Starting phenix.real_space_refine
on Fri Sep 11 00:08:09 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8fzr_29638/09_2026/8fzr_29638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fzr_29638/09_2026/8fzr_29638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fzr_29638/09_2026/8fzr_29638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fzr_29638/09_2026/8fzr_29638.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fzr_29638/09_2026/8fzr_29638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fzr_29638/09_2026/8fzr_29638.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8fzr_29638/09_2026/8fzr_29638.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8fzr_29638/09_2026/8fzr_29638.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
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=   0.000 sd=   0.000
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
     Zn      1      6.06       5
     P      76      5.49       5
     S      32      5.16       5
     C    3342      2.51       5
     N     966      2.21       5
     O    1294      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5711
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 503, 4071
          Classifications: {'peptide': 503}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 25, 'TRANS': 477}
    Chain: "R"
      Number of atoms: 1639
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 1639
          Classifications: {'RNAv2': 77}
          Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 33}
          Link IDs: {'rna2p': 9, 'rna3p': 67}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    158  SG  CYS A  20      22.510  31.353  95.799  1.00  0.00           S
  ATOM    180  SG  CYS A  23      23.297  28.877  95.832  1.00  0.00           S
  ATOM    754  SG  CYS A  94      24.926  28.690  98.909  1.00  0.00           S
  ATOM    760  SG  CYS A  95      25.270  30.234  95.400  1.00  0.00           S

  Time building chain proxies: 1.64, per 1000 atoms: 0.29
  Number of scatterers: 5711
  At special positions: 0
  Unit cell: (66.3176, 78.534, 136.126, 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)
     Zn      1     29.99
     S      32     16.00
     P      76     15.00
     O    1294      8.00
     N     966      7.00
     C    3342      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: 0.58
  Conformation dependent library (CDL) restraints added in 362.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A  23 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A  95 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A  20 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A  94 "
      Number of angles added : 6


  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  940

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 3 sheets defined
      40.4% alpha, 10.1% beta
      4 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 1.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 20
    Processing helix  chain 'A' and resid 30 through 35
      removed outlier: 3.651A  pdb=" N   LEU A  34 " --> pdb=" O   ASN A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 37 through 45
      removed outlier: 3.988A  pdb=" N   ARG A  43 " --> pdb=" O   SER A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 77
      removed outlier: 4.139A  pdb=" N   ARG A  72 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   MET A  73 " --> pdb=" O   THR A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 125
      removed outlier: 3.807A  pdb=" N   ILE A 117 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   SER A 118 " --> pdb=" O   LYS A 114 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ARG A 119 " --> pdb=" O   LYS A 115 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   PHE A 120 " --> pdb=" O   CYS A 116 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   ALA A 121 " --> pdb=" O   ILE A 117 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   THR A 122 " --> pdb=" O   SER A 118 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ARG A 123 " --> pdb=" O   ARG A 119 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ILE A 124 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   THR A 125 " --> pdb=" O   ALA A 121 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 113 through 125'
    Processing helix  chain 'A' and resid 140 through 145
      removed outlier: 3.992A  pdb=" N   ASN A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 166 through 178
      removed outlier: 3.503A  pdb=" N   LYS A 172 " --> pdb=" O   HIS A 168 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLN A 174 " --> pdb=" O   PHE A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 194
      removed outlier: 3.610A  pdb=" N   LYS A 189 " --> pdb=" O   PRO A 185 " (cutoff:3.500A)
      removed outlier: 4.210A  pdb=" N   PHE A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ASP A 194 " --> pdb=" O   ARG A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 204
    Processing helix  chain 'A' and resid 205 through 214
      removed outlier: 3.773A  pdb=" N   TRP A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 276
      removed outlier: 3.930A  pdb=" N   LEU A 272 " --> pdb=" O   SER A 268 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   SER A 273 " --> pdb=" O   LEU A 269 " (cutoff:3.500A)
      removed outlier: 4.584A  pdb=" N   ALA A 274 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 284
      removed outlier: 3.590A  pdb=" N   ARG A 283 " --> pdb=" O   ALA A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 308
      removed outlier: 4.039A  pdb=" N   TYR A 303 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 326
    Processing helix  chain 'A' and resid 329 through 333
      removed outlier: 3.845A  pdb=" N   GLY A 332 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LYS A 333 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 329 through 333'
    Processing helix  chain 'A' and resid 372 through 376
    Processing helix  chain 'A' and resid 382 through 396
      removed outlier: 3.836A  pdb=" N   SER A 386 " --> pdb=" O   CYS A 382 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU A 392 " --> pdb=" O   ASN A 388 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLU A 393 " --> pdb=" O   GLU A 389 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
      removed outlier: 3.509A  pdb=" N   THR A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ILE A 410 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 406 through 410'
    Processing helix  chain 'A' and resid 413 through 418
      removed outlier: 3.671A  pdb=" N   ASN A 417 " --> pdb=" O   LYS A 414 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   GLY A 418 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 444
      removed outlier: 3.709A  pdb=" N   LEU A 437 " --> pdb=" O   PRO A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 4.245A  pdb=" N   ASP A 448 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   LEU A 449 " --> pdb=" O   LYS A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.838A  pdb=" N   GLU A 472 " --> pdb=" O   PHE A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 485
      removed outlier: 3.715A  pdb=" N   VAL A 483 " --> pdb=" O   ARG A 479 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A 484 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 493
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8
      removed outlier: 6.313A  pdb=" N   PHE A   5 " --> pdb=" O   VAL A 496 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   LEU A 498 " --> pdb=" O   PHE A   5 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ILE A   7 " --> pdb=" O   LEU A 498 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 61
    Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 102
      removed outlier: 6.474A  pdb=" N   TYR A  98 " --> pdb=" O   TYR A 293 " (cutoff:3.500A)
      removed outlier: 5.416A  pdb=" N   TYR A 293 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 7.164A  pdb=" N   ILE A 100 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   ILE A 253 " --> pdb=" O   TYR A 290 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   GLY A 292 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   SER A 255 " --> pdb=" O   GLY A 292 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   TYR A 294 " --> pdb=" O   SER A 255 " (cutoff:3.500A)
      removed outlier: 13.408A  pdb=" N   TYR A 257 " --> pdb=" O   TYR A 294 " (cutoff:3.500A)
      removed outlier: 7.721A  pdb=" N   VAL A 245 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 5.014A  pdb=" N   PHE A 258 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   ILE A 243 " --> pdb=" O   PHE A 258 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   TRP A 260 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   ILE A 241 " --> pdb=" O   TRP A 260 " (cutoff:3.500A)
      removed outlier: 4.932A  pdb=" N   LEU A 240 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   TYR A 236 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   ALA A 242 " --> pdb=" O   TYR A 234 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ARG A 156 " --> pdb=" O   CYS A 233 " (cutoff:3.500A)

    93 hydrogen bonds defined for protein.
    219 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      9 hydrogen bonds
      18 hydrogen bond angles
      0 basepair planarities
      4 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 0.95

  Time building geometry restraints manager: 0.75 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: 1507
        1.34 -     1.46: 1549
        1.46 -     1.57: 2749
        1.57 -     1.69: 152
        1.69 -     1.81: 49
  Bond restraints: 6006
  Sorted by residual:
  bond pdb=" N   GLU A 490 "
       pdb=" CA  GLU A 490 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.29e-02 6.01e+03 5.73e+00
  bond pdb=" N   THR A 491 "
       pdb=" CA  THR A 491 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.29e-02 6.01e+03 4.73e+00
  bond pdb=" N   PHE A 487 "
       pdb=" CA  PHE A 487 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.61e-02 3.86e+03 4.05e+00
  bond pdb=" N   GLY A 488 "
       pdb=" CA  GLY A 488 "
    ideal  model  delta    sigma   weight residual
    1.449  1.475 -0.026 1.45e-02 4.76e+03 3.24e+00
  bond pdb=" C3'   C R  49 "
       pdb=" O3'   C R  49 "
    ideal  model  delta    sigma   weight residual
    1.415  1.447 -0.032 2.00e-02 2.50e+03 2.50e+00
  ... (remaining 6001 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 8164
        1.55 -     3.10: 271
        3.10 -     4.65: 46
        4.65 -     6.20: 15
        6.20 -     7.75: 1
  Bond angle restraints: 8497
  Sorted by residual:
  angle pdb=" C3'   C R  49 "
        pdb=" O3'   C R  49 "
        pdb=" P     G R  50 "
      ideal   model   delta    sigma   weight residual
     119.70  125.42   -5.72 1.20e+00 6.94e-01 2.27e+01
  angle pdb=" N   PHE A 487 "
        pdb=" CA  PHE A 487 "
        pdb=" C   PHE A 487 "
      ideal   model   delta    sigma   weight residual
     109.11  115.29   -6.18 1.42e+00 4.96e-01 1.89e+01
  angle pdb=" N   VAL A 177 "
        pdb=" CA  VAL A 177 "
        pdb=" C   VAL A 177 "
      ideal   model   delta    sigma   weight residual
     113.53  110.45    3.08 9.80e-01 1.04e+00 9.86e+00
  angle pdb=" CA  PHE A 487 "
        pdb=" C   PHE A 487 "
        pdb=" O   PHE A 487 "
      ideal   model   delta    sigma   weight residual
     121.86  117.92    3.94 1.39e+00 5.18e-01 8.03e+00
  angle pdb=" C   GLY A 488 "
        pdb=" N   PHE A 489 "
        pdb=" CA  PHE A 489 "
      ideal   model   delta    sigma   weight residual
     121.54  116.45    5.09 1.91e+00 2.74e-01 7.10e+00
  ... (remaining 8492 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.82: 3226
       34.82 -    69.63: 187
       69.63 -   104.45: 13
      104.45 -   139.26: 0
      139.26 -   174.08: 1
  Dihedral angle restraints: 3427
    sinusoidal: 1953
      harmonic: 1474
  Sorted by residual:
  dihedral pdb=" C4'   C R  75 "
           pdb=" C3'   C R  75 "
           pdb=" C2'   C R  75 "
           pdb=" C1'   C R  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -36.05   72.39     1      3.10e+00 1.04e-01 6.97e+02
  dihedral pdb=" C4'   U R   7 "
           pdb=" C3'   U R   7 "
           pdb=" C2'   U R   7 "
           pdb=" C1'   U R   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -35.39   71.74     1      3.10e+00 1.04e-01 6.86e+02
  dihedral pdb=" C4'   U R  17 "
           pdb=" C3'   U R  17 "
           pdb=" C2'   U R  17 "
           pdb=" C1'   U R  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -35.27   71.62     1      3.10e+00 1.04e-01 6.84e+02
  ... (remaining 3424 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 812
       0.065 -    0.129: 69
       0.129 -    0.194: 1
       0.194 -    0.258: 81
       0.258 -    0.323: 14
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" P     G R  50 "
            pdb=" OP1   G R  50 "
            pdb=" OP2   G R  50 "
            pdb=" O5'   G R  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.50   -0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" C2'   C R  49 "
            pdb=" C3'   C R  49 "
            pdb=" O2'   C R  49 "
            pdb=" C1'   C R  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.49   -0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" C2'   U R   7 "
            pdb=" C3'   U R   7 "
            pdb=" O2'   U R   7 "
            pdb=" C1'   U R   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.51   -0.28 2.00e-01 2.50e+01 1.91e+00
  ... (remaining 974 not shown)

  Planarity restraints: 803
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 486 "    0.011 2.00e-02 2.50e+03   2.19e-02 4.80e+00
        pdb=" C   LEU A 486 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   LEU A 486 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PHE A 487 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 487 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   PHE A 487 "    0.029 2.00e-02 2.50e+03
        pdb=" O   PHE A 487 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLY A 488 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 249 "    0.020 5.00e-02 4.00e+02   3.07e-02 1.51e+00
        pdb=" N   PRO A 250 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 250 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 250 "    0.017 5.00e-02 4.00e+02
  ... (remaining 800 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1065
        2.77 -     3.30: 5148
        3.30 -     3.83: 9289
        3.83 -     4.37: 10496
        4.37 -     4.90: 16735
  Nonbonded interactions: 42733
  Sorted by model distance:
  nonbonded pdb=" N   ASP A  89 "
            pdb=" OD1 ASP A  89 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" O   ILE A 253 "
            pdb=" N   TYR A 290 "
     model   vdw
     2.252 3.120
  nonbonded pdb=" O2'   G R  15 "
            pdb=" OP1   G R  19 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   GLY A  77 "
            pdb=" OH  TYR A 293 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   ASP A  71 "
            pdb=" ND2 ASN A  75 "
     model   vdw
     2.290 3.120
  ... (remaining 42728 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.660
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2369
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      :  0.003   0.127   6010  Z= 0.150
  Angle     :  1.137  46.512   8503  Z= 0.365
  Chirality :  0.083   0.323    977
  Planarity :  0.004   0.031    803
  Dihedral  : 17.830 174.077   2487
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  1.00 %
    Allowed  :  4.59 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 10.56 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.87 (0.37), residues: 501
  helix: -0.88 (0.55), residues: 93
  sheet: -2.68 (0.69), residues: 45
  loop : -1.19 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 276 
 TYR   0.007   0.001   TYR A 173 
 PHE   0.008   0.001   PHE A 139 
 TRP   0.005   0.001   TRP A 267 
 HIS   0.002   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.13 ( 6006)
  covalent geometry    : angle       0.67862 /  0.32 ( 8497)
  hydrogen bonds       : bond        0.32909 / 21.01 (  102)
  hydrogen bonds       : angle      11.40266 /  8.15 (  237)
  metal coordination   : bond        0.08025 /  4.04 (    4)
  metal coordination   : angle      34.34967 / 16.83 (    6)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 PHE cc_start: 0.5898 (OUTLIER) cc_final: 0.5271 (p90)
REVERT: A  293 TYR cc_start: 0.4648 (OUTLIER) cc_final: 0.3979 (m-80)
REVERT: A  310 GLU cc_start: 0.3033 (OUTLIER) cc_final: 0.2778 (tp30)
REVERT: A  361 PHE cc_start: 0.4508 (OUTLIER) cc_final: 0.4082 (m-80)
  outliers start: 31
  outliers final: 8
  residues processed: 108
  average time/residue: 0.0900
  time to fit residues: 12.3884
Evaluate side-chains
  55 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 43
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 56 optimal weight:   10.0000
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 168 HIS
A 174 GLN
A 183 ASN
** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 216 GLN
A 326 GLN
A 416 HIS
A 442 GLN
A 475 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.149632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.131291 restraints weight = 36562.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.133205 restraints weight = 28346.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4716 r_free = 0.4716 target = 0.134513 restraints weight = 23304.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.135579 restraints weight = 20148.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.4744 r_free = 0.4744 target = 0.136423 restraints weight = 17925.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.4564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6088
moved from start:          0.3321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6010  Z= 0.192
  Angle     :  1.075  14.823   8503  Z= 0.449
  Chirality :  0.080   0.659    977
  Planarity :  0.005   0.031    803
  Dihedral  : 17.375 164.975   1500
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  7.19 %
    Allowed  : 18.88 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.38), residues: 501
  helix: -0.77 (0.52), residues: 87
  sheet: -2.94 (0.63), residues: 55
  loop : -0.96 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  79 
 TYR   0.019   0.002   TYR A 162 
 PHE   0.017   0.002   PHE A 469 
 TRP   0.011   0.002   TRP A 215 
 HIS   0.003   0.001   HIS A 168 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.19 ( 6006)
  covalent geometry    : angle       1.05926 /  0.45 ( 8497)
  hydrogen bonds       : bond        0.06379 /  4.46 (  102)
  hydrogen bonds       : angle       7.69214 /  5.71 (  237)
  metal coordination   : bond        0.01261 /  0.62 (    4)
  metal coordination   : angle       6.89581 /  3.02 (    6)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 46
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8371 (mmp) cc_final: 0.7466 (tpt)
REVERT: A   44 TYR cc_start: -0.3111 (OUTLIER) cc_final: -0.3590 (m-80)
REVERT: A   48 MET cc_start: 0.8565 (tpp) cc_final: 0.8285 (mmm)
REVERT: A   67 VAL cc_start: 0.8880 (m) cc_final: 0.8539 (p)
REVERT: A  223 LYS cc_start: 0.8857 (tttp) cc_final: 0.8606 (tmtt)
REVERT: A  258 PHE cc_start: -0.0640 (OUTLIER) cc_final: -0.1232 (t80)
REVERT: A  293 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6282 (m-80)
REVERT: A  310 GLU cc_start: 0.5724 (OUTLIER) cc_final: 0.4659 (tp30)
REVERT: A  361 PHE cc_start: 0.5539 (OUTLIER) cc_final: 0.4782 (m-80)
REVERT: A  394 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9072 (pp)
  outliers start: 32
  outliers final: 18
  residues processed: 75
  average time/residue: 0.0810
  time to fit residues: 7.8089
Evaluate side-chains
  64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 40
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 TYR
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  164 GLU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 20 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   chunk 52 optimal weight:    7.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    5.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 ASN
A 302 ASN
A 316 HIS
** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 502 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4718 r_free = 0.4718 target = 0.130304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.112621 restraints weight = 38101.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.114373 restraints weight = 29006.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.115742 restraints weight = 23707.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4524 r_free = 0.4524 target = 0.116545 restraints weight = 20479.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.117359 restraints weight = 18415.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6690
moved from start:          0.5966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.059   6010  Z= 0.353
  Angle     :  1.235  13.025   8503  Z= 0.531
  Chirality :  0.076   0.487    977
  Planarity :  0.007   0.057    803
  Dihedral  : 17.927 141.339   1496
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 37.60
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.58 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  8.54 %
    Allowed  : 19.10 %
    Favored  : 72.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.16 (0.36), residues: 501
  helix: -1.30 (0.49), residues: 83
  sheet: -2.49 (0.75), residues: 39
  loop : -1.44 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 485 
 TYR   0.019   0.003   TYR A 257 
 PHE   0.024   0.003   PHE A  78 
 TRP   0.027   0.003   TRP A 215 
 HIS   0.008   0.002   HIS A 168 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00733 /  0.35 ( 6006)
  covalent geometry    : angle       1.21748 /  0.53 ( 8497)
  hydrogen bonds       : bond        0.08181 /  5.52 (  102)
  hydrogen bonds       : angle       8.07401 /  6.17 (  237)
  metal coordination   : bond        0.01521 /  0.76 (    4)
  metal coordination   : angle       7.84119 /  3.60 (    6)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 42
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6290 (tpt)
REVERT: A   31 MET cc_start: 0.8553 (mmp) cc_final: 0.7699 (tpt)
REVERT: A   44 TYR cc_start: -0.2383 (OUTLIER) cc_final: -0.3922 (m-80)
REVERT: A   67 VAL cc_start: 0.8982 (m) cc_final: 0.8602 (m)
REVERT: A   73 MET cc_start: 0.8408 (ptm) cc_final: 0.8208 (ptm)
REVERT: A  147 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8265 (pm20)
REVERT: A  183 ASN cc_start: 0.8654 (OUTLIER) cc_final: 0.8340 (m110)
REVERT: A  223 LYS cc_start: 0.8914 (tttp) cc_final: 0.8563 (tmtt)
REVERT: A  260 TRP cc_start: 0.3837 (OUTLIER) cc_final: 0.2994 (m-10)
REVERT: A  289 TYR cc_start: 0.7323 (t80) cc_final: 0.6357 (t80)
REVERT: A  361 PHE cc_start: 0.5827 (OUTLIER) cc_final: 0.5135 (m-80)
  outliers start: 38
  outliers final: 24
  residues processed: 77
  average time/residue: 0.0736
  time to fit residues: 7.5878
Evaluate side-chains
  67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 37
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 MET
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   44 TYR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  147 GLU
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  260 TRP
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  351 VAL
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 21 optimal weight:    0.0870
   chunk 17 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 27 optimal weight:    1.9990
   chunk 45 optimal weight:   30.0000
   chunk 35 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.5562

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 178 HIS
A 417 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4814 r_free = 0.4814 target = 0.138329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4593 r_free = 0.4593 target = 0.120549 restraints weight = 37242.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.122377 restraints weight = 28854.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4638 r_free = 0.4638 target = 0.123671 restraints weight = 23784.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.124318 restraints weight = 20578.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4663 r_free = 0.4663 target = 0.125299 restraints weight = 18819.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.4447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6442
moved from start:          0.5897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6010  Z= 0.151
  Angle     :  0.913  11.690   8503  Z= 0.389
  Chirality :  0.065   0.399    977
  Planarity :  0.005   0.042    803
  Dihedral  : 17.697 137.881   1493
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 16.33
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  5.19 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 21.12 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.38), residues: 501
  helix: -0.24 (0.57), residues: 80
  sheet: -2.83 (0.70), residues: 39
  loop : -1.06 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 276 
 TYR   0.017   0.002   TYR A 162 
 PHE   0.027   0.002   PHE A 456 
 TRP   0.010   0.001   TRP A  40 
 HIS   0.005   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.15 ( 6006)
  covalent geometry    : angle       0.90796 /  0.39 ( 8497)
  hydrogen bonds       : bond        0.05269 /  3.71 (  102)
  hydrogen bonds       : angle       7.06987 /  5.46 (  237)
  metal coordination   : bond        0.00636 /  0.31 (    4)
  metal coordination   : angle       3.87812 /  1.73 (    6)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 41
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8301 (mmp) cc_final: 0.7161 (tpt)
REVERT: A   48 MET cc_start: 0.8262 (mmm) cc_final: 0.7268 (mmm)
REVERT: A   71 ASP cc_start: 0.9158 (t0) cc_final: 0.8634 (p0)
REVERT: A   73 MET cc_start: 0.8222 (ptm) cc_final: 0.7988 (ptp)
REVERT: A   91 LEU cc_start: 0.7144 (tp) cc_final: 0.6617 (pt)
REVERT: A  183 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.7298 (m-40)
REVERT: A  186 LYS cc_start: 0.9041 (pttm) cc_final: 0.8504 (mmtt)
REVERT: A  223 LYS cc_start: 0.8956 (tttp) cc_final: 0.8622 (tmmt)
REVERT: A  258 PHE cc_start: 0.0453 (OUTLIER) cc_final: 0.0225 (t80)
REVERT: A  289 TYR cc_start: 0.7333 (t80) cc_final: 0.6317 (t80)
REVERT: A  310 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5576 (tm-30)
REVERT: A  361 PHE cc_start: 0.5765 (OUTLIER) cc_final: 0.5082 (m-80)
  outliers start: 34
  outliers final: 21
  residues processed: 73
  average time/residue: 0.0754
  time to fit residues: 7.3922
Evaluate side-chains
  64 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 39
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 13 optimal weight:    4.9990
   chunk 40 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    2.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.134171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.116874 restraints weight = 38104.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4574 r_free = 0.4574 target = 0.118684 restraints weight = 28841.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.119744 restraints weight = 23663.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.120869 restraints weight = 20635.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.121689 restraints weight = 18262.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.4406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6520
moved from start:          0.6580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6010  Z= 0.192
  Angle     :  0.917  11.970   8503  Z= 0.395
  Chirality :  0.062   0.383    977
  Planarity :  0.005   0.035    803
  Dihedral  : 17.753 136.263   1492
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 21.74
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  7.58 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 21.57 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.37), residues: 501
  helix: -0.29 (0.55), residues: 86
  sheet: -2.58 (0.75), residues: 39
  loop : -1.23 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 276 
 TYR   0.018   0.002   TYR A  44 
 PHE   0.018   0.002   PHE A  78 
 TRP   0.026   0.002   TRP A  40 
 HIS   0.005   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.19 ( 6006)
  covalent geometry    : angle       0.91140 /  0.39 ( 8497)
  hydrogen bonds       : bond        0.05342 /  3.74 (  102)
  hydrogen bonds       : angle       7.11232 /  5.45 (  237)
  metal coordination   : bond        0.00756 /  0.38 (    4)
  metal coordination   : angle       4.05530 /  1.89 (    6)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 38
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8605 (mmp) cc_final: 0.7742 (tpt)
REVERT: A   48 MET cc_start: 0.8186 (mmm) cc_final: 0.7800 (mmm)
REVERT: A   71 ASP cc_start: 0.9131 (t0) cc_final: 0.8584 (p0)
REVERT: A   73 MET cc_start: 0.8286 (ptm) cc_final: 0.8049 (ptp)
REVERT: A   91 LEU cc_start: 0.7064 (tp) cc_final: 0.6504 (pt)
REVERT: A  223 LYS cc_start: 0.8932 (tttp) cc_final: 0.8615 (tmmt)
REVERT: A  226 HIS cc_start: 0.6132 (p90) cc_final: 0.5673 (t-90)
REVERT: A  258 PHE cc_start: 0.0787 (OUTLIER) cc_final: 0.0523 (t80)
REVERT: A  289 TYR cc_start: 0.7435 (t80) cc_final: 0.6393 (t80)
REVERT: A  310 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.5750 (tm-30)
REVERT: A  361 PHE cc_start: 0.5902 (OUTLIER) cc_final: 0.5206 (m-80)
REVERT: A  394 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9159 (pp)
  outliers start: 31
  outliers final: 21
  residues processed: 67
  average time/residue: 0.0724
  time to fit residues: 6.6413
Evaluate side-chains
  62 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 37
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   89 ASP
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  268 SER
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  307 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    4.9990
   chunk 8 optimal weight:    8.9990
   chunk 43 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0870
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    2.0166

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4783 r_free = 0.4783 target = 0.135077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.118162 restraints weight = 37639.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.119971 restraints weight = 28610.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.121183 restraints weight = 23366.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.122280 restraints weight = 20120.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.122768 restraints weight = 17784.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.4434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6467
moved from start:          0.6920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6010  Z= 0.156
  Angle     :  0.858  12.801   8503  Z= 0.370
  Chirality :  0.060   0.371    977
  Planarity :  0.004   0.035    803
  Dihedral  : 17.860 138.129   1492
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.59 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  7.19 %
    Allowed  : 21.80 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.37), residues: 501
  helix: -0.40 (0.53), residues: 91
  sheet: -2.45 (0.74), residues: 39
  loop : -1.18 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 276 
 TYR   0.015   0.002   TYR A 162 
 PHE   0.015   0.001   PHE A  78 
 TRP   0.015   0.002   TRP A  40 
 HIS   0.004   0.001   HIS A  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.16 ( 6006)
  covalent geometry    : angle       0.85422 /  0.37 ( 8497)
  hydrogen bonds       : bond        0.04779 /  3.37 (  102)
  hydrogen bonds       : angle       6.84114 /  5.26 (  237)
  metal coordination   : bond        0.00600 /  0.30 (    4)
  metal coordination   : angle       3.33269 /  1.51 (    6)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 38
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 MET cc_start: 0.5425 (tpt) cc_final: 0.4703 (tpt)
REVERT: A   31 MET cc_start: 0.8468 (mmp) cc_final: 0.7595 (tpt)
REVERT: A   48 MET cc_start: 0.8583 (mmm) cc_final: 0.8241 (mmm)
REVERT: A   71 ASP cc_start: 0.9112 (t0) cc_final: 0.8579 (p0)
REVERT: A   73 MET cc_start: 0.8213 (ptm) cc_final: 0.8011 (ptp)
REVERT: A  186 LYS cc_start: 0.9031 (pttm) cc_final: 0.8447 (mmtt)
REVERT: A  203 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7189 (tm)
REVERT: A  223 LYS cc_start: 0.8931 (tttp) cc_final: 0.8635 (tmmt)
REVERT: A  226 HIS cc_start: 0.5978 (p90) cc_final: 0.5255 (t-90)
REVERT: A  258 PHE cc_start: 0.0961 (OUTLIER) cc_final: 0.0729 (t80)
REVERT: A  289 TYR cc_start: 0.7486 (t80) cc_final: 0.6580 (t80)
REVERT: A  310 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.5623 (tm-30)
REVERT: A  361 PHE cc_start: 0.5900 (OUTLIER) cc_final: 0.5196 (m-10)
  outliers start: 32
  outliers final: 23
  residues processed: 67
  average time/residue: 0.0755
  time to fit residues: 6.7958
Evaluate side-chains
  61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 34
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  225 LYS
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 43 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9980
   chunk 31 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 29 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4770 r_free = 0.4770 target = 0.133948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.116886 restraints weight = 37918.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.118687 restraints weight = 28835.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.119997 restraints weight = 23637.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4619 r_free = 0.4619 target = 0.121036 restraints weight = 20265.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.121526 restraints weight = 17916.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.4425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6482
moved from start:          0.7283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6010  Z= 0.158
  Angle     :  0.867  13.587   8503  Z= 0.373
  Chirality :  0.059   0.341    977
  Planarity :  0.004   0.034    803
  Dihedral  : 17.891 137.987   1492
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 18.51
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  7.78 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 21.57 %
    Favored  : 71.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.37), residues: 501
  helix: -0.49 (0.53), residues: 96
  sheet: -2.19 (0.77), residues: 39
  loop : -1.15 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 276 
 TYR   0.014   0.002   TYR A 162 
 PHE   0.015   0.001   PHE A  78 
 TRP   0.015   0.002   TRP A 215 
 HIS   0.004   0.001   HIS A  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.16 ( 6006)
  covalent geometry    : angle       0.86313 /  0.37 ( 8497)
  hydrogen bonds       : bond        0.04624 /  3.25 (  102)
  hydrogen bonds       : angle       6.81198 /  5.22 (  237)
  metal coordination   : bond        0.00631 /  0.32 (    4)
  metal coordination   : angle       3.37531 /  1.55 (    6)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 38
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.8540 (mmp) cc_final: 0.7637 (tpt)
REVERT: A   48 MET cc_start: 0.8624 (mmm) cc_final: 0.8283 (mmm)
REVERT: A   71 ASP cc_start: 0.9077 (t0) cc_final: 0.8583 (m-30)
REVERT: A  203 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7153 (tm)
REVERT: A  223 LYS cc_start: 0.8924 (tttp) cc_final: 0.8618 (tmmt)
REVERT: A  258 PHE cc_start: 0.0813 (OUTLIER) cc_final: 0.0533 (t80)
REVERT: A  289 TYR cc_start: 0.7447 (t80) cc_final: 0.6519 (t80)
REVERT: A  294 TYR cc_start: 0.4906 (t80) cc_final: 0.4652 (t80)
REVERT: A  310 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5559 (tm-30)
REVERT: A  361 PHE cc_start: 0.5928 (OUTLIER) cc_final: 0.5209 (m-10)
  outliers start: 29
  outliers final: 22
  residues processed: 65
  average time/residue: 0.0748
  time to fit residues: 6.4832
Evaluate side-chains
  60 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 34
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  225 LYS
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 56 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 38 optimal weight:   20.0000
   chunk 34 optimal weight:   20.0000
   chunk 41 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 37 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   overall best weight:    2.2584

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4759 r_free = 0.4759 target = 0.132974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.116059 restraints weight = 37851.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.117758 restraints weight = 28834.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.119196 restraints weight = 23575.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.120212 restraints weight = 20075.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.120869 restraints weight = 17802.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.4419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6484
moved from start:          0.7615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6010  Z= 0.167
  Angle     :  0.883  14.098   8503  Z= 0.384
  Chirality :  0.060   0.343    977
  Planarity :  0.004   0.035    803
  Dihedral  : 17.884 136.348   1490
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 19.75
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.79 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  6.74 %
    Allowed  : 22.02 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.80 (0.37), residues: 501
  helix: -0.88 (0.49), residues: 99
  sheet: -2.22 (0.75), residues: 40
  loop : -1.21 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 276 
 TYR   0.014   0.002   TYR A 162 
 PHE   0.019   0.002   PHE A  78 
 TRP   0.015   0.002   TRP A 215 
 HIS   0.005   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.17 ( 6006)
  covalent geometry    : angle       0.87912 /  0.38 ( 8497)
  hydrogen bonds       : bond        0.04729 /  3.28 (  102)
  hydrogen bonds       : angle       6.69949 /  5.20 (  237)
  metal coordination   : bond        0.00636 /  0.32 (    4)
  metal coordination   : angle       3.35590 /  1.55 (    6)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 36
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 MET cc_start: 0.5294 (tpt) cc_final: 0.4649 (tpt)
REVERT: A   31 MET cc_start: 0.8486 (mmp) cc_final: 0.7529 (tpt)
REVERT: A   48 MET cc_start: 0.8662 (mmm) cc_final: 0.8350 (mmm)
REVERT: A   71 ASP cc_start: 0.9114 (t0) cc_final: 0.8609 (m-30)
REVERT: A  186 LYS cc_start: 0.8898 (pttm) cc_final: 0.8256 (mmtt)
REVERT: A  203 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7177 (tm)
REVERT: A  223 LYS cc_start: 0.8894 (tttp) cc_final: 0.8600 (tmtt)
REVERT: A  227 MET cc_start: 0.6579 (tpt) cc_final: 0.6050 (tpp)
REVERT: A  258 PHE cc_start: 0.0966 (OUTLIER) cc_final: 0.0754 (t80)
REVERT: A  294 TYR cc_start: 0.5079 (t80) cc_final: 0.4818 (t80)
REVERT: A  310 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5443 (tm-30)
REVERT: A  361 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5182 (m-10)
  outliers start: 30
  outliers final: 20
  residues processed: 62
  average time/residue: 0.0646
  time to fit residues: 5.5609
Evaluate side-chains
  57 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 33
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  153 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0000
   chunk 29 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0870
   chunk 56 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 10 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   overall best weight:    1.3364

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.135579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4589 r_free = 0.4589 target = 0.118710 restraints weight = 37909.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4612 r_free = 0.4612 target = 0.120467 restraints weight = 28769.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.121842 restraints weight = 23463.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.122852 restraints weight = 20105.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.123424 restraints weight = 17794.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.4459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6410
moved from start:          0.7754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6010  Z= 0.134
  Angle     :  0.860  14.906   8503  Z= 0.366
  Chirality :  0.059   0.375    977
  Planarity :  0.004   0.036    803
  Dihedral  : 17.803 134.571   1490
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 17.28
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  7.19 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 23.82 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.37), residues: 501
  helix: -0.91 (0.51), residues: 99
  sheet: -1.83 (0.80), residues: 40
  loop : -1.15 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 276 
 TYR   0.014   0.001   TYR A 162 
 PHE   0.014   0.001   PHE A  78 
 TRP   0.012   0.002   TRP A  40 
 HIS   0.005   0.001   HIS A 226 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00291 /  0.13 ( 6006)
  covalent geometry    : angle       0.85679 /  0.37 ( 8497)
  hydrogen bonds       : bond        0.04417 /  3.06 (  102)
  hydrogen bonds       : angle       6.68217 /  5.17 (  237)
  metal coordination   : bond        0.00516 /  0.26 (    4)
  metal coordination   : angle       2.98262 /  1.31 (    6)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 38
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 MET cc_start: 0.4819 (tpt) cc_final: 0.4250 (tpt)
REVERT: A   31 MET cc_start: 0.8508 (mmp) cc_final: 0.7573 (tpt)
REVERT: A   48 MET cc_start: 0.8697 (mmm) cc_final: 0.8397 (mmm)
REVERT: A   71 ASP cc_start: 0.9021 (t0) cc_final: 0.8616 (m-30)
REVERT: A  186 LYS cc_start: 0.8833 (pttm) cc_final: 0.8070 (mmtt)
REVERT: A  203 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7158 (tm)
REVERT: A  223 LYS cc_start: 0.8927 (tttp) cc_final: 0.8654 (tmtt)
REVERT: A  227 MET cc_start: 0.6677 (tpt) cc_final: 0.6275 (tpp)
REVERT: A  247 ASP cc_start: 0.7648 (t0) cc_final: 0.7302 (t0)
REVERT: A  258 PHE cc_start: 0.0787 (OUTLIER) cc_final: 0.0508 (t80)
REVERT: A  289 TYR cc_start: 0.7383 (t80) cc_final: 0.6498 (t80)
REVERT: A  294 TYR cc_start: 0.4962 (t80) cc_final: 0.4624 (t80)
REVERT: A  310 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5016 (tm-30)
REVERT: A  361 PHE cc_start: 0.5790 (OUTLIER) cc_final: 0.5141 (m-10)
  outliers start: 23
  outliers final: 19
  residues processed: 57
  average time/residue: 0.0712
  time to fit residues: 5.4586
Evaluate side-chains
  59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 36
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue   99 THR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  407 LEU
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 46 optimal weight:   30.0000
   chunk 3 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 11 optimal weight:    7.9990
   chunk 47 optimal weight:    5.9990
   chunk 14 optimal weight:    0.0770
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0000
   overall best weight:    3.2148

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.128605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.111574 restraints weight = 39192.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.113397 restraints weight = 29605.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.114688 restraints weight = 24146.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4556 r_free = 0.4556 target = 0.115696 restraints weight = 20706.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.116178 restraints weight = 18317.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.4344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6614
moved from start:          0.8337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   6010  Z= 0.220
  Angle     :  0.981  15.151   8503  Z= 0.423
  Chirality :  0.061   0.370    977
  Planarity :  0.006   0.105    803
  Dihedral  : 17.997 135.100   1488
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 28.10
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.58 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 24.72 %
    Favored  : 70.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.97 (0.37), residues: 501
  helix: -1.09 (0.49), residues: 99
  sheet: -2.07 (0.80), residues: 40
  loop : -1.35 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 276 
 TYR   0.013   0.002   TYR A 319 
 PHE   0.027   0.002   PHE A  78 
 TRP   0.021   0.002   TRP A 215 
 HIS   0.004   0.001   HIS A 231 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00468 /  0.22 ( 6006)
  covalent geometry    : angle       0.97515 /  0.42 ( 8497)
  hydrogen bonds       : bond        0.05044 /  3.40 (  102)
  hydrogen bonds       : angle       6.97169 /  5.35 (  237)
  metal coordination   : bond        0.00836 /  0.42 (    4)
  metal coordination   : angle       4.15712 /  1.90 (    6)

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

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

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1002 Ramachandran restraints generated.
    501 Oldfield, 0 Emsley, 501 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 38
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 MET cc_start: 0.5449 (tpt) cc_final: 0.4788 (tpt)
REVERT: A   31 MET cc_start: 0.8418 (mmp) cc_final: 0.7596 (tpp)
REVERT: A   71 ASP cc_start: 0.9028 (t0) cc_final: 0.8556 (m-30)
REVERT: A  203 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7033 (tm)
REVERT: A  223 LYS cc_start: 0.8875 (tttp) cc_final: 0.8534 (tmtt)
REVERT: A  227 MET cc_start: 0.6810 (tpt) cc_final: 0.6501 (tpp)
REVERT: A  258 PHE cc_start: 0.1125 (OUTLIER) cc_final: 0.0900 (t80)
REVERT: A  310 GLU cc_start: 0.6324 (OUTLIER) cc_final: 0.5535 (tm-30)
  outliers start: 21
  outliers final: 16
  residues processed: 56
  average time/residue: 0.0695
  time to fit residues: 5.3316
Evaluate side-chains
  55 residues out of total 445 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 36
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   83 LYS
Chi-restraints excluded: chain A residue   98 TYR
Chi-restraints excluded: chain A residue  139 PHE
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  248 ILE
Chi-restraints excluded: chain A residue  258 PHE
Chi-restraints excluded: chain A residue  293 TYR
Chi-restraints excluded: chain A residue  310 GLU
Chi-restraints excluded: chain A residue  316 HIS
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  353 SER
Chi-restraints excluded: chain A residue  361 PHE
Chi-restraints excluded: chain A residue  432 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  496 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    0.0570
   chunk 44 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 38 optimal weight:    9.9990
   chunk 22 optimal weight:    0.4980
   chunk 39 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 40 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   overall best weight:    2.1102

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4745 r_free = 0.4745 target = 0.131516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.114703 restraints weight = 37820.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.116492 restraints weight = 28760.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.117790 restraints weight = 23503.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.118789 restraints weight = 20086.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4610 r_free = 0.4610 target = 0.119431 restraints weight = 17787.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6507
moved from start:          0.8463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6010  Z= 0.161
  Angle     :  0.892  15.993   8503  Z= 0.383
  Chirality :  0.060   0.413    977
  Planarity :  0.005   0.078    803
  Dihedral  : 18.003 133.309   1488
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 19.84
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  7.58 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 24.49 %
    Favored  : 71.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.99 (0.37), residues: 501
  helix: -1.01 (0.48), residues: 111
  sheet: -2.06 (0.78), residues: 40
  loop : -1.38 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 276 
 TYR   0.014   0.002   TYR A 162 
 PHE   0.019   0.001   PHE A  78 
 TRP   0.012   0.002   TRP A  40 
 HIS   0.003   0.001   HIS A  64 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.16 ( 6006)
  covalent geometry    : angle       0.88854 /  0.38 ( 8497)
  hydrogen bonds       : bond        0.04534 /  3.14 (  102)
  hydrogen bonds       : angle       6.79548 /  5.26 (  237)
  metal coordination   : bond        0.00595 /  0.30 (    4)
  metal coordination   : angle       3.20257 /  1.47 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1485.66 seconds
wall clock time: 26 minutes 15.84 seconds (1575.84 seconds total)