Starting phenix.real_space_refine
on Wed Aug  5 19:00:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p0g_17333/08_2026/8p0g_17333.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p0g_17333/08_2026/8p0g_17333.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p0g_17333/08_2026/8p0g_17333.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p0g_17333/08_2026/8p0g_17333.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p0g_17333/08_2026/8p0g_17333.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p0g_17333/08_2026/8p0g_17333.cif"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.018
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: 6
    Type Number    sf(0)   Gaussians
     P      19      5.49       5
     Mg      1      5.21       5
     S      68      5.16       5
     C    7119      2.51       5
     N    1979      2.21       5
     O    2145      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11331
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3644
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 453, 3644
          Classifications: {'peptide': 453}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 426}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 5307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 662, 5307
          Classifications: {'peptide': 662}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 628}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 1966
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 241, 1954
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 16, 'TRANS': 224}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 241, 1954
          Classifications: {'peptide': 241}
          Link IDs: {'PTRANS': 16, 'TRANS': 224}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1989
    Chain: "V"
      Number of atoms: 307
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 307
          Classifications: {'RNA': 14}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 8, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 3, 'rna3p': 10}
    Chain: "R"
      Number of atoms: 106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 106
          Classifications: {'RNA': 5}
          Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3}
          Link IDs: {'rna3p': 4}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR C  59 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR C  59 " occ=0.50
  Time building chain proxies: 2.92, per 1000 atoms: 0.26
  Number of scatterers: 11331
  At special positions: 0
  Unit cell: (102.548, 110.818, 95.932, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      68     16.00
     P      19     15.00
     Mg      1     11.99
     O    2145      8.00
     N    1979      7.00
     C    7119      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Conformation dependent library (CDL) restraints added in 607.7 milliseconds
  

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2588

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 16 sheets defined
      50.9% alpha, 10.2% beta
      5 base pairs and 12 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 176 through 184
    Processing helix  chain 'A' and resid 246 through 257
    Processing helix  chain 'A' and resid 270 through 272
      No H-bonds generated for 'chain 'A' and resid 270 through 272'
    Processing helix  chain 'A' and resid 273 through 286
      removed outlier: 3.706A  pdb=" N   LEU A 277 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 301
    Processing helix  chain 'A' and resid 304 through 316
      removed outlier: 3.715A  pdb=" N   GLU A 308 " --> pdb=" O   ASN A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 345
      removed outlier: 4.215A  pdb=" N   GLU A 339 " --> pdb=" O   PRO A 335 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ARG A 345 " --> pdb=" O   MET A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 381
      removed outlier: 4.555A  pdb=" N   ARG A 381 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 401
    Processing helix  chain 'A' and resid 485 through 493
    Processing helix  chain 'A' and resid 494 through 497
    Processing helix  chain 'A' and resid 498 through 515
      removed outlier: 3.615A  pdb=" N   ILE A 504 " --> pdb=" O   GLN A 500 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 557
    Processing helix  chain 'A' and resid 559 through 581
      removed outlier: 4.356A  pdb=" N   ARG A 571 " --> pdb=" O   ALA A 567 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   LEU A 572 " --> pdb=" O   ASN A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 592 through 599
      removed outlier: 3.532A  pdb=" N   GLU A 599 " --> pdb=" O   ASP A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 617
    Processing helix  chain 'B' and resid 13 through 20
      removed outlier: 4.024A  pdb=" N   GLU B  17 " --> pdb=" O   THR B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 49
      Proline residue:  B  44  - end of helix
      removed outlier: 4.453A  pdb=" N   TYR B  49 " --> pdb=" O   TYR B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 58
      removed outlier: 3.609A  pdb=" N   ALA B  57 " --> pdb=" O   ASN B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 70
    Processing helix  chain 'B' and resid 80 through 95
    Processing helix  chain 'B' and resid 95 through 108
    Processing helix  chain 'B' and resid 109 through 113
    Processing helix  chain 'B' and resid 114 through 121
    Processing helix  chain 'B' and resid 134 through 151
    Processing helix  chain 'B' and resid 157 through 171
      removed outlier: 3.843A  pdb=" N   GLU B 170 " --> pdb=" O   ALA B 166 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU B 171 " --> pdb=" O   ASP B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 225
    Processing helix  chain 'B' and resid 247 through 249
      No H-bonds generated for 'chain 'B' and resid 247 through 249'
    Processing helix  chain 'B' and resid 250 through 266
    Processing helix  chain 'B' and resid 277 through 287
    Processing helix  chain 'B' and resid 310 through 326
      removed outlier: 3.655A  pdb=" N   MET B 314 " --> pdb=" O   ASP B 310 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 344
      Proline residue:  B 338  - end of helix
    Processing helix  chain 'B' and resid 373 through 380
      removed outlier: 4.454A  pdb=" N   ARG B 378 " --> pdb=" O   ASP B 375 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL B 380 " --> pdb=" O   VAL B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 409
      removed outlier: 3.710A  pdb=" N   SER B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ILE B 408 " --> pdb=" O   ALA B 404 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLU B 409 " --> pdb=" O   LEU B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 451
    Processing helix  chain 'B' and resid 496 through 514
    Processing helix  chain 'B' and resid 518 through 537
    Processing helix  chain 'B' and resid 543 through 552
    Processing helix  chain 'B' and resid 558 through 562
    Processing helix  chain 'B' and resid 575 through 583
    Processing helix  chain 'B' and resid 587 through 596
    Processing helix  chain 'B' and resid 646 through 666
      removed outlier: 4.143A  pdb=" N   ASN B 650 " --> pdb=" O   LYS B 646 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   LYS B 651 " --> pdb=" O   ALA B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 694
    Processing helix  chain 'B' and resid 698 through 708
      removed outlier: 3.510A  pdb=" N   ARG B 708 " --> pdb=" O   ARG B 704 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 27
    Processing helix  chain 'C' and resid 27 through 32
      removed outlier: 3.667A  pdb=" N   SER C  32 " --> pdb=" O   PRO C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 33 through 35
      No H-bonds generated for 'chain 'C' and resid 33 through 35'
    Processing helix  chain 'C' and resid 36 through 42
      removed outlier: 4.136A  pdb=" N   THR C  40 " --> pdb=" O   THR C  36 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 52 through 62
      removed outlier: 3.706A  pdb=" N   ARG C  56 " --> pdb=" O   ALA C  52 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   VAL C  58 " --> pdb=" O   GLN C  54 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N  ATYR C  59 " --> pdb=" O   MET C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 108
      removed outlier: 4.303A  pdb=" N   ASP C 105 " --> pdb=" O   ILE C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 123
    Processing helix  chain 'C' and resid 123 through 135
    Processing helix  chain 'C' and resid 163 through 165
      No H-bonds generated for 'chain 'C' and resid 163 through 165'
    Processing helix  chain 'C' and resid 166 through 176
    Processing helix  chain 'C' and resid 177 through 180
      removed outlier: 3.834A  pdb=" N   THR C 180 " --> pdb=" O   PRO C 177 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 177 through 180'
    Processing helix  chain 'C' and resid 181 through 186
    Processing helix  chain 'C' and resid 189 through 200
    Processing helix  chain 'C' and resid 208 through 221
      removed outlier: 3.816A  pdb=" N   HIS C 214 " --> pdb=" O   GLU C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 245
      removed outlier: 4.077A  pdb=" N   MET C 240 " --> pdb=" O   ARG C 236 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   HIS C 242 " --> pdb=" O   ALA C 238 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   PHE C 243 " --> pdb=" O   GLU C 239 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   LEU C 244 " --> pdb=" O   MET C 240 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   CYS C 245 " --> pdb=" O   ALA C 241 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 242
      removed outlier: 7.585A  pdb=" N   TRP A 426 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   LEU A 475 " --> pdb=" O   MET A 451 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   VAL A 464 " --> pdb=" O   ILE A 263 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 242
      removed outlier: 6.840A  pdb=" N   ILE A 414 " --> pdb=" O   TRP A 426 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   MET A 428 " --> pdb=" O   CYS A 412 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   CYS A 412 " --> pdb=" O   MET A 428 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   LEU A 430 " --> pdb=" O   THR A 410 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   THR A 410 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 323
      removed outlier: 3.531A  pdb=" N   LYS A 322 " --> pdb=" O   THR B 356 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 445
    Processing sheet with id=AA5, first strand: chain 'A' and resid 526 through 528
    Processing sheet with id=AA6, first strand: chain 'A' and resid 584 through 586
    Processing sheet with id=AA7, first strand: chain 'B' and resid 124 through 126
      removed outlier: 3.648A  pdb=" N   ARG B 131 " --> pdb=" O   SER B 126 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 173 through 178
    Processing sheet with id=AA9, first strand: chain 'B' and resid 227 through 230
    Processing sheet with id=AB1, first strand: chain 'B' and resid 302 through 303
      removed outlier: 4.712A  pdb=" N   ASN B 453 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 345 through 348
      removed outlier: 3.619A  pdb=" N   LYS B 345 " --> pdb=" O   CYS B 387 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 470
    Processing sheet with id=AB4, first strand: chain 'C' and resid 67 through 69
    Processing sheet with id=AB5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AB6, first strand: chain 'C' and resid 142 through 143
    Processing sheet with id=AB7, first strand: chain 'C' and resid 150 through 154

    523 hydrogen bonds defined for protein.
    1441 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      14 hydrogen bonds
      28 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      12 stacking parallelities
  Total time for adding SS restraints: 2.09

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3620
        1.34 -     1.46: 1723
        1.46 -     1.57: 6124
        1.57 -     1.69: 36
        1.69 -     1.81: 114
  Bond restraints: 11617
  Sorted by residual:
  bond pdb=" N   MET B   1 "
       pdb=" CA  MET B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.91e+00
  bond pdb=" CB  PRO B 464 "
       pdb=" CG  PRO B 464 "
    ideal  model  delta    sigma   weight residual
    1.506  1.477  0.029 3.90e-02 6.57e+02 5.35e-01
  bond pdb=" C   LEU A 171 "
       pdb=" N   GLN A 172 "
    ideal  model  delta    sigma   weight residual
    1.332  1.322  0.010 1.40e-02 5.10e+03 5.21e-01
  bond pdb=" C   GLU C 201 "
       pdb=" N   PRO C 202 "
    ideal  model  delta    sigma   weight residual
    1.334  1.350 -0.016 2.34e-02 1.83e+03 4.85e-01
  bond pdb=" CB  PRO B 274 "
       pdb=" CG  PRO B 274 "
    ideal  model  delta    sigma   weight residual
    1.492  1.526 -0.034 5.00e-02 4.00e+02 4.59e-01
  ... (remaining 11612 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 15341
        0.98 -     1.96: 327
        1.96 -     2.94: 83
        2.94 -     3.92: 51
        3.92 -     4.89: 8
  Bond angle restraints: 15810
  Sorted by residual:
  angle pdb=" O4'   A V   7 "
        pdb=" C1'   A V   7 "
        pdb=" N9    A V   7 "
      ideal   model   delta    sigma   weight residual
     108.20  110.89   -2.69 8.00e-01 1.56e+00 1.13e+01
  angle pdb=" O5'   A V   7 "
        pdb=" C5'   A V   7 "
        pdb=" C4'   A V   7 "
      ideal   model   delta    sigma   weight residual
     109.40  111.99   -2.59 8.00e-01 1.56e+00 1.05e+01
  angle pdb=" O5'   A V   6 "
        pdb=" C5'   A V   6 "
        pdb=" C4'   A V   6 "
      ideal   model   delta    sigma   weight residual
     109.40  111.72   -2.32 8.00e-01 1.56e+00 8.38e+00
  angle pdb=" O5'   A V  10 "
        pdb=" C5'   A V  10 "
        pdb=" C4'   A V  10 "
      ideal   model   delta    sigma   weight residual
     109.40  111.69   -2.29 8.00e-01 1.56e+00 8.20e+00
  angle pdb=" O5'   G V  13 "
        pdb=" C5'   G V  13 "
        pdb=" C4'   G V  13 "
      ideal   model   delta    sigma   weight residual
     109.40  111.67   -2.27 8.00e-01 1.56e+00 8.03e+00
  ... (remaining 15805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.71: 6162
       16.71 -    33.42: 698
       33.42 -    50.13: 177
       50.13 -    66.84: 68
       66.84 -    83.55: 18
  Dihedral angle restraints: 7123
    sinusoidal: 3138
      harmonic: 3985
  Sorted by residual:
  dihedral pdb=" CA  GLU C 201 "
           pdb=" C   GLU C 201 "
           pdb=" N   PRO C 202 "
           pdb=" CA  PRO C 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.62  -22.38     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CG  ARG B 581 "
           pdb=" CD  ARG B 581 "
           pdb=" NE  ARG B 581 "
           pdb=" CZ  ARG B 581 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.06   44.94     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CG  ARG A 323 "
           pdb=" CD  ARG A 323 "
           pdb=" NE  ARG A 323 "
           pdb=" CZ  ARG A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.58   44.42     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 7120 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1162
       0.028 -    0.055: 404
       0.055 -    0.083: 93
       0.083 -    0.110: 92
       0.110 -    0.138: 23
  Chirality restraints: 1774
  Sorted by residual:
  chirality pdb=" CA  VAL B 491 "
            pdb=" N   VAL B 491 "
            pdb=" C   VAL B 491 "
            pdb=" CB  VAL B 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality pdb=" CA  ILE A 192 "
            pdb=" N   ILE A 192 "
            pdb=" C   ILE A 192 "
            pdb=" CB  ILE A 192 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" CA  ILE A 527 "
            pdb=" N   ILE A 527 "
            pdb=" C   ILE A 527 "
            pdb=" CB  ILE A 527 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.02e-01
  ... (remaining 1771 not shown)

  Planarity restraints: 1953
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A V   7 "    0.017 2.00e-02 2.50e+03   7.91e-03 1.72e+00
        pdb=" N9    A V   7 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8    A V   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A V   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A V   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A V   7 "    0.002 2.00e-02 2.50e+03
        pdb=" N6    A V   7 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    A V   7 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A V   7 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A V   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A V   7 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 201 "   -0.021 5.00e-02 4.00e+02   3.14e-02 1.58e+00
        pdb=" N   PRO C 202 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C 202 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 202 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  96 "    0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO B  97 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B  97 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B  97 "    0.017 5.00e-02 4.00e+02
  ... (remaining 1950 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 100
        2.55 -     3.14: 8783
        3.14 -     3.73: 17692
        3.73 -     4.31: 24963
        4.31 -     4.90: 42634
  Nonbonded interactions: 94172
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 423 "
            pdb="MG    MG B 801 "
     model   vdw
     1.965 2.170
  nonbonded pdb=" OD1 ASN A 516 "
            pdb=" OG  SER A 518 "
     model   vdw
     2.070 3.040
  nonbonded pdb=" OE1 GLU C  74 "
            pdb=" OG  SER C 112 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" OE1 GLU A 369 "
            pdb=" NH2 ARG B 527 "
     model   vdw
     2.168 3.120
  nonbonded pdb=" OG1 THR B  62 "
            pdb=" OD2 ASP B 312 "
     model   vdw
     2.220 3.040
  ... (remaining 94167 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=0.50 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:             2.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.970
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
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   0.034  11617  Z= 0.093
  Angle     :  0.432   4.895  15810  Z= 0.244
  Chirality :  0.037   0.138   1774
  Planarity :  0.003   0.031   1953
  Dihedral  : 16.061  83.552   4535
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.65 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  : 12.29 %
    Favored  : 87.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.93 (0.24), residues: 1345
  helix:  2.17 (0.22), residues: 625
  sheet: -0.44 (0.44), residues: 127
  loop : -0.87 (0.26), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 198 
 TYR   0.013   0.001   TYR B  22 
 PHE   0.015   0.001   PHE C  41 
 TRP   0.005   0.001   TRP A 336 
 HIS   0.002   0.000   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00198 /  0.09 (11617)
  covalent geometry    : angle       0.43221 /  0.24 (15810)
  hydrogen bonds       : bond        0.14411 /  9.81 (  533)
  hydrogen bonds       : angle       5.37939 /  3.92 ( 1469)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  101 ILE cc_start: 0.8204 (pt) cc_final: 0.7930 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 129
  average time/residue: 0.1549
  time to fit residues: 26.5233
Evaluate side-chains
  72 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain B residue  289 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0070
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.0870
   chunk 77 optimal weight:    9.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    2.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 453 ASN
B 582 HIS
C 131 GLN
C 242 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.052450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.040113 restraints weight = 72568.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.2774 rms_B_bonded: 4.05
r_work: 0.2618 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2622
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2622 r_free = 0.2622    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2622 r_free = 0.2622    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8945
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  11617  Z= 0.194
  Angle     :  0.574   7.515  15810  Z= 0.296
  Chirality :  0.041   0.223   1774
  Planarity :  0.005   0.061   1953
  Dihedral  :  9.733  73.289   1771
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.58 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.27 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.93 (0.24), residues: 1345
  helix:  2.21 (0.22), residues: 616
  sheet: -0.57 (0.44), residues: 127
  loop : -0.82 (0.25), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 701 
 TYR   0.023   0.002   TYR B 533 
 PHE   0.025   0.002   PHE C  41 
 TRP   0.011   0.001   TRP A 253 
 HIS   0.006   0.001   HIS A 434 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.19 (11617)
  covalent geometry    : angle       0.57408 /  0.30 (15810)
  hydrogen bonds       : bond        0.04415 /  2.95 (  533)
  hydrogen bonds       : angle       4.68180 /  3.37 ( 1469)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   11 CYS cc_start: 0.9242 (m) cc_final: 0.8993 (p)
  outliers start: 21
  outliers final: 11
  residues processed: 88
  average time/residue: 0.1138
  time to fit residues: 14.8600
Evaluate side-chains
  81 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 135 optimal weight:   10.0000
   chunk 121 optimal weight:    3.9990
   chunk 71 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 75 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   chunk 50 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 214 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.052416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.040276 restraints weight = 72514.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 4.02
r_work: 0.2621 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2626
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2626
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8940
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  11617  Z= 0.137
  Angle     :  0.520   6.343  15810  Z= 0.267
  Chirality :  0.039   0.190   1774
  Planarity :  0.004   0.040   1953
  Dihedral  :  9.614  73.285   1769
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.73 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.11 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.81 (0.23), residues: 1345
  helix:  2.04 (0.21), residues: 624
  sheet: -0.71 (0.43), residues: 127
  loop : -0.83 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  43 
 TYR   0.020   0.001   TYR B 533 
 PHE   0.026   0.001   PHE C  41 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00314 /  0.14 (11617)
  covalent geometry    : angle       0.52044 /  0.27 (15810)
  hydrogen bonds       : bond        0.03786 /  2.54 (  533)
  hydrogen bonds       : angle       4.43204 /  3.18 ( 1469)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 70
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   11 CYS cc_start: 0.9250 (m) cc_final: 0.8947 (p)
  outliers start: 30
  outliers final: 14
  residues processed: 93
  average time/residue: 0.0984
  time to fit residues: 14.1707
Evaluate side-chains
  81 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue  146 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 21 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 39 optimal weight:    0.4980
   chunk 111 optimal weight:    0.0030
   chunk 34 optimal weight:    6.9990
   chunk 14 optimal weight:    6.9990
   chunk 119 optimal weight:    8.9990
   chunk 132 optimal weight:    4.9990
   chunk 57 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   overall best weight:    2.6996

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.050899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.038843 restraints weight = 66926.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.2737 rms_B_bonded: 3.84
r_work: 0.2583 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8985
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  11617  Z= 0.226
  Angle     :  0.565   5.717  15810  Z= 0.288
  Chirality :  0.041   0.243   1774
  Planarity :  0.004   0.041   1953
  Dihedral  :  9.642  73.244   1769
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.55 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.93 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.75 (0.23), residues: 1345
  helix:  1.94 (0.21), residues: 626
  sheet: -0.65 (0.43), residues: 125
  loop : -0.82 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  43 
 TYR   0.023   0.001   TYR B 533 
 PHE   0.024   0.002   PHE C  41 
 TRP   0.010   0.001   TRP A 253 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00520 /  0.23 (11617)
  covalent geometry    : angle       0.56541 /  0.29 (15810)
  hydrogen bonds       : bond        0.03969 /  2.67 (  533)
  hydrogen bonds       : angle       4.45493 /  3.18 ( 1469)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 67
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  617 MET cc_start: 0.9346 (mtm) cc_final: 0.8955 (mtm)
  outliers start: 30
  outliers final: 20
  residues processed: 87
  average time/residue: 0.0919
  time to fit residues: 12.8094
Evaluate side-chains
  86 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  399 THR
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 115 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 116 optimal weight:    0.8980
   overall best weight:    1.2782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.051618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.039278 restraints weight = 88889.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.2752 rms_B_bonded: 4.44
r_work: 0.2585 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.2585
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8973
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11617  Z= 0.131
  Angle     :  0.509   6.700  15810  Z= 0.260
  Chirality :  0.039   0.174   1774
  Planarity :  0.004   0.043   1953
  Dihedral  :  9.604  73.172   1768
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.10 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.59 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.84 (0.23), residues: 1345
  helix:  1.97 (0.21), residues: 626
  sheet: -0.49 (0.43), residues: 121
  loop : -0.75 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  43 
 TYR   0.020   0.001   TYR B 533 
 PHE   0.030   0.001   PHE C  41 
 TRP   0.010   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 (11617)
  covalent geometry    : angle       0.50908 /  0.26 (15810)
  hydrogen bonds       : bond        0.03528 /  2.38 (  533)
  hydrogen bonds       : angle       4.33091 /  3.10 ( 1469)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 69
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  604 ASN cc_start: 0.9259 (OUTLIER) cc_final: 0.8995 (t0)
REVERT: C  101 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.8026 (tt)
  outliers start: 29
  outliers final: 20
  residues processed: 89
  average time/residue: 0.0916
  time to fit residues: 12.8866
Evaluate side-chains
  89 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 67
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain A residue  604 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  601 VAL
Chi-restraints excluded: chain B residue  620 ILE
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 115 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 31 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 127 optimal weight:    0.7980
   chunk 110 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    1.7184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.051230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.038748 restraints weight = 89504.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.2736 rms_B_bonded: 4.51
r_work: 0.2562 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.2562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2566
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2566 r_free = 0.2566    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2566 r_free = 0.2566    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2566
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8996
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  11617  Z= 0.160
  Angle     :  0.523   7.977  15810  Z= 0.264
  Chirality :  0.040   0.285   1774
  Planarity :  0.004   0.042   1953
  Dihedral  :  9.585  73.195   1768
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.55 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.92 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.86 (0.23), residues: 1345
  helix:  2.01 (0.21), residues: 625
  sheet: -0.51 (0.43), residues: 121
  loop : -0.75 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 198 
 TYR   0.021   0.001   TYR B 533 
 PHE   0.029   0.001   PHE C  41 
 TRP   0.009   0.001   TRP B 230 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00371 /  0.16 (11617)
  covalent geometry    : angle       0.52292 /  0.26 (15810)
  hydrogen bonds       : bond        0.03570 /  2.40 (  533)
  hydrogen bonds       : angle       4.33739 /  3.10 ( 1469)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 68
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  569 MET cc_start: 0.9332 (mmm) cc_final: 0.8806 (tpp)
REVERT: A  604 ASN cc_start: 0.9283 (OUTLIER) cc_final: 0.9007 (t0)
REVERT: A  617 MET cc_start: 0.9344 (mtm) cc_final: 0.8967 (mtm)
REVERT: C  101 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8075 (tt)
  outliers start: 33
  outliers final: 24
  residues processed: 91
  average time/residue: 0.0883
  time to fit residues: 12.9187
Evaluate side-chains
  95 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 69
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  526 GLU
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain A residue  604 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  399 THR
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  601 VAL
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue   73 LYS
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   chunk 45 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 85 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    2.0584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.050646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.038732 restraints weight = 77302.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.2736 rms_B_bonded: 4.10
r_work: 0.2569 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.2569
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2573
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2573 r_free = 0.2573    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2573 r_free = 0.2573    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2573
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8988
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11617  Z= 0.179
  Angle     :  0.534   9.361  15810  Z= 0.269
  Chirality :  0.040   0.151   1774
  Planarity :  0.004   0.042   1953
  Dihedral  :  9.604  73.114   1768
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.09 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.84 (0.23), residues: 1345
  helix:  1.99 (0.21), residues: 625
  sheet: -0.52 (0.43), residues: 121
  loop : -0.77 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  43 
 TYR   0.021   0.001   TYR B 533 
 PHE   0.028   0.001   PHE C  41 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.18 (11617)
  covalent geometry    : angle       0.53363 /  0.27 (15810)
  hydrogen bonds       : bond        0.03631 /  2.44 (  533)
  hydrogen bonds       : angle       4.33958 /  3.10 ( 1469)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 69
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  569 MET cc_start: 0.9318 (mmm) cc_final: 0.8798 (tpp)
REVERT: A  604 ASN cc_start: 0.9283 (OUTLIER) cc_final: 0.8995 (t0)
REVERT: A  617 MET cc_start: 0.9310 (mtm) cc_final: 0.8882 (mtm)
REVERT: B  652 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8464 (tt0)
REVERT: C  101 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8115 (tt)
  outliers start: 31
  outliers final: 23
  residues processed: 90
  average time/residue: 0.0948
  time to fit residues: 13.7194
Evaluate side-chains
  93 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 67
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  483 PHE
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain A residue  604 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  211 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  601 VAL
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0040
   chunk 112 optimal weight:    4.9990
   chunk 129 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 130 optimal weight:    7.9990
   chunk 121 optimal weight:    1.9990
   chunk 47 optimal weight:    0.3980
   chunk 83 optimal weight:    0.9990
   overall best weight:    0.6394

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.051626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.039321 restraints weight = 99024.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 4.67
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8893
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  11617  Z= 0.103
  Angle     :  0.513  10.739  15810  Z= 0.257
  Chirality :  0.038   0.159   1774
  Planarity :  0.004   0.045   1953
  Dihedral  :  9.604  73.135   1768
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.34 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.90 (0.23), residues: 1345
  helix:  2.03 (0.21), residues: 626
  sheet: -0.47 (0.43), residues: 121
  loop : -0.72 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 545 
 TYR   0.017   0.001   TYR B 533 
 PHE   0.031   0.001   PHE C  41 
 TRP   0.010   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.10 (11617)
  covalent geometry    : angle       0.51306 /  0.26 (15810)
  hydrogen bonds       : bond        0.03263 /  2.19 (  533)
  hydrogen bonds       : angle       4.24328 /  3.04 ( 1469)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  569 MET cc_start: 0.8938 (mmm) cc_final: 0.8426 (tpp)
REVERT: A  604 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8898 (t0)
REVERT: A  617 MET cc_start: 0.8909 (mtm) cc_final: 0.8633 (mtm)
REVERT: B  652 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8377 (tt0)
REVERT: C  101 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7905 (tt)
  outliers start: 27
  outliers final: 17
  residues processed: 85
  average time/residue: 0.0889
  time to fit residues: 12.2819
Evaluate side-chains
  88 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain A residue  604 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  385 ILE
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 130 optimal weight:    0.1980
   chunk 135 optimal weight:   10.0000
   chunk 118 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9980
   chunk 128 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 120 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  51 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.051759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.039608 restraints weight = 92235.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.2766 rms_B_bonded: 4.52
r_work: 0.2594 rms_B_bonded: 4.94 restraints_weight: 0.5000
r_work (final): 0.2594
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2598
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2598 r_free = 0.2598    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2598 r_free = 0.2598    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2598
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8962
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11617  Z= 0.107
  Angle     :  0.509  11.993  15810  Z= 0.256
  Chirality :  0.038   0.152   1774
  Planarity :  0.004   0.045   1953
  Dihedral  :  9.573  73.194   1768
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.42 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.96 (0.23), residues: 1345
  helix:  2.07 (0.21), residues: 626
  sheet: -0.40 (0.43), residues: 121
  loop : -0.70 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 198 
 TYR   0.017   0.001   TYR B 533 
 PHE   0.029   0.001   PHE C  41 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.026   0.001   HIS C  51 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 (11617)
  covalent geometry    : angle       0.50934 /  0.26 (15810)
  hydrogen bonds       : bond        0.03187 /  2.14 (  533)
  hydrogen bonds       : angle       4.19047 /  3.00 ( 1469)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  569 MET cc_start: 0.9300 (mmm) cc_final: 0.8776 (tpp)
REVERT: A  617 MET cc_start: 0.9286 (mtm) cc_final: 0.8890 (mtm)
REVERT: C  101 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8047 (tt)
  outliers start: 24
  outliers final: 19
  residues processed: 82
  average time/residue: 0.0871
  time to fit residues: 11.5884
Evaluate side-chains
  88 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  399 THR
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 94 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 104 optimal weight:    9.9990
   chunk 98 optimal weight:    2.9990
   chunk 114 optimal weight:    3.9990
   chunk 131 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  51 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.051298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.038745 restraints weight = 93523.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.2741 rms_B_bonded: 4.63
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8910
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11617  Z= 0.167
  Angle     :  0.540  12.362  15810  Z= 0.270
  Chirality :  0.039   0.158   1774
  Planarity :  0.004   0.044   1953
  Dihedral  :  9.579  73.136   1768
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.50 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.94 (0.23), residues: 1345
  helix:  2.05 (0.21), residues: 630
  sheet: -0.40 (0.43), residues: 121
  loop : -0.72 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 545 
 TYR   0.020   0.001   TYR B 533 
 PHE   0.029   0.001   PHE C  41 
 TRP   0.009   0.001   TRP B 230 
 HIS   0.027   0.001   HIS C  51 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.17 (11617)
  covalent geometry    : angle       0.53999 /  0.27 (15810)
  hydrogen bonds       : bond        0.03369 /  2.26 (  533)
  hydrogen bonds       : angle       4.22713 /  3.02 ( 1469)

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

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

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2690 Ramachandran restraints generated.
    1345 Oldfield, 0 Emsley, 1345 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 67
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  569 MET cc_start: 0.8968 (mmm) cc_final: 0.8478 (tpp)
REVERT: A  604 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8890 (t0)
REVERT: A  617 MET cc_start: 0.8925 (mtm) cc_final: 0.8612 (mtm)
REVERT: C  101 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7897 (tt)
  outliers start: 26
  outliers final: 22
  residues processed: 82
  average time/residue: 0.0851
  time to fit residues: 11.4209
Evaluate side-chains
  91 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ASP
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  574 MET
Chi-restraints excluded: chain A residue  604 ASN
Chi-restraints excluded: chain B residue   22 TYR
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  349 MET
Chi-restraints excluded: chain B residue  395 MET
Chi-restraints excluded: chain B residue  399 THR
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  555 THR
Chi-restraints excluded: chain B residue  649 LEU
Chi-restraints excluded: chain B residue  652 GLU
Chi-restraints excluded: chain B residue  679 THR
Chi-restraints excluded: chain C residue   51 HIS
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 115 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   chunk 135 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0370
   chunk 119 optimal weight:    6.9990
   chunk 127 optimal weight:    0.4980
   overall best weight:    0.6658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  51 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.051881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.039618 restraints weight = 77494.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.2768 rms_B_bonded: 4.22
r_work: 0.2607 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2611
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2611 r_free = 0.2611    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2611
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8959
moved from start:          0.2440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11617  Z= 0.107
  Angle     :  0.521  12.498  15810  Z= 0.261
  Chirality :  0.038   0.150   1774
  Planarity :  0.004   0.045   1953
  Dihedral  :  9.594  73.162   1768
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.58 %
    Favored  : 81.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.97 (0.23), residues: 1345
  helix:  2.07 (0.21), residues: 629
  sheet: -0.38 (0.43), residues: 121
  loop : -0.71 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  43 
 TYR   0.017   0.001   TYR B 533 
 PHE   0.031   0.001   PHE C  41 
 TRP   0.009   0.001   TRP A 336 
 HIS   0.026   0.001   HIS C  51 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 (11617)
  covalent geometry    : angle       0.52069 /  0.26 (15810)
  hydrogen bonds       : bond        0.03204 /  2.15 (  533)
  hydrogen bonds       : angle       4.19810 /  3.00 ( 1469)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2742.75 seconds
wall clock time: 48 minutes 3.10 seconds (2883.10 seconds total)