Starting phenix.real_space_refine
on Tue Jul 29 11:28:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p0g_17333/07_2025/8p0g_17333.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p0g_17333/07_2025/8p0g_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_17333/07_2025/8p0g_17333.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p0g_17333/07_2025/8p0g_17333.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p0g_17333/07_2025/8p0g_17333.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p0g_17333/07_2025/8p0g_17333.cif"
  }
  resolution = 3.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.86, per 1000 atoms: 0.69
  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: 2.61
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 3.51
  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: 4.08

  Time building geometry restraints manager: 3.17 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: 15402
        0.98 -     1.96: 298
        1.96 -     2.94: 51
        2.94 -     3.92: 51
        3.92 -     4.89: 8
  Bond angle restraints: 15810
  Sorted by residual:
  angle pdb=" N   GLU C 201 "
        pdb=" CA  GLU C 201 "
        pdb=" C   GLU C 201 "
      ideal   model   delta    sigma   weight residual
     109.81  114.70   -4.89 2.21e+00 2.05e-01 4.89e+00
  angle pdb=" C   ASP A 405 "
        pdb=" N   ARG A 406 "
        pdb=" CA  ARG A 406 "
      ideal   model   delta    sigma   weight residual
     121.54  125.43   -3.89 1.91e+00 2.74e-01 4.15e+00
  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 1.50e+00 4.44e-01 3.21e+00
  angle pdb=" N   GLU B 668 "
        pdb=" CA  GLU B 668 "
        pdb=" C   GLU B 668 "
      ideal   model   delta    sigma   weight residual
     114.75  112.71    2.04 1.26e+00 6.30e-01 2.62e+00
  angle pdb=" C   PHE B 666 "
        pdb=" N   PRO B 667 "
        pdb=" CA  PRO B 667 "
      ideal   model   delta    sigma   weight residual
     121.91  119.80    2.11 1.35e+00 5.49e-01 2.44e+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: 1165
       0.028 -    0.055: 423
       0.055 -    0.083: 90
       0.083 -    0.110: 73
       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:             2.350
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     31.670
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
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= 0.087
  Angle     :  0.417   4.895  15810  Z= 0.209
  Chirality :  0.036   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 : 5.02
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.24), 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
 TRP   0.005   0.001   TRP A 336 
 HIS   0.002   0.000   HIS B 291 
 PHE   0.015   0.001   PHE C  41 
 TYR   0.013   0.001   TYR B  22 
 ARG   0.001   0.000   ARG C 198 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14411 (  533)
  hydrogen bonds       : angle       5.37939 ( 1469)
  covalent geometry    : bond        0.00196 (11617)
  covalent geometry    : angle       0.41650 (15810)

*********************** 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  : 1.235 
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: 0.3274
  time to fit residues: 55.9692
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  : 1.228 
-------------------------------------------------------------------------------
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 114 optimal weight:    0.9990
   chunk 103 optimal weight:    7.9990
   chunk 57 optimal weight:    9.9990
   chunk 35 optimal weight:    8.9990
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 106 optimal weight:    0.5980
   chunk 41 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3176 r_free = 0.3176 target = 0.052867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.040368 restraints weight = 77349.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.2782 rms_B_bonded: 4.24
r_work: 0.2616 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2616
-------------------------------------------------------------------------------
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 = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2622
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8812
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11617  Z= 0.153
  Angle     :  0.540   6.170  15810  Z= 0.277
  Chirality :  0.039   0.171   1774
  Planarity :  0.004   0.052   1953
  Dihedral  :  9.745  73.367   1771
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  3.58 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 14.11 %
    Favored  : 84.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.24), residues: 1345
  helix:  2.21 (0.22), residues: 616
  sheet: -0.59 (0.44), residues: 127
  loop : -0.77 (0.26), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 253 
 HIS   0.005   0.001   HIS B 291 
 PHE   0.026   0.001   PHE C  41 
 TYR   0.019   0.001   TYR B 533 
 ARG   0.007   0.001   ARG B 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04074 (  533)
  hydrogen bonds       : angle       4.53446 ( 1469)
  covalent geometry    : bond        0.00352 (11617)
  covalent geometry    : angle       0.53988 (15810)

*********************** 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
  97 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 76
  time to evaluate  : 1.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  449 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7997 (mt-10)
REVERT: C   11 CYS cc_start: 0.9289 (m) cc_final: 0.9016 (p)
  outliers start: 21
  outliers final: 9
  residues processed: 90
  average time/residue: 0.2356
  time to fit residues: 31.2648
Evaluate side-chains
  79 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
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  449 GLU
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  407 SER
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain C residue   73 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 119 optimal weight:    0.0000
   chunk 51 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 29 optimal weight:    6.9990
   chunk 72 optimal weight:    8.9990
   chunk 54 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 135 optimal weight:    8.9990
   chunk 96 optimal weight:    0.6980
   chunk 95 optimal weight:    3.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
C 214 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.051918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.039471 restraints weight = 80866.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 4.30
r_work: 0.2593 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.2593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2597
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2597 r_free = 0.2597    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2597 r_free = 0.2597    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2597
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8833
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11617  Z= 0.162
  Angle     :  0.522   6.141  15810  Z= 0.267
  Chirality :  0.039   0.186   1774
  Planarity :  0.004   0.040   1953
  Dihedral  :  9.645  73.272   1769
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.25 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 13.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.24), residues: 1345
  helix:  2.07 (0.21), residues: 619
  sheet: -0.49 (0.44), residues: 121
  loop : -0.77 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 253 
 HIS   0.006   0.001   HIS B 291 
 PHE   0.031   0.001   PHE C  41 
 TYR   0.021   0.001   TYR B 533 
 ARG   0.004   0.000   ARG C  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03699 (  533)
  hydrogen bonds       : angle       4.37885 ( 1469)
  covalent geometry    : bond        0.00374 (11617)
  covalent geometry    : angle       0.52245 (15810)

*********************** 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: 33
    poor density    : 67
  time to evaluate  : 1.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  652 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8554 (tt0)
  outliers start: 33
  outliers final: 18
  residues processed: 91
  average time/residue: 0.2069
  time to fit residues: 29.0156
Evaluate side-chains
  83 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
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  286 GLU
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   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  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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 52 optimal weight:    0.4980
   chunk 19 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 96 optimal weight:    0.4980
   chunk 27 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.5984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.051513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.040030 restraints weight = 52111.585|
|-----------------------------------------------------------------------------|
r_work (start): 0.2778 rms_B_bonded: 3.35
r_work: 0.2635 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11617  Z= 0.151
  Angle     :  0.515   6.262  15810  Z= 0.261
  Chirality :  0.039   0.155   1774
  Planarity :  0.004   0.041   1953
  Dihedral  :  9.607  73.217   1768
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  4.17 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 14.77 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.24), residues: 1345
  helix:  2.05 (0.21), residues: 621
  sheet: -0.41 (0.44), residues: 121
  loop : -0.72 (0.26), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 
 PHE   0.029   0.001   PHE C  41 
 TYR   0.021   0.001   TYR B 533 
 ARG   0.004   0.000   ARG C  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03515 (  533)
  hydrogen bonds       : angle       4.34596 ( 1469)
  covalent geometry    : bond        0.00348 (11617)
  covalent geometry    : angle       0.51516 (15810)

*********************** 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
  98 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 68
  time to evaluate  : 2.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  449 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7895 (mt-10)
REVERT: B  652 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8501 (tt0)
REVERT: C  101 ILE cc_start: 0.8434 (OUTLIER) cc_final: 0.8053 (tt)
  outliers start: 30
  outliers final: 18
  residues processed: 88
  average time/residue: 0.2576
  time to fit residues: 36.3864
Evaluate side-chains
  87 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 1.328 
-------------------------------------------------------------------------------
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  286 GLU
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  449 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  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  450 VAL
Chi-restraints excluded: chain B residue  491 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 119 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 129 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.051591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.039377 restraints weight = 78160.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.2756 rms_B_bonded: 4.21
r_work: 0.2593 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.2593
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2597
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2597 r_free = 0.2597    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 = 0.2597 r_free = 0.2597    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2597
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11617  Z= 0.136
  Angle     :  0.506   8.474  15810  Z= 0.255
  Chirality :  0.039   0.208   1774
  Planarity :  0.004   0.043   1953
  Dihedral  :  9.599  73.193   1768
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.55 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.10 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.24), residues: 1345
  helix:  2.10 (0.21), residues: 619
  sheet: -0.40 (0.43), residues: 121
  loop : -0.73 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 
 PHE   0.028   0.001   PHE C  41 
 TYR   0.020   0.001   TYR B 533 
 ARG   0.002   0.000   ARG C  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03361 (  533)
  hydrogen bonds       : angle       4.30533 ( 1469)
  covalent geometry    : bond        0.00316 (11617)
  covalent geometry    : angle       0.50558 (15810)

*********************** 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
  100 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 68
  time to evaluate  : 1.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  617 MET cc_start: 0.9258 (mtm) cc_final: 0.8597 (mtm)
REVERT: B  652 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8480 (tt0)
REVERT: C  101 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8078 (tt)
  outliers start: 32
  outliers final: 22
  residues processed: 90
  average time/residue: 0.2771
  time to fit residues: 41.1407
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  : 2.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  276 CYS
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  483 PHE
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  450 VAL
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  101 ILE
Chi-restraints excluded: chain C residue  146 MET
Chi-restraints excluded: chain C residue  181 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 121 optimal weight:    3.9990
   chunk 133 optimal weight:    0.8980
   chunk 51 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.1582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.051551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.039387 restraints weight = 88810.832|
|-----------------------------------------------------------------------------|
r_work (start): 0.2758 rms_B_bonded: 4.45
r_work: 0.2588 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2588
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2592
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2592 r_free = 0.2592    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 = 0.2592 r_free = 0.2592    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2592
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8835
moved from start:          0.2312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11617  Z= 0.123
  Angle     :  0.499   8.453  15810  Z= 0.250
  Chirality :  0.038   0.141   1774
  Planarity :  0.004   0.044   1953
  Dihedral  :  9.595  73.177   1768
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.32 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.18 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.24), residues: 1345
  helix:  2.14 (0.21), residues: 621
  sheet: -0.35 (0.43), residues: 121
  loop : -0.69 (0.26), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 
 PHE   0.031   0.001   PHE C  41 
 TYR   0.019   0.001   TYR B 533 
 ARG   0.003   0.000   ARG C  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03241 (  533)
  hydrogen bonds       : angle       4.23194 ( 1469)
  covalent geometry    : bond        0.00283 (11617)
  covalent geometry    : angle       0.49940 (15810)

*********************** 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
  98 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 70
  time to evaluate  : 1.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  449 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8022 (mt-10)
REVERT: A  604 ASN cc_start: 0.9263 (OUTLIER) cc_final: 0.9002 (t0)
REVERT: A  617 MET cc_start: 0.9290 (mtm) cc_final: 0.8564 (mtm)
REVERT: B  652 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8497 (tt0)
REVERT: C  101 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8098 (tt)
  outliers start: 28
  outliers final: 19
  residues processed: 88
  average time/residue: 0.1950
  time to fit residues: 27.6057
Evaluate side-chains
  92 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 1.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  276 CYS
Chi-restraints excluded: chain A residue  286 GLU
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  449 GLU
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  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  450 VAL
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  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 11 optimal weight:    5.9990
   chunk 114 optimal weight:    5.9990
   chunk 123 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 100 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    1.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.051120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.039224 restraints weight = 76828.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.2752 rms_B_bonded: 4.09
r_work: 0.2591 rms_B_bonded: 4.58 restraints_weight: 0.5000
r_work (final): 0.2591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2596
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2596 r_free = 0.2596    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 = 0.2596 r_free = 0.2596    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2596
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8835
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  11617  Z= 0.143
  Angle     :  0.515   8.230  15810  Z= 0.258
  Chirality :  0.038   0.141   1774
  Planarity :  0.004   0.043   1953
  Dihedral  :  9.617  73.146   1768
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.55 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.92 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.23), residues: 1345
  helix:  2.06 (0.21), residues: 627
  sheet: -0.34 (0.43), residues: 121
  loop : -0.70 (0.26), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 
 PHE   0.030   0.001   PHE C  41 
 TYR   0.020   0.001   TYR B 533 
 ARG   0.004   0.000   ARG B 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03340 (  533)
  hydrogen bonds       : angle       4.25581 ( 1469)
  covalent geometry    : bond        0.00332 (11617)
  covalent geometry    : angle       0.51455 (15810)

*********************** 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
  97 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 1.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  449 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7997 (mt-10)
REVERT: A  569 MET cc_start: 0.9299 (mmm) cc_final: 0.8821 (tpp)
REVERT: A  604 ASN cc_start: 0.9274 (OUTLIER) cc_final: 0.9000 (t0)
REVERT: A  617 MET cc_start: 0.9283 (mtm) cc_final: 0.8560 (mtm)
REVERT: C  101 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8106 (tt)
  outliers start: 27
  outliers final: 22
  residues processed: 87
  average time/residue: 0.2200
  time to fit residues: 30.3116
Evaluate side-chains
  94 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
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  286 GLU
Chi-restraints excluded: chain A residue  294 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  449 GLU
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  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  450 VAL
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 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 78 optimal weight:    0.8980
   chunk 118 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 128 optimal weight:    9.9990
   chunk 57 optimal weight:    0.3980
   chunk 76 optimal weight:    4.9990
   chunk 81 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
C  51 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.051708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.038975 restraints weight = 105895.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.2750 rms_B_bonded: 4.94
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2747
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.2464

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= 0.116
  Angle     :  0.508   9.249  15810  Z= 0.255
  Chirality :  0.038   0.141   1774
  Planarity :  0.004   0.045   1953
  Dihedral  :  9.616  73.136   1768
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.01 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.24), residues: 1345
  helix:  2.11 (0.21), residues: 626
  sheet: -0.49 (0.42), residues: 125
  loop : -0.70 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.023   0.001   HIS C  51 
 PHE   0.031   0.001   PHE C  41 
 TYR   0.018   0.001   TYR B 533 
 ARG   0.004   0.000   ARG B 681 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03163 (  533)
  hydrogen bonds       : angle       4.20860 ( 1469)
  covalent geometry    : bond        0.00267 (11617)
  covalent geometry    : angle       0.50848 (15810)

*********************** 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
  94 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  604 ASN cc_start: 0.9191 (OUTLIER) cc_final: 0.8901 (t0)
REVERT: C  101 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7911 (tt)
  outliers start: 26
  outliers final: 22
  residues processed: 84
  average time/residue: 0.1915
  time to fit residues: 25.9010
Evaluate side-chains
  92 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 68
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
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  286 GLU
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   32 THR
Chi-restraints excluded: chain B residue  169 MET
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  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  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 17 optimal weight:    0.0060
   chunk 101 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   chunk 121 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.1602

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.051660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.039576 restraints weight = 69001.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 3.97
r_work: 0.2612 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.2612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2618
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2618 r_free = 0.2618    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 = 0.2618 r_free = 0.2618    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2618
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11617  Z= 0.125
  Angle     :  0.508   9.321  15810  Z= 0.256
  Chirality :  0.038   0.143   1774
  Planarity :  0.004   0.045   1953
  Dihedral  :  9.621  73.137   1768
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.17 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.24), residues: 1345
  helix:  2.09 (0.21), residues: 627
  sheet: -0.46 (0.42), residues: 125
  loop : -0.70 (0.26), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.006   0.001   HIS B 291 
 PHE   0.031   0.001   PHE C  41 
 TYR   0.019   0.001   TYR B 533 
 ARG   0.003   0.000   ARG A 536 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03179 (  533)
  hydrogen bonds       : angle       4.18106 ( 1469)
  covalent geometry    : bond        0.00289 (11617)
  covalent geometry    : angle       0.50787 (15810)

*********************** 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
  94 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 1.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  617 MET cc_start: 0.9113 (mtm) cc_final: 0.8173 (mtm)
REVERT: C  101 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.8089 (tt)
  outliers start: 26
  outliers final: 22
  residues processed: 84
  average time/residue: 0.2200
  time to fit residues: 29.6440
Evaluate side-chains
  90 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
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  286 GLU
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 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  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  450 VAL
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  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 34 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 130 optimal weight:    6.9990
   chunk 81 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 44 optimal weight:    0.1980
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.8388

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

Flipped N/Q/H residues before XYZ refinement:
C  51 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.050798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.039046 restraints weight = 59410.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.2751 rms_B_bonded: 3.63
r_work: 0.2604 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2610
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2610 r_free = 0.2610    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 = 0.2610 r_free = 0.2610    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2610
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.2556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  11617  Z= 0.166
  Angle     :  0.536   9.542  15810  Z= 0.270
  Chirality :  0.039   0.141   1774
  Planarity :  0.004   0.043   1953
  Dihedral  :  9.645  73.062   1768
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.23), residues: 1345
  helix:  2.04 (0.21), residues: 627
  sheet: -0.34 (0.43), residues: 121
  loop : -0.70 (0.26), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 336 
 HIS   0.023   0.001   HIS C  51 
 PHE   0.030   0.002   PHE C  41 
 TYR   0.021   0.001   TYR B 533 
 ARG   0.002   0.000   ARG C  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03418 (  533)
  hydrogen bonds       : angle       4.24308 ( 1469)
  covalent geometry    : bond        0.00384 (11617)
  covalent geometry    : angle       0.53590 (15810)

********************** 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
  92 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 67
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  617 MET cc_start: 0.9191 (mtm) cc_final: 0.8256 (mtm)
REVERT: C  101 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8109 (tt)
  outliers start: 25
  outliers final: 23
  residues processed: 81
  average time/residue: 0.1896
  time to fit residues: 24.6681
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  : 1.216 
-------------------------------------------------------------------------------
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  286 GLU
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 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  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  450 VAL
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 70 optimal weight:    0.6980
   chunk 29 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 72 optimal weight:    5.9990
   chunk 127 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
B 476 HIS
C  51 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.051244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.038557 restraints weight = 106926.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.2736 rms_B_bonded: 4.93
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2734
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2734 r_free = 0.2734    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2734
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8746
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11617  Z= 0.123
  Angle     :  0.512   9.428  15810  Z= 0.258
  Chirality :  0.038   0.142   1774
  Planarity :  0.004   0.044   1953
  Dihedral  :  9.644  73.072   1768
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.01 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.23), residues: 1345
  helix:  2.05 (0.21), residues: 627
  sheet: -0.31 (0.43), residues: 121
  loop : -0.70 (0.26), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 336 
 HIS   0.022   0.001   HIS C  51 
 PHE   0.031   0.001   PHE C  41 
 TYR   0.019   0.001   TYR B 533 
 ARG   0.002   0.000   ARG C  43 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03226 (  533)
  hydrogen bonds       : angle       4.20144 ( 1469)
  covalent geometry    : bond        0.00283 (11617)
  covalent geometry    : angle       0.51163 (15810)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5826.79 seconds
wall clock time: 103 minutes 7.75 seconds (6187.75 seconds total)