Starting phenix.real_space_refine
on Wed Mar  4 03:08:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r89_24312/03_2026/7r89_24312.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r89_24312/03_2026/7r89_24312.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r89_24312/03_2026/7r89_24312.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r89_24312/03_2026/7r89_24312.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r89_24312/03_2026/7r89_24312.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r89_24312/03_2026/7r89_24312.map"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    6811      2.51       5
     N    1778      2.21       5
     O    1876      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10531
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 584, 4596
          Classifications: {'peptide': 584}
          Link IDs: {'PTRANS': 22, 'TRANS': 561}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 529, 4202
          Classifications: {'peptide': 529}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 504}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 901
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 3, 'TRANS': 110}
    Chain: "D"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 803
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 2, 'PTRANS': 2, 'TRANS': 100}
    Chain: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'ERG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.25, per 1000 atoms: 0.21
  Number of scatterers: 10531
  At special positions: 0
  Unit cell: (116.48, 101.504, 123.968, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    1876      8.00
     N    1778      7.00
     C    6811      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 587 " - pdb=" SG  CYS A 600 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  41 " - pdb=" SG  CYS C 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  43 " - pdb=" SG  CYS D 108 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 502.1 milliseconds
  

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2468

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 10 sheets defined
      53.5% alpha, 15.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 101
    Processing helix  chain 'A' and resid 143 through 156
    Processing helix  chain 'A' and resid 160 through 175
      removed outlier: 4.377A  pdb=" N   PHE A 164 " --> pdb=" O   ASN A 160 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU A 175 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 208
    Processing helix  chain 'A' and resid 224 through 241
    Processing helix  chain 'A' and resid 253 through 257
    Processing helix  chain 'A' and resid 276 through 287
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 311 through 331
    Processing helix  chain 'A' and resid 332 through 347
      removed outlier: 3.866A  pdb=" N   HIS A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 381
    Processing helix  chain 'A' and resid 382 through 405
      removed outlier: 5.475A  pdb=" N   ASN A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   LEU A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   PHE A 403 " --> pdb=" O   PHE A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 454
      Proline residue:  A 431  - end of helix
      Proline residue:  A 443  - end of helix
      removed outlier: 4.054A  pdb=" N   GLN A 454 " --> pdb=" O   ASP A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 491
      Proline residue:  A 473  - end of helix
      removed outlier: 4.993A  pdb=" N   TRP A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   THR A 489 " --> pdb=" O   VAL A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 524
      Proline residue:  A 509  - end of helix
    Processing helix  chain 'A' and resid 526 through 545
      removed outlier: 3.511A  pdb=" N   VAL A 530 " --> pdb=" O   ASN A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 555
    Processing helix  chain 'A' and resid 556 through 564
      removed outlier: 3.638A  pdb=" N   TYR A 564 " --> pdb=" O   LYS A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 580
      removed outlier: 4.241A  pdb=" N   TYR A 570 " --> pdb=" O   THR A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 613
      removed outlier: 3.658A  pdb=" N   PHE A 608 " --> pdb=" O   GLN A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 618
      No H-bonds generated for 'chain 'A' and resid 616 through 618'
    Processing helix  chain 'A' and resid 619 through 649
      Proline residue:  A 632  - end of helix
    Processing helix  chain 'B' and resid 113 through 120
    Processing helix  chain 'B' and resid 140 through 147
      removed outlier: 3.730A  pdb=" N   ARG B 145 " --> pdb=" O   PRO B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 175
    Processing helix  chain 'B' and resid 180 through 195
    Processing helix  chain 'B' and resid 214 through 228
    Processing helix  chain 'B' and resid 244 through 260
    Processing helix  chain 'B' and resid 276 through 280
    Processing helix  chain 'B' and resid 299 through 306
    Processing helix  chain 'B' and resid 316 through 324
    Processing helix  chain 'B' and resid 394 through 411
    Processing helix  chain 'B' and resid 413 through 435
    Processing helix  chain 'B' and resid 444 through 459
      removed outlier: 4.638A  pdb=" N   ILE B 459 " --> pdb=" O   ILE B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 473
    Processing helix  chain 'B' and resid 474 through 485
    Processing helix  chain 'B' and resid 490 through 517
      removed outlier: 3.844A  pdb=" N   PHE B 494 " --> pdb=" O   GLY B 490 " (cutoff:3.500A)
      Proline residue:  B 502  - end of helix
      Proline residue:  B 514  - end of helix
      removed outlier: 4.042A  pdb=" N   TRP B 517 " --> pdb=" O   MET B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 525 through 553
    Processing helix  chain 'B' and resid 555 through 573
    Processing helix  chain 'B' and resid 585 through 593
    Processing helix  chain 'B' and resid 594 through 609
    Processing helix  chain 'B' and resid 627 through 633
      removed outlier: 3.804A  pdb=" N   MET B 633 " --> pdb=" O   ILE B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 639 through 665
    Processing helix  chain 'C' and resid 47 through 51
      removed outlier: 3.955A  pdb=" N   PHE C  51 " --> pdb=" O   PHE C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 76
    Processing helix  chain 'D' and resid 99 through 103
      removed outlier: 3.663A  pdb=" N   LEU D 103 " --> pdb=" O   SER D 100 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 77
      removed outlier: 6.624A  pdb=" N   LYS A  70 " --> pdb=" O   SER A  44 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   SER A  44 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   VAL A  72 " --> pdb=" O   HIS A  42 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   ILE A  40 " --> pdb=" O   TYR A 114 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   TYR A 114 " --> pdb=" O   ILE A  40 " (cutoff:3.500A)
      removed outlier: 5.431A  pdb=" N   HIS A  42 " --> pdb=" O   GLU A 112 " (cutoff:3.500A)
      removed outlier: 5.031A  pdb=" N   GLU A 112 " --> pdb=" O   HIS A  42 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 132
      removed outlier: 6.354A  pdb=" N   MET A 214 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   THR A 248 " --> pdb=" O   MET A 214 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   PHE A 216 " --> pdb=" O   THR A 248 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   PHE A 273 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   SER A 267 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   LEU A 271 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 88 through 96
      removed outlier: 5.242A  pdb=" N   LEU B  52 " --> pdb=" O   ASN B  90 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   SER B  92 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ARG B  50 " --> pdb=" O   SER B  92 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   LYS B  94 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLU B  48 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ARG B  96 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   THR B  46 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   GLN B  55 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ILE B 127 " --> pdb=" O   GLN B  55 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 88 through 96
      removed outlier: 5.242A  pdb=" N   LEU B  52 " --> pdb=" O   ASN B  90 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   SER B  92 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ARG B  50 " --> pdb=" O   SER B  92 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   LYS B  94 " --> pdb=" O   GLU B  48 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLU B  48 " --> pdb=" O   LYS B  94 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ARG B  96 " --> pdb=" O   THR B  46 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   THR B  46 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151
      removed outlier: 6.319A  pdb=" N   ALA B 149 " --> pdb=" O   ILE B 235 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   ASP B 237 " --> pdb=" O   ALA B 149 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   VAL B 151 " --> pdb=" O   ASP B 237 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   LEU B 101 " --> pdb=" O   ILE B 267 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   MET B 100 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   LEU B 284 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ALA B 102 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   MET B 286 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ILE B 104 " --> pdb=" O   MET B 286 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   TYR B 293 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   THR B 287 " --> pdb=" O   PRO B 291 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 22 through 26
    Processing sheet with id=AA7, first strand: chain 'C' and resid 79 through 81
      removed outlier: 5.133A  pdb=" N   TRP C  66 " --> pdb=" O   ARG C  57 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   ARG C  57 " --> pdb=" O   TRP C  66 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27
    Processing sheet with id=AA9, first strand: chain 'D' and resid 30 through 32
      removed outlier: 6.348A  pdb=" N   LEU D  31 " --> pdb=" O   GLU D 125 " (cutoff:3.500A)
      removed outlier: 6.647A  pdb=" N   LEU D  53 " --> pdb=" O   TYR D  69 " (cutoff:3.500A)
      removed outlier: 4.831A  pdb=" N   TYR D  69 " --> pdb=" O   LEU D  53 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   TRP D  55 " --> pdb=" O   LEU D  67 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 30 through 32
      removed outlier: 6.348A  pdb=" N   LEU D  31 " --> pdb=" O   GLU D 125 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   THR D 117 " --> pdb=" O   GLN D 110 " (cutoff:3.500A)

    596 hydrogen bonds defined for protein.
    1710 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.62

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3342
        1.35 -     1.46: 2562
        1.46 -     1.58: 4752
        1.58 -     1.70: 0
        1.70 -     1.82: 105
  Bond restraints: 10761
  Sorted by residual:
  bond pdb=" C10 ERG B 901 "
       pdb=" C9  ERG B 901 "
    ideal  model  delta    sigma   weight residual
    1.556  1.507  0.049 2.00e-02 2.50e+03 6.12e+00
  bond pdb=" N   ARG C  63 "
       pdb=" CA  ARG C  63 "
    ideal  model  delta    sigma   weight residual
    1.459  1.473 -0.015 1.16e-02 7.43e+03 1.61e+00
  bond pdb=" C10 ERG B 901 "
       pdb=" C5  ERG B 901 "
    ideal  model  delta    sigma   weight residual
    1.519  1.496  0.023 2.00e-02 2.50e+03 1.37e+00
  bond pdb=" N   THR B 489 "
       pdb=" CA  THR B 489 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.014 1.29e-02 6.01e+03 1.15e+00
  bond pdb=" C   ILE B 459 "
       pdb=" N   PRO B 460 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.014 1.28e-02 6.10e+03 1.14e+00
  ... (remaining 10756 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 14277
        1.58 -     3.15: 230
        3.15 -     4.73: 39
        4.73 -     6.30: 21
        6.30 -     7.88: 4
  Bond angle restraints: 14571
  Sorted by residual:
  angle pdb=" C   PRO A 556 "
        pdb=" N   ILE A 557 "
        pdb=" CA  ILE A 557 "
      ideal   model   delta    sigma   weight residual
     120.33  123.30   -2.97 8.00e-01 1.56e+00 1.38e+01
  angle pdb=" N   VAL B 205 "
        pdb=" CA  VAL B 205 "
        pdb=" CB  VAL B 205 "
      ideal   model   delta    sigma   weight residual
     112.39  108.80    3.59 1.17e+00 7.31e-01 9.42e+00
  angle pdb=" C   ARG C  63 "
        pdb=" CA  ARG C  63 "
        pdb=" CB  ARG C  63 "
      ideal   model   delta    sigma   weight residual
     110.92  115.60   -4.68 1.59e+00 3.96e-01 8.66e+00
  angle pdb=" C   THR B 488 "
        pdb=" N   THR B 489 "
        pdb=" CA  THR B 489 "
      ideal   model   delta    sigma   weight residual
     121.54  127.03   -5.49 1.91e+00 2.74e-01 8.27e+00
  angle pdb=" N   ILE B 459 "
        pdb=" CA  ILE B 459 "
        pdb=" C   ILE B 459 "
      ideal   model   delta    sigma   weight residual
     108.88  115.05   -6.17 2.16e+00 2.14e-01 8.16e+00
  ... (remaining 14566 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 5818
       17.96 -    35.91: 460
       35.91 -    53.86: 133
       53.86 -    71.82: 30
       71.82 -    89.77: 11
  Dihedral angle restraints: 6452
    sinusoidal: 2608
      harmonic: 3844
  Sorted by residual:
  dihedral pdb=" CB  CYS A 587 "
           pdb=" SG  CYS A 587 "
           pdb=" SG  CYS A 600 "
           pdb=" CB  CYS A 600 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -159.55   73.55     1      1.00e+01 1.00e-02 6.88e+01
  dihedral pdb=" CB  CYS D  43 "
           pdb=" SG  CYS D  43 "
           pdb=" SG  CYS D 108 "
           pdb=" CB  CYS D 108 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   65.05   27.95     1      1.00e+01 1.00e-02 1.12e+01
  dihedral pdb=" CB  GLU B 483 "
           pdb=" CG  GLU B 483 "
           pdb=" CD  GLU B 483 "
           pdb=" OE1 GLU B 483 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.77  -89.77     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 6449 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 1638
       0.111 -    0.222: 22
       0.222 -    0.334: 0
       0.334 -    0.445: 1
       0.445 -    0.556: 1
  Chirality restraints: 1662
  Sorted by residual:
  chirality pdb=" C14 ERG B 901 "
            pdb=" C13 ERG B 901 "
            pdb=" C15 ERG B 901 "
            pdb=" C8  ERG B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.26   -2.82    0.56 2.00e-01 2.50e+01 7.73e+00
  chirality pdb=" C10 ERG B 901 "
            pdb=" C1  ERG B 901 "
            pdb=" C5  ERG B 901 "
            pdb=" C9  ERG B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.77   -2.38   -0.40 2.00e-01 2.50e+01 3.91e+00
  chirality pdb=" C13 ERG B 901 "
            pdb=" C12 ERG B 901 "
            pdb=" C14 ERG B 901 "
            pdb=" C17 ERG B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.71   -0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1659 not shown)

  Planarity restraints: 1828
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C20 ERG B 901 "    0.146 2.00e-02 2.50e+03   1.47e-01 2.15e+02
        pdb=" C22 ERG B 901 "   -0.141 2.00e-02 2.50e+03
        pdb=" C23 ERG B 901 "   -0.152 2.00e-02 2.50e+03
        pdb=" C24 ERG B 901 "    0.148 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 513 "    0.026 5.00e-02 4.00e+02   3.99e-02 2.55e+00
        pdb=" N   PRO B 514 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO B 514 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 514 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 276 "    0.022 5.00e-02 4.00e+02   3.41e-02 1.86e+00
        pdb=" N   PRO A 277 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 277 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 277 "    0.019 5.00e-02 4.00e+02
  ... (remaining 1825 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1396
        2.76 -     3.29: 10098
        3.29 -     3.83: 18206
        3.83 -     4.36: 21016
        4.36 -     4.90: 37151
  Nonbonded interactions: 87867
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 573 "
            pdb=" OG  SER B 591 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER D  83 "
            pdb=" OG1 THR D  94 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OG  SER B 428 "
            pdb=" OG1 THR B 515 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG  SER B 428 "
            pdb=" O   TYR B 511 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OH  TYR B 293 "
            pdb=" O   ALA B 296 "
     model   vdw
     2.312 3.040
  ... (remaining 87862 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.710
  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:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.160
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
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      :  0.002   0.049  10764  Z= 0.121
  Angle     :  0.563   7.876  14577  Z= 0.319
  Chirality :  0.041   0.556   1662
  Planarity :  0.005   0.147   1828
  Dihedral  : 14.779  89.774   3975
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 16.67 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.22), residues: 1308
  helix:  0.26 (0.19), residues: 681
  sheet: -1.46 (0.33), residues: 178
  loop : -2.63 (0.26), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 108 
 TYR   0.008   0.001   TYR A 487 
 PHE   0.013   0.001   PHE B 493 
 TRP   0.005   0.001   TRP C  55 
 HIS   0.003   0.001   HIS B 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 (10761)
  covalent geometry    : angle       0.56112 (14571)
  SS BOND              : bond        0.00147 (    3)
  SS BOND              : angle       2.07155 (    6)
  hydrogen bonds       : bond        0.12640 (  591)
  hydrogen bonds       : angle       5.27759 ( 1710)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 224
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A  435 MET cc_start: 0.8706 (tmm) cc_final: 0.8408 (tmm)
REVERT: B  146 LYS cc_start: 0.8680 (tmmt) cc_final: 0.8391 (tttm)
REVERT: B  156 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7316 (mm-40)
REVERT: B  517 TRP cc_start: 0.7264 (m100) cc_final: 0.6768 (t60)
REVERT: B  577 MET cc_start: 0.6459 (OUTLIER) cc_final: 0.5841 (mtp)
  outliers start: 39
  outliers final: 14
  residues processed: 255
  average time/residue: 0.5642
  time to fit residues: 154.6411
Evaluate side-chains
  167 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  587 CYS
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  577 MET
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  635 LEU
Chi-restraints excluded: chain C residue   44 SER
Chi-restraints excluded: chain C residue  100 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.0870
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    0.0470
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5660

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

Flipped N/Q/H residues before XYZ refinement:
A 206 GLN
A 378 ASN
A 425 GLN
A 459 GLN
A 462 GLN
A 493 HIS
A 578 ASN
B  99 GLN
B 155 ASN
B 199 GLN
B 249 HIS
B 270 HIS
B 271 GLN
B 302 GLN
B 409 ASN
B 438 HIS
B 568 ASN
C  58 GLN
C  75 ASN
C 103 GLN
D  26 GLN
D  47 GLN
D  58 GLN
D  65 GLN

Total number of N/Q/H flips: 24

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.115195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.090411 restraints weight = 14515.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.21
r_work: 0.2941 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10764  Z= 0.118
  Angle     :  0.533   6.749  14577  Z= 0.270
  Chirality :  0.039   0.145   1662
  Planarity :  0.004   0.052   1828
  Dihedral  :  5.818  59.203   1549
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 19.36 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.24), residues: 1308
  helix:  1.36 (0.20), residues: 691
  sheet: -1.02 (0.35), residues: 182
  loop : -1.79 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 419 
 TYR   0.016   0.001   TYR A 114 
 PHE   0.015   0.001   PHE B 493 
 TRP   0.008   0.001   TRP C 128 
 HIS   0.005   0.001   HIS B 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10761)
  covalent geometry    : angle       0.53284 (14571)
  SS BOND              : bond        0.00296 (    3)
  SS BOND              : angle       0.67474 (    6)
  hydrogen bonds       : bond        0.03750 (  591)
  hydrogen bonds       : angle       4.06764 ( 1710)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 160
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
REVERT: A  435 MET cc_start: 0.9076 (tmm) cc_final: 0.8792 (tmm)
REVERT: A  529 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8904 (mp)
REVERT: A  630 PHE cc_start: 0.7360 (m-80) cc_final: 0.7057 (t80)
REVERT: B  145 ARG cc_start: 0.8255 (ptp90) cc_final: 0.8013 (ptp-170)
REVERT: B  156 GLN cc_start: 0.7924 (pm20) cc_final: 0.7655 (pm20)
REVERT: B  392 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7400 (mpp)
REVERT: B  474 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8487 (mt-10)
REVERT: B  517 TRP cc_start: 0.7659 (m100) cc_final: 0.6773 (t60)
REVERT: C   26 SER cc_start: 0.8890 (OUTLIER) cc_final: 0.8511 (m)
REVERT: C  103 GLN cc_start: 0.8435 (tp40) cc_final: 0.7996 (tp40)
  outliers start: 52
  outliers final: 21
  residues processed: 199
  average time/residue: 0.5539
  time to fit residues: 118.7007
Evaluate side-chains
  169 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 145
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain B residue  635 LEU
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  116 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 126 optimal weight:    0.0980
   chunk 91 optimal weight:    0.7980
   chunk 122 optimal weight:    9.9990
   chunk 129 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0470
   chunk 6 optimal weight:    7.9990
   chunk 92 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 63 optimal weight:   10.0000
   chunk 78 optimal weight:    0.9990
   overall best weight:    1.1882

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

Flipped N/Q/H residues before XYZ refinement:
A 393 ASN
A 410 ASN
B 302 GLN
B 607 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.108249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.082405 restraints weight = 14421.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.2935 rms_B_bonded: 2.21
r_work: 0.2801 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2670 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10764  Z= 0.165
  Angle     :  0.584   7.949  14577  Z= 0.296
  Chirality :  0.041   0.141   1662
  Planarity :  0.004   0.053   1828
  Dihedral  :  5.080  56.117   1534
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 19.62 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.24), residues: 1308
  helix:  1.65 (0.20), residues: 687
  sheet: -0.68 (0.36), residues: 187
  loop : -1.60 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 240 
 TYR   0.015   0.002   TYR A 114 
 PHE   0.017   0.002   PHE B 493 
 TRP   0.008   0.001   TRP B 598 
 HIS   0.006   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (10761)
  covalent geometry    : angle       0.58379 (14571)
  SS BOND              : bond        0.00374 (    3)
  SS BOND              : angle       0.96211 (    6)
  hydrogen bonds       : bond        0.04791 (  591)
  hydrogen bonds       : angle       4.12237 ( 1710)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 147
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  134 GLN cc_start: 0.7014 (pm20) cc_final: 0.6774 (pm20)
REVERT: A  435 MET cc_start: 0.9223 (tmm) cc_final: 0.8968 (tmm)
REVERT: B  156 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7792 (pm20)
REVERT: B  244 ASP cc_start: 0.7865 (t0) cc_final: 0.7656 (t70)
REVERT: B  392 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7536 (mpp)
REVERT: B  441 ILE cc_start: 0.8947 (mt) cc_final: 0.8737 (mm)
REVERT: B  474 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8431 (mt-10)
REVERT: B  517 TRP cc_start: 0.7834 (m100) cc_final: 0.7009 (t60)
REVERT: B  582 SER cc_start: 0.7547 (OUTLIER) cc_final: 0.7133 (p)
REVERT: C   26 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8542 (m)
REVERT: C   99 ILE cc_start: 0.8910 (mt) cc_final: 0.8470 (mp)
REVERT: C  103 GLN cc_start: 0.8429 (tp40) cc_final: 0.7969 (tp40)
  outliers start: 53
  outliers final: 20
  residues processed: 187
  average time/residue: 0.5185
  time to fit residues: 104.6766
Evaluate side-chains
  159 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  116 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 106 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B 607 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.107943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.082450 restraints weight = 14500.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.18
r_work: 0.2807 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2677 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10764  Z= 0.144
  Angle     :  0.560   7.571  14577  Z= 0.283
  Chirality :  0.040   0.144   1662
  Planarity :  0.004   0.056   1828
  Dihedral  :  4.654  53.598   1529
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 19.62 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.24), residues: 1308
  helix:  1.83 (0.20), residues: 685
  sheet: -0.51 (0.37), residues: 188
  loop : -1.44 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  44 
 TYR   0.017   0.001   TYR A 114 
 PHE   0.016   0.001   PHE B 493 
 TRP   0.007   0.001   TRP B 598 
 HIS   0.004   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (10761)
  covalent geometry    : angle       0.55995 (14571)
  SS BOND              : bond        0.00318 (    3)
  SS BOND              : angle       0.75162 (    6)
  hydrogen bonds       : bond        0.04455 (  591)
  hydrogen bonds       : angle       4.04191 ( 1710)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 139
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 ILE cc_start: 0.8108 (mm) cc_final: 0.7858 (mt)
REVERT: A  345 MET cc_start: 0.7706 (pp-130) cc_final: 0.7118 (tpp)
REVERT: A  435 MET cc_start: 0.9185 (tmm) cc_final: 0.8972 (tmm)
REVERT: A  647 HIS cc_start: 0.6727 (OUTLIER) cc_final: 0.6467 (t70)
REVERT: B  156 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7782 (pm20)
REVERT: B  244 ASP cc_start: 0.7879 (t0) cc_final: 0.7662 (t70)
REVERT: B  392 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7547 (mpp)
REVERT: B  441 ILE cc_start: 0.8945 (mt) cc_final: 0.8733 (mm)
REVERT: B  474 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8413 (mt-10)
REVERT: B  503 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8275 (tt0)
REVERT: B  517 TRP cc_start: 0.7826 (m100) cc_final: 0.7013 (t60)
REVERT: B  582 SER cc_start: 0.7498 (OUTLIER) cc_final: 0.7141 (p)
REVERT: C   26 SER cc_start: 0.8914 (t) cc_final: 0.8554 (m)
REVERT: C   32 GLN cc_start: 0.6105 (OUTLIER) cc_final: 0.5884 (mm110)
REVERT: C   88 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7723 (mtm-85)
REVERT: C   99 ILE cc_start: 0.8927 (mt) cc_final: 0.8508 (mp)
REVERT: C  103 GLN cc_start: 0.8492 (tp40) cc_final: 0.8015 (tp40)
REVERT: C  123 MET cc_start: 0.9174 (mmp) cc_final: 0.8947 (mmm)
  outliers start: 53
  outliers final: 26
  residues processed: 181
  average time/residue: 0.5060
  time to fit residues: 99.4644
Evaluate side-chains
  167 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 134
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  647 HIS
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  290 THR
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  429 MET
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  503 GLU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain C residue   32 GLN
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   88 ARG
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  116 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
A 392 GLN
A 425 GLN
B 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.104430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.078800 restraints weight = 14275.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 2.13
r_work: 0.2742 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10764  Z= 0.232
  Angle     :  0.636   9.364  14577  Z= 0.324
  Chirality :  0.043   0.148   1662
  Planarity :  0.004   0.057   1828
  Dihedral  :  4.988  54.014   1529
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 19.70 %
    Favored  : 75.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.24), residues: 1308
  helix:  1.67 (0.20), residues: 686
  sheet: -0.44 (0.37), residues: 188
  loop : -1.36 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  44 
 TYR   0.015   0.002   TYR A 114 
 PHE   0.018   0.002   PHE B 493 
 TRP   0.009   0.001   TRP B 584 
 HIS   0.005   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 (10761)
  covalent geometry    : angle       0.63570 (14571)
  SS BOND              : bond        0.00390 (    3)
  SS BOND              : angle       1.03755 (    6)
  hydrogen bonds       : bond        0.05409 (  591)
  hydrogen bonds       : angle       4.22978 ( 1710)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 143
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ILE cc_start: 0.8101 (mm) cc_final: 0.7860 (mt)
REVERT: A  345 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.7178 (tpp)
REVERT: A  647 HIS cc_start: 0.6811 (OUTLIER) cc_final: 0.6528 (t70)
REVERT: B   26 ARG cc_start: 0.6338 (ptt180) cc_final: 0.6112 (ptt180)
REVERT: B  121 ARG cc_start: 0.6993 (mpt180) cc_final: 0.6669 (mpt-90)
REVERT: B  244 ASP cc_start: 0.7936 (t0) cc_final: 0.7691 (t70)
REVERT: B  392 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7517 (mpp)
REVERT: B  441 ILE cc_start: 0.8884 (mt) cc_final: 0.8666 (mm)
REVERT: B  461 PHE cc_start: 0.7879 (t80) cc_final: 0.7663 (t80)
REVERT: B  474 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8337 (mt-10)
REVERT: B  503 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8333 (tt0)
REVERT: B  517 TRP cc_start: 0.7799 (m100) cc_final: 0.6974 (t60)
REVERT: B  582 SER cc_start: 0.7639 (OUTLIER) cc_final: 0.7258 (p)
REVERT: C   26 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8517 (m)
REVERT: C   88 ARG cc_start: 0.8439 (OUTLIER) cc_final: 0.7620 (mtm-85)
REVERT: C   99 ILE cc_start: 0.8883 (mt) cc_final: 0.8435 (mp)
REVERT: C  103 GLN cc_start: 0.8417 (tp40) cc_final: 0.7568 (tp-100)
REVERT: C  130 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8050 (pm20)
REVERT: D   97 SER cc_start: 0.8271 (t) cc_final: 0.7988 (p)
  outliers start: 56
  outliers final: 32
  residues processed: 184
  average time/residue: 0.5560
  time to fit residues: 110.1965
Evaluate side-chains
  173 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 133
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  647 HIS
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  200 CYS
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  324 LEU
Chi-restraints excluded: chain B residue  325 THR
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  501 LEU
Chi-restraints excluded: chain B residue  503 GLU
Chi-restraints excluded: chain B residue  545 MET
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   88 ARG
Chi-restraints excluded: chain C residue   92 SER
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  130 GLN
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain D residue   32 SER
Chi-restraints excluded: chain D residue   38 ARG
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  116 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 5 optimal weight:    0.0870
   chunk 72 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 95 optimal weight:    3.9990
   chunk 128 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 119 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 127 optimal weight:    2.9990
   overall best weight:    0.7964

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

Flipped N/Q/H residues before XYZ refinement:
A  36 HIS
A 251 GLN
A 425 GLN
B 607 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.107360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.081894 restraints weight = 14300.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 2.14
r_work: 0.2800 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2669 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10764  Z= 0.130
  Angle     :  0.559   7.795  14577  Z= 0.284
  Chirality :  0.040   0.141   1662
  Planarity :  0.004   0.058   1828
  Dihedral  :  4.729  54.167   1529
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 20.75 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.24), residues: 1308
  helix:  1.88 (0.20), residues: 685
  sheet: -0.39 (0.37), residues: 188
  loop : -1.26 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  44 
 TYR   0.018   0.001   TYR A 114 
 PHE   0.017   0.001   PHE B 493 
 TRP   0.008   0.001   TRP A 461 
 HIS   0.004   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10761)
  covalent geometry    : angle       0.55866 (14571)
  SS BOND              : bond        0.00308 (    3)
  SS BOND              : angle       0.71775 (    6)
  hydrogen bonds       : bond        0.04390 (  591)
  hydrogen bonds       : angle       4.05675 ( 1710)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 142
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ILE cc_start: 0.8058 (mm) cc_final: 0.7847 (mt)
REVERT: A  345 MET cc_start: 0.7644 (pp-130) cc_final: 0.7100 (tpp)
REVERT: A  353 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7357 (mmt)
REVERT: A  529 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8811 (mp)
REVERT: A  647 HIS cc_start: 0.6741 (OUTLIER) cc_final: 0.6446 (t70)
REVERT: B  121 ARG cc_start: 0.6896 (mpt180) cc_final: 0.6624 (mpt-90)
REVERT: B  244 ASP cc_start: 0.7847 (t0) cc_final: 0.7615 (t70)
REVERT: B  392 MET cc_start: 0.7701 (OUTLIER) cc_final: 0.7481 (mpp)
REVERT: B  441 ILE cc_start: 0.8951 (mt) cc_final: 0.8733 (mm)
REVERT: B  474 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8291 (mt-10)
REVERT: B  503 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8229 (tt0)
REVERT: B  517 TRP cc_start: 0.7762 (m100) cc_final: 0.6957 (t60)
REVERT: B  582 SER cc_start: 0.7570 (OUTLIER) cc_final: 0.7191 (p)
REVERT: C   26 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8515 (m)
REVERT: C   88 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7631 (mtm-85)
REVERT: C   99 ILE cc_start: 0.8873 (mt) cc_final: 0.8442 (mp)
REVERT: C  103 GLN cc_start: 0.8393 (tp40) cc_final: 0.7575 (tp-100)
REVERT: D   38 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7859 (ptm-80)
REVERT: D   97 SER cc_start: 0.8235 (t) cc_final: 0.7993 (p)
  outliers start: 46
  outliers final: 22
  residues processed: 179
  average time/residue: 0.5391
  time to fit residues: 104.1198
Evaluate side-chains
  167 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 136
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  647 HIS
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  503 GLU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   88 ARG
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain D residue   38 ARG
Chi-restraints excluded: chain D residue  116 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 111 optimal weight:    0.3980
   chunk 123 optimal weight:    3.9990
   chunk 128 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 127 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 80 optimal weight:    5.9990
   chunk 110 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
A 425 GLN
B 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.106610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.081630 restraints weight = 14759.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 2.13
r_work: 0.2810 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8809
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10764  Z= 0.163
  Angle     :  0.586   9.908  14577  Z= 0.296
  Chirality :  0.041   0.144   1662
  Planarity :  0.004   0.058   1828
  Dihedral  :  4.748  50.758   1529
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 21.27 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.24), residues: 1308
  helix:  1.88 (0.20), residues: 685
  sheet: -0.32 (0.38), residues: 188
  loop : -1.22 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  44 
 TYR   0.017   0.001   TYR A 114 
 PHE   0.017   0.001   PHE B 493 
 TRP   0.008   0.001   TRP A 461 
 HIS   0.004   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (10761)
  covalent geometry    : angle       0.58632 (14571)
  SS BOND              : bond        0.00304 (    3)
  SS BOND              : angle       0.79130 (    6)
  hydrogen bonds       : bond        0.04690 (  591)
  hydrogen bonds       : angle       4.07749 ( 1710)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 136
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 ILE cc_start: 0.8097 (mm) cc_final: 0.7879 (mt)
REVERT: A  345 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7120 (tpp)
REVERT: A  353 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7382 (mmt)
REVERT: A  529 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8869 (mp)
REVERT: A  647 HIS cc_start: 0.6707 (OUTLIER) cc_final: 0.6408 (t70)
REVERT: B  121 ARG cc_start: 0.6999 (mpt180) cc_final: 0.6771 (mpt-90)
REVERT: B  244 ASP cc_start: 0.7911 (t0) cc_final: 0.7679 (t70)
REVERT: B  392 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.7535 (mpp)
REVERT: B  441 ILE cc_start: 0.8954 (mt) cc_final: 0.8732 (mm)
REVERT: B  474 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8324 (mt-10)
REVERT: B  503 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8267 (tt0)
REVERT: B  517 TRP cc_start: 0.7829 (m100) cc_final: 0.6989 (t60)
REVERT: B  582 SER cc_start: 0.7596 (OUTLIER) cc_final: 0.7190 (p)
REVERT: C   26 SER cc_start: 0.8873 (OUTLIER) cc_final: 0.8495 (m)
REVERT: C   88 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7620 (mtm-85)
REVERT: C   99 ILE cc_start: 0.8890 (mt) cc_final: 0.8452 (mp)
REVERT: C  103 GLN cc_start: 0.8388 (tp40) cc_final: 0.7540 (tp-100)
REVERT: D   38 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7847 (ptm-80)
REVERT: D   97 SER cc_start: 0.8253 (t) cc_final: 0.8006 (p)
  outliers start: 45
  outliers final: 24
  residues processed: 170
  average time/residue: 0.5345
  time to fit residues: 98.3074
Evaluate side-chains
  169 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 135
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  366 SER
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  647 HIS
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  503 GLU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   88 ARG
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain D residue   38 ARG
Chi-restraints excluded: chain D residue  116 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 13 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 101 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
A 425 GLN
B 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.106847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.082017 restraints weight = 14281.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 2.06
r_work: 0.2807 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2677 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10764  Z= 0.135
  Angle     :  0.562   7.192  14577  Z= 0.284
  Chirality :  0.040   0.143   1662
  Planarity :  0.004   0.059   1828
  Dihedral  :  4.626  47.326   1529
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 21.44 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.24), residues: 1308
  helix:  1.99 (0.20), residues: 685
  sheet: -0.30 (0.38), residues: 189
  loop : -1.15 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  44 
 TYR   0.017   0.001   TYR A 114 
 PHE   0.017   0.001   PHE B 493 
 TRP   0.008   0.001   TRP A 461 
 HIS   0.004   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (10761)
  covalent geometry    : angle       0.56158 (14571)
  SS BOND              : bond        0.00301 (    3)
  SS BOND              : angle       0.80907 (    6)
  hydrogen bonds       : bond        0.04368 (  591)
  hydrogen bonds       : angle       4.01930 ( 1710)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 147
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ILE cc_start: 0.8079 (mm) cc_final: 0.7871 (mt)
REVERT: A  345 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7106 (tpp)
REVERT: A  353 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7445 (mmt)
REVERT: A  529 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8803 (mp)
REVERT: A  647 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.6364 (t70)
REVERT: B  121 ARG cc_start: 0.6996 (mpt180) cc_final: 0.6574 (mpt-90)
REVERT: B  244 ASP cc_start: 0.7839 (t0) cc_final: 0.7620 (t70)
REVERT: B  392 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7440 (mpp)
REVERT: B  441 ILE cc_start: 0.8961 (mt) cc_final: 0.8741 (mm)
REVERT: B  474 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8285 (mt-10)
REVERT: B  503 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8173 (tt0)
REVERT: B  517 TRP cc_start: 0.7763 (m100) cc_final: 0.6945 (t60)
REVERT: B  582 SER cc_start: 0.7473 (OUTLIER) cc_final: 0.7092 (p)
REVERT: C   26 SER cc_start: 0.8902 (OUTLIER) cc_final: 0.8522 (m)
REVERT: C   88 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7234 (mtm-85)
REVERT: C   99 ILE cc_start: 0.8884 (mt) cc_final: 0.8437 (mp)
REVERT: C  103 GLN cc_start: 0.8387 (tp40) cc_final: 0.7557 (tp-100)
REVERT: D   38 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7935 (ptm-80)
REVERT: D   97 SER cc_start: 0.8237 (t) cc_final: 0.8005 (p)
  outliers start: 43
  outliers final: 26
  residues processed: 179
  average time/residue: 0.5387
  time to fit residues: 104.4940
Evaluate side-chains
  177 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 141
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  647 HIS
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  503 GLU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   88 ARG
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain D residue   38 ARG
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  116 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 84 optimal weight:    0.3980
   chunk 39 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 23 optimal weight:    0.4980
   chunk 62 optimal weight:    0.8980
   chunk 124 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   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 251 GLN
A 425 GLN
B 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.108141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.082743 restraints weight = 14207.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 2.14
r_work: 0.2812 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10764  Z= 0.125
  Angle     :  0.558   9.418  14577  Z= 0.280
  Chirality :  0.040   0.143   1662
  Planarity :  0.004   0.059   1828
  Dihedral  :  4.562  46.811   1529
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 21.35 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.04 (0.24), residues: 1308
  helix:  2.02 (0.20), residues: 690
  sheet: -0.24 (0.38), residues: 189
  loop : -1.10 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  44 
 TYR   0.018   0.001   TYR A 114 
 PHE   0.017   0.001   PHE B 493 
 TRP   0.008   0.001   TRP A 461 
 HIS   0.004   0.001   HIS B 531 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (10761)
  covalent geometry    : angle       0.55806 (14571)
  SS BOND              : bond        0.00286 (    3)
  SS BOND              : angle       0.72246 (    6)
  hydrogen bonds       : bond        0.04232 (  591)
  hydrogen bonds       : angle       3.97806 ( 1710)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 142
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 ILE cc_start: 0.8067 (mm) cc_final: 0.7859 (mt)
REVERT: A  345 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7115 (tpp)
REVERT: A  353 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7443 (mmt)
REVERT: A  406 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7931 (mtt180)
REVERT: A  529 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8803 (mp)
REVERT: B  121 ARG cc_start: 0.6992 (mpt180) cc_final: 0.6583 (mpt-90)
REVERT: B  244 ASP cc_start: 0.7838 (t0) cc_final: 0.7634 (t70)
REVERT: B  441 ILE cc_start: 0.8959 (mt) cc_final: 0.8737 (mm)
REVERT: B  474 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8296 (mt-10)
REVERT: B  503 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8160 (tt0)
REVERT: B  517 TRP cc_start: 0.7755 (m100) cc_final: 0.6930 (t60)
REVERT: B  582 SER cc_start: 0.7455 (OUTLIER) cc_final: 0.7058 (p)
REVERT: C   26 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8517 (m)
REVERT: C   99 ILE cc_start: 0.8864 (mt) cc_final: 0.8429 (mp)
REVERT: C  103 GLN cc_start: 0.8389 (tp40) cc_final: 0.7576 (tp-100)
REVERT: D   38 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7927 (ptm-80)
REVERT: D   97 SER cc_start: 0.8242 (t) cc_final: 0.8011 (p)
  outliers start: 44
  outliers final: 23
  residues processed: 176
  average time/residue: 0.5330
  time to fit residues: 101.4486
Evaluate side-chains
  171 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 140
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  351 LEU
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  406 ARG
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  529 ILE
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  503 GLU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain D residue   38 ARG
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  116 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 111 optimal weight:    7.9990
   chunk 117 optimal weight:    3.9990
   chunk 98 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 63 optimal weight:    8.9990
   chunk 3 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
A 425 GLN
B 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.104875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.080019 restraints weight = 14130.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 2.06
r_work: 0.2769 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2639 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10764  Z= 0.190
  Angle     :  0.623   8.299  14577  Z= 0.312
  Chirality :  0.043   0.293   1662
  Planarity :  0.004   0.058   1828
  Dihedral  :  4.767  47.210   1529
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 21.88 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.24), residues: 1308
  helix:  1.88 (0.20), residues: 685
  sheet: -0.11 (0.39), residues: 178
  loop : -1.18 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D  44 
 TYR   0.017   0.002   TYR A 114 
 PHE   0.018   0.002   PHE B 493 
 TRP   0.008   0.001   TRP B 584 
 HIS   0.005   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (10761)
  covalent geometry    : angle       0.62233 (14571)
  SS BOND              : bond        0.00348 (    3)
  SS BOND              : angle       0.95341 (    6)
  hydrogen bonds       : bond        0.04967 (  591)
  hydrogen bonds       : angle       4.11699 ( 1710)

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

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

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2616 Ramachandran restraints generated.
    1308 Oldfield, 0 Emsley, 1308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 136
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ILE cc_start: 0.8115 (mm) cc_final: 0.7892 (mt)
REVERT: A  345 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7154 (tpp)
REVERT: A  353 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7378 (mmm)
REVERT: A  412 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8008 (tm)
REVERT: A  647 HIS cc_start: 0.6577 (OUTLIER) cc_final: 0.6320 (t70)
REVERT: B  121 ARG cc_start: 0.7090 (mpt180) cc_final: 0.6622 (mpt-90)
REVERT: B  244 ASP cc_start: 0.7858 (t0) cc_final: 0.7626 (t70)
REVERT: B  441 ILE cc_start: 0.8968 (mt) cc_final: 0.8741 (mm)
REVERT: B  474 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8274 (mt-10)
REVERT: B  503 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8280 (tt0)
REVERT: B  517 TRP cc_start: 0.7776 (m100) cc_final: 0.6960 (t60)
REVERT: B  582 SER cc_start: 0.7606 (OUTLIER) cc_final: 0.7180 (p)
REVERT: C   26 SER cc_start: 0.8922 (OUTLIER) cc_final: 0.8528 (m)
REVERT: C   99 ILE cc_start: 0.8894 (mt) cc_final: 0.8453 (mp)
REVERT: C  103 GLN cc_start: 0.8403 (tp40) cc_final: 0.7595 (tp-100)
REVERT: D   97 SER cc_start: 0.8283 (t) cc_final: 0.8039 (p)
  outliers start: 38
  outliers final: 24
  residues processed: 165
  average time/residue: 0.5322
  time to fit residues: 94.6605
Evaluate side-chains
  165 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 134
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  345 MET
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  425 GLN
Chi-restraints excluded: chain A residue  439 VAL
Chi-restraints excluded: chain A residue  470 HIS
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  613 CYS
Chi-restraints excluded: chain A residue  647 HIS
Chi-restraints excluded: chain B residue   41 SER
Chi-restraints excluded: chain B residue   52 LEU
Chi-restraints excluded: chain B residue  113 SER
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  256 SER
Chi-restraints excluded: chain B residue  458 LEU
Chi-restraints excluded: chain B residue  503 GLU
Chi-restraints excluded: chain B residue  582 SER
Chi-restraints excluded: chain B residue  629 ILE
Chi-restraints excluded: chain C residue   26 SER
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   96 SER
Chi-restraints excluded: chain C residue  134 VAL
Chi-restraints excluded: chain D residue   38 ARG
Chi-restraints excluded: chain D residue  109 LEU
Chi-restraints excluded: chain D residue  116 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 129 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 60 optimal weight:    4.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN
B 607 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.104885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.079927 restraints weight = 14257.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 2.07
r_work: 0.2770 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2640 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8806
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.129  10764  Z= 0.213
  Angle     :  0.910  59.094  14577  Z= 0.510
  Chirality :  0.042   0.311   1662
  Planarity :  0.004   0.058   1828
  Dihedral  :  4.765  47.188   1529
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 21.70 %
    Favored  : 75.09 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 5.66 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.24), residues: 1308
  helix:  1.87 (0.20), residues: 685
  sheet: -0.11 (0.39), residues: 178
  loop : -1.18 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  44 
 TYR   0.015   0.001   TYR A 114 
 PHE   0.018   0.002   PHE B 493 
 TRP   0.008   0.001   TRP B 584 
 HIS   0.004   0.001   HIS A 510 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (10761)
  covalent geometry    : angle       0.90991 (14571)
  SS BOND              : bond        0.00342 (    3)
  SS BOND              : angle       0.93385 (    6)
  hydrogen bonds       : bond        0.05007 (  591)
  hydrogen bonds       : angle       4.11903 ( 1710)

===============================================================================
Job complete
usr+sys time: 3811.18 seconds
wall clock time: 65 minutes 31.43 seconds (3931.43 seconds total)