Starting phenix.real_space_refine
on Tue Mar  3 19:00:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lre_23496/03_2026/7lre_23496.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lre_23496/03_2026/7lre_23496.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lre_23496/03_2026/7lre_23496.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lre_23496/03_2026/7lre_23496.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lre_23496/03_2026/7lre_23496.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lre_23496/03_2026/7lre_23496.cif"
  }
  resolution = 2.76
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      58      5.16       5
     C    5194      2.51       5
     N    1378      2.21       5
     O    1512      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8144
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4071
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 502, 4071
          Classifications: {'peptide': 502}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 491}
          Chain breaks: 2
    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   2161  SG  CYS A 277      78.410  62.514  53.924  1.00 52.28           S
  ATOM   2434  SG  CYS A 311      79.178  61.360  50.357  1.00 41.08           S
  ATOM   2440  SG  CYS A 312      75.929  60.277  52.068  1.00 39.93           S

  Restraints were copied for chains:
    B
  Time building chain proxies: 2.71, per 1000 atoms: 0.33
  Number of scatterers: 8144
  At special positions: 0
  Unit cell: (120.119, 90.355, 89.292, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      58     16.00
     O    1512      8.00
     N    1378      7.00
     C    5194      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: 0.60
  Conformation dependent library (CDL) restraints added in 337.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 601 "
        pdb="ZN    ZN A 601 " - pdb=" ND1 HIS A 275 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 277 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 311 "
        pdb="ZN    ZN A 601 " - pdb=" SG  CYS A 312 "
      pdb="  ZN B 601 "
        pdb="ZN    ZN B 601 " - pdb=" ND1 HIS B 275 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 277 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 311 "
        pdb="ZN    ZN B 601 " - pdb=" SG  CYS B 312 "
      Number of angles added : 6


  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1908

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 12 sheets defined
      41.0% alpha, 19.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 30
    Processing helix  chain 'A' and resid 33 through 54
    Processing helix  chain 'A' and resid 69 through 74
    Processing helix  chain 'A' and resid 76 through 87
    Processing helix  chain 'A' and resid 89 through 93
      removed outlier: 3.754A  pdb=" N   TYR A  93 " --> pdb=" O   PHE A  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 89 through 93'
    Processing helix  chain 'A' and resid 138 through 152
    Processing helix  chain 'A' and resid 173 through 186
      removed outlier: 3.745A  pdb=" N   MET A 177 " --> pdb=" O   GLU A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 233
      removed outlier: 4.448A  pdb=" N   LEU A 215 " --> pdb=" O   THR A 211 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLN A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLU A 220 " --> pdb=" O   GLN A 216 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU A 222 " --> pdb=" O   ILE A 218 " (cutoff:3.500A)
      Proline residue:  A 223  - end of helix
    Processing helix  chain 'A' and resid 253 through 271
      removed outlier: 3.514A  pdb=" N   MET A 271 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 343
    Processing helix  chain 'A' and resid 392 through 403
    Processing helix  chain 'A' and resid 403 through 415
      removed outlier: 3.979A  pdb=" N   LYS A 407 " --> pdb=" O   HIS A 403 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN A 408 " --> pdb=" O   GLU A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 432
      removed outlier: 3.631A  pdb=" N   ASP A 431 " --> pdb=" O   SER A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 483
    Processing helix  chain 'A' and resid 519 through 524
      removed outlier: 3.800A  pdb=" N   PHE A 524 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 541
    Processing helix  chain 'B' and resid 24 through 30
    Processing helix  chain 'B' and resid 33 through 54
    Processing helix  chain 'B' and resid 69 through 74
    Processing helix  chain 'B' and resid 76 through 87
    Processing helix  chain 'B' and resid 89 through 93
      removed outlier: 3.754A  pdb=" N   TYR B  93 " --> pdb=" O   PHE B  89 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 89 through 93'
    Processing helix  chain 'B' and resid 138 through 152
    Processing helix  chain 'B' and resid 173 through 186
      removed outlier: 3.745A  pdb=" N   MET B 177 " --> pdb=" O   GLU B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 233
      removed outlier: 4.448A  pdb=" N   LEU B 215 " --> pdb=" O   THR B 211 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLN B 216 " --> pdb=" O   GLU B 212 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS B 219 " --> pdb=" O   LEU B 215 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLU B 220 " --> pdb=" O   GLN B 216 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LEU B 222 " --> pdb=" O   ILE B 218 " (cutoff:3.500A)
      Proline residue:  B 223  - end of helix
    Processing helix  chain 'B' and resid 253 through 271
      removed outlier: 3.514A  pdb=" N   MET B 271 " --> pdb=" O   SER B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 333 through 343
    Processing helix  chain 'B' and resid 392 through 403
    Processing helix  chain 'B' and resid 403 through 415
      removed outlier: 3.979A  pdb=" N   LYS B 407 " --> pdb=" O   HIS B 403 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN B 408 " --> pdb=" O   GLU B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 432
      removed outlier: 3.631A  pdb=" N   ASP B 431 " --> pdb=" O   SER B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 483
    Processing helix  chain 'B' and resid 519 through 524
      removed outlier: 3.800A  pdb=" N   PHE B 524 " --> pdb=" O   SER B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 541
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5
      removed outlier: 6.633A  pdb=" N   VAL A  58 " --> pdb=" O   VAL A  15 " (cutoff:3.500A)
      removed outlier: 5.663A  pdb=" N   ASP A  17 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   LYS A  60 " --> pdb=" O   ASP A  17 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   GLY A  19 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 130
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172
      removed outlier: 6.633A  pdb=" N   VAL B  58 " --> pdb=" O   VAL B  15 " (cutoff:3.500A)
      removed outlier: 5.663A  pdb=" N   ASP B  17 " --> pdb=" O   VAL B  58 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   LYS B  60 " --> pdb=" O   ASP B  17 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   GLY B  19 " --> pdb=" O   LYS B  60 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 191
      removed outlier: 6.663A  pdb=" N   LEU A 190 " --> pdb=" O   TYR A 293 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   SER A 286 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   LEU A 305 " --> pdb=" O   SER A 286 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   LYS A 288 " --> pdb=" O   CYS A 303 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   CYS A 303 " --> pdb=" O   LYS A 288 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LEU A 290 " --> pdb=" O   TYR A 301 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   TYR A 301 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   VAL A 292 " --> pdb=" O   CYS A 299 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 274
    Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 325
    Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 391
      removed outlier: 5.803A  pdb=" N   THR A 389 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   PHE A 424 " --> pdb=" O   THR A 389 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   THR A 391 " --> pdb=" O   PHE A 424 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   CYS A 442 " --> pdb=" O   PHE A 458 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR A 510 " --> pdb=" O   ILE A 497 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   TYR A 499 " --> pdb=" O   CYS A 508 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   CYS A 508 " --> pdb=" O   TYR A 499 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 127 through 130
    Processing sheet with id=AA9, first strand: chain 'B' and resid 189 through 191
      removed outlier: 6.663A  pdb=" N   LEU B 190 " --> pdb=" O   TYR B 293 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   SER B 286 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   LEU B 305 " --> pdb=" O   SER B 286 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   LYS B 288 " --> pdb=" O   CYS B 303 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   CYS B 303 " --> pdb=" O   LYS B 288 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   LEU B 290 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   TYR B 301 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   VAL B 292 " --> pdb=" O   CYS B 299 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 274
    Processing sheet with id=AB2, first strand: chain 'B' and resid 322 through 325
    Processing sheet with id=AB3, first strand: chain 'B' and resid 388 through 391
      removed outlier: 5.803A  pdb=" N   THR B 389 " --> pdb=" O   LEU B 422 " (cutoff:3.500A)
      removed outlier: 7.074A  pdb=" N   PHE B 424 " --> pdb=" O   THR B 389 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   THR B 391 " --> pdb=" O   PHE B 424 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   CYS B 442 " --> pdb=" O   PHE B 458 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   TYR B 510 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   TYR B 499 " --> pdb=" O   CYS B 508 " (cutoff:3.500A)
      removed outlier: 6.191A  pdb=" N   CYS B 508 " --> pdb=" O   TYR B 499 " (cutoff:3.500A)

    372 hydrogen bonds defined for protein.
    1050 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.18

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2199
        1.33 -     1.45: 1321
        1.45 -     1.57: 4674
        1.57 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 8282
  Sorted by residual:
  bond pdb=" N   LYS A 150 "
       pdb=" CA  LYS A 150 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.80e+00
  bond pdb=" N   LYS B 150 "
       pdb=" CA  LYS B 150 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.21e-02 6.83e+03 5.80e+00
  bond pdb=" C   ILE A 131 "
       pdb=" O   ILE A 131 "
    ideal  model  delta    sigma   weight residual
    1.236  1.215  0.022 1.19e-02 7.06e+03 3.29e+00
  bond pdb=" C   ILE B 131 "
       pdb=" O   ILE B 131 "
    ideal  model  delta    sigma   weight residual
    1.236  1.216  0.021 1.19e-02 7.06e+03 3.02e+00
  bond pdb=" CA  ASP B 130 "
       pdb=" C   ASP B 130 "
    ideal  model  delta    sigma   weight residual
    1.530  1.511  0.018 1.11e-02 8.12e+03 2.77e+00
  ... (remaining 8277 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.25: 10894
        1.25 -     2.50: 164
        2.50 -     3.76: 39
        3.76 -     5.01: 9
        5.01 -     6.26: 6
  Bond angle restraints: 11112
  Sorted by residual:
  angle pdb=" N   ARG B 129 "
        pdb=" CA  ARG B 129 "
        pdb=" C   ARG B 129 "
      ideal   model   delta    sigma   weight residual
     107.99  113.51   -5.52 1.77e+00 3.19e-01 9.74e+00
  angle pdb=" N   ARG A 129 "
        pdb=" CA  ARG A 129 "
        pdb=" C   ARG A 129 "
      ideal   model   delta    sigma   weight residual
     107.99  113.51   -5.52 1.77e+00 3.19e-01 9.74e+00
  angle pdb=" N   SER A 133 "
        pdb=" CA  SER A 133 "
        pdb=" C   SER A 133 "
      ideal   model   delta    sigma   weight residual
     109.95  114.71   -4.76 1.59e+00 3.96e-01 8.95e+00
  angle pdb=" N   SER B 133 "
        pdb=" CA  SER B 133 "
        pdb=" C   SER B 133 "
      ideal   model   delta    sigma   weight residual
     109.95  114.71   -4.76 1.59e+00 3.96e-01 8.95e+00
  angle pdb=" C   ASP B 130 "
        pdb=" N   ILE B 131 "
        pdb=" CA  ILE B 131 "
      ideal   model   delta    sigma   weight residual
     121.97  127.16   -5.19 1.80e+00 3.09e-01 8.31e+00
  ... (remaining 11107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.67: 4960
       16.67 -    33.34: 96
       33.34 -    50.01: 16
       50.01 -    66.68: 0
       66.68 -    83.36: 2
  Dihedral angle restraints: 5074
    sinusoidal: 2126
      harmonic: 2948
  Sorted by residual:
  dihedral pdb=" CB  GLU A 205 "
           pdb=" CG  GLU A 205 "
           pdb=" CD  GLU A 205 "
           pdb=" OE1 GLU A 205 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.36   83.36     1      3.00e+01 1.11e-03 9.43e+00
  dihedral pdb=" CB  GLU B 205 "
           pdb=" CG  GLU B 205 "
           pdb=" CD  GLU B 205 "
           pdb=" OE1 GLU B 205 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -83.36   83.36     1      3.00e+01 1.11e-03 9.43e+00
  dihedral pdb=" CA  ILE A 221 "
           pdb=" CB  ILE A 221 "
           pdb=" CG1 ILE A 221 "
           pdb=" CD1 ILE A 221 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  102.63  -42.63     3      1.50e+01 4.44e-03 7.65e+00
  ... (remaining 5071 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1038
       0.048 -    0.096: 127
       0.096 -    0.144: 63
       0.144 -    0.192: 2
       0.192 -    0.239: 2
  Chirality restraints: 1232
  Sorted by residual:
  chirality pdb=" CB  ILE B 131 "
            pdb=" CA  ILE B 131 "
            pdb=" CG1 ILE B 131 "
            pdb=" CG2 ILE B 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CB  ILE A 131 "
            pdb=" CA  ILE A 131 "
            pdb=" CG1 ILE A 131 "
            pdb=" CG2 ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  ILE A  59 "
            pdb=" N   ILE A  59 "
            pdb=" C   ILE A  59 "
            pdb=" CB  ILE A  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.26e-01
  ... (remaining 1229 not shown)

  Planarity restraints: 1400
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 130 "    0.007 2.00e-02 2.50e+03   1.51e-02 2.28e+00
        pdb=" C   ASP A 130 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ASP A 130 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ILE A 131 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 130 "   -0.007 2.00e-02 2.50e+03   1.51e-02 2.28e+00
        pdb=" C   ASP B 130 "    0.026 2.00e-02 2.50e+03
        pdb=" O   ASP B 130 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE B 131 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 222 "    0.017 5.00e-02 4.00e+02   2.58e-02 1.07e+00
        pdb=" N   PRO A 223 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 223 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 223 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1397 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2311
        2.82 -     3.34: 6916
        3.34 -     3.86: 13220
        3.86 -     4.38: 15692
        4.38 -     4.90: 27727
  Nonbonded interactions: 65866
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  68 "
            pdb=" O   GLY B  74 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OH  TYR A  68 "
            pdb=" O   GLY A  74 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OE1 GLU B  13 "
            pdb=" NZ  LYS B 478 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" OE1 GLU A  13 "
            pdb=" NZ  LYS A 478 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" OD2 ASP B   6 "
            pdb=" NZ  LYS B  60 "
     model   vdw
     2.327 3.120
  ... (remaining 65861 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.590
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.710
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:7.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
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   0.051   8290  Z= 0.135
  Angle     :  0.437   6.259  11118  Z= 0.275
  Chirality :  0.040   0.239   1232
  Planarity :  0.003   0.026   1400
  Dihedral  :  7.410  83.356   3166
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.88 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.20 (0.26), residues: 992
  helix:  2.92 (0.28), residues: 376
  sheet:  1.81 (0.40), residues: 164
  loop :  0.06 (0.26), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 309 
 TYR   0.006   0.001   TYR A 236 
 PHE   0.012   0.001   PHE A 145 
 TRP   0.003   0.001   TRP B 110 
 HIS   0.001   0.000   HIS A 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8282)
  covalent geometry    : angle       0.43657 (11112)
  hydrogen bonds       : bond        0.12221 (  372)
  hydrogen bonds       : angle       4.50855 ( 1050)
  metal coordination   : bond        0.00344 (    8)
  metal coordination   : angle       0.85354 (    6)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.336 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 42
  average time/residue: 0.6551
  time to fit residues: 29.3218
Evaluate side-chains
  34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 323 HIS
B 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.042578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.032450 restraints weight = 33005.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.2667 rms_B_bonded: 3.66
r_work: 0.2507 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8855
moved from start:          0.0716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8290  Z= 0.116
  Angle     :  0.418   6.204  11118  Z= 0.223
  Chirality :  0.038   0.135   1232
  Planarity :  0.003   0.024   1400
  Dihedral  :  3.490  15.232   1094
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  2.64 %
    Favored  : 96.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.25 (0.26), residues: 992
  helix:  3.12 (0.28), residues: 366
  sheet:  1.83 (0.39), residues: 164
  loop :  0.02 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 155 
 TYR   0.006   0.001   TYR B 293 
 PHE   0.018   0.001   PHE A 145 
 TRP   0.004   0.001   TRP A 428 
 HIS   0.003   0.001   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 8282)
  covalent geometry    : angle       0.41423 (11112)
  hydrogen bonds       : bond        0.03103 (  372)
  hydrogen bonds       : angle       3.80107 ( 1050)
  metal coordination   : bond        0.00888 (    8)
  metal coordination   : angle       2.39438 (    6)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 34
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9588 (mpp) cc_final: 0.9288 (mpp)
REVERT: B  414 MET cc_start: 0.9587 (mpp) cc_final: 0.9291 (mpp)
  outliers start: 10
  outliers final: 0
  residues processed: 36
  average time/residue: 0.6535
  time to fit residues: 25.1170
Evaluate side-chains
  34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 25 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 68 optimal weight:    0.7980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS
** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.041410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.031344 restraints weight = 32676.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.2628 rms_B_bonded: 3.64
r_work: 0.2466 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8889
moved from start:          0.1033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8290  Z= 0.185
  Angle     :  0.437   7.792  11118  Z= 0.232
  Chirality :  0.038   0.132   1232
  Planarity :  0.003   0.032   1400
  Dihedral  :  3.619  15.118   1094
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  3.30 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.32 (0.27), residues: 992
  helix:  3.26 (0.28), residues: 366
  sheet:  1.78 (0.39), residues: 164
  loop :  0.03 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 526 
 TYR   0.006   0.001   TYR B 293 
 PHE   0.018   0.001   PHE A 145 
 TRP   0.002   0.000   TRP A 337 
 HIS   0.004   0.001   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 8282)
  covalent geometry    : angle       0.43519 (11112)
  hydrogen bonds       : bond        0.02953 (  372)
  hydrogen bonds       : angle       3.72081 ( 1050)
  metal coordination   : bond        0.01671 (    8)
  metal coordination   : angle       1.59586 (    6)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 34
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9645 (mpp) cc_final: 0.9319 (mpp)
REVERT: B  414 MET cc_start: 0.9645 (mpp) cc_final: 0.9324 (mpp)
  outliers start: 6
  outliers final: 0
  residues processed: 36
  average time/residue: 0.5958
  time to fit residues: 22.9446
Evaluate side-chains
  32 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 70 optimal weight:    4.9990
   chunk 76 optimal weight:    0.4980
   chunk 41 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 45 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 99 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 323 HIS
B 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.042030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.031821 restraints weight = 33462.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.2649 rms_B_bonded: 3.73
r_work: 0.2493 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.2493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.1127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   8290  Z= 0.105
  Angle     :  0.407   8.597  11118  Z= 0.216
  Chirality :  0.037   0.137   1232
  Planarity :  0.002   0.025   1400
  Dihedral  :  3.581  16.070   1094
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.41 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  3.52 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.32 (0.27), residues: 992
  helix:  3.23 (0.28), residues: 366
  sheet:  1.72 (0.40), residues: 164
  loop :  0.07 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 155 
 TYR   0.005   0.001   TYR A 487 
 PHE   0.016   0.001   PHE B 145 
 TRP   0.002   0.000   TRP A 337 
 HIS   0.003   0.001   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 8282)
  covalent geometry    : angle       0.40534 (11112)
  hydrogen bonds       : bond        0.02576 (  372)
  hydrogen bonds       : angle       3.62844 ( 1050)
  metal coordination   : bond        0.01130 (    8)
  metal coordination   : angle       1.69342 (    6)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A   13 GLU cc_start: 0.8925 (pt0) cc_final: 0.8706 (pm20)
REVERT: A  414 MET cc_start: 0.9652 (mpp) cc_final: 0.9387 (mpp)
REVERT: B   13 GLU cc_start: 0.8913 (pt0) cc_final: 0.8701 (pm20)
REVERT: B  414 MET cc_start: 0.9652 (mpp) cc_final: 0.9391 (mpp)
  outliers start: 4
  outliers final: 0
  residues processed: 36
  average time/residue: 0.6578
  time to fit residues: 25.2556
Evaluate side-chains
  34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 65 optimal weight:    0.1980
   chunk 75 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 323 HIS
B 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.041720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.031614 restraints weight = 33489.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.2648 rms_B_bonded: 3.75
r_work: 0.2492 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8895
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8290  Z= 0.120
  Angle     :  0.418  10.009  11118  Z= 0.219
  Chirality :  0.038   0.134   1232
  Planarity :  0.002   0.025   1400
  Dihedral  :  3.532  15.940   1094
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.81 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  3.74 %
    Favored  : 95.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.32 (0.27), residues: 992
  helix:  3.25 (0.28), residues: 364
  sheet:  1.75 (0.40), residues: 164
  loop :  0.07 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 155 
 TYR   0.004   0.001   TYR B 529 
 PHE   0.010   0.001   PHE A 145 
 TRP   0.002   0.000   TRP A 337 
 HIS   0.003   0.001   HIS A 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 8282)
  covalent geometry    : angle       0.41735 (11112)
  hydrogen bonds       : bond        0.02541 (  372)
  hydrogen bonds       : angle       3.60831 ( 1050)
  metal coordination   : bond        0.01014 (    8)
  metal coordination   : angle       0.98698 (    6)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 34
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9666 (mpp) cc_final: 0.9346 (mpp)
REVERT: B  414 MET cc_start: 0.9663 (mpp) cc_final: 0.9345 (mpp)
  outliers start: 4
  outliers final: 0
  residues processed: 36
  average time/residue: 0.7447
  time to fit residues: 28.5331
Evaluate side-chains
  32 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 323 HIS
** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.040972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.030730 restraints weight = 33399.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.2612 rms_B_bonded: 3.75
r_work: 0.2456 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8935
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8290  Z= 0.231
  Angle     :  0.496  10.473  11118  Z= 0.258
  Chirality :  0.039   0.139   1232
  Planarity :  0.003   0.036   1400
  Dihedral  :  3.724  15.130   1094
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.12 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  3.74 %
    Favored  : 95.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.36 (0.27), residues: 992
  helix:  3.25 (0.28), residues: 364
  sheet:  1.72 (0.39), residues: 164
  loop :  0.13 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 526 
 TYR   0.007   0.001   TYR B 293 
 PHE   0.019   0.001   PHE A 145 
 TRP   0.002   0.001   TRP A 322 
 HIS   0.004   0.001   HIS B 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00514 ( 8282)
  covalent geometry    : angle       0.49579 (11112)
  hydrogen bonds       : bond        0.02962 (  372)
  hydrogen bonds       : angle       3.74034 ( 1050)
  metal coordination   : bond        0.02182 (    8)
  metal coordination   : angle       1.01835 (    6)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.333 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9691 (mpp) cc_final: 0.9396 (mpp)
REVERT: B  414 MET cc_start: 0.9692 (mpp) cc_final: 0.9398 (mpp)
  outliers start: 8
  outliers final: 2
  residues processed: 36
  average time/residue: 0.6235
  time to fit residues: 24.0443
Evaluate side-chains
  34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0070
   chunk 12 optimal weight:    4.9990
   chunk 90 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0870
   chunk 27 optimal weight:    0.1980
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.3376

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

Flipped N/Q/H residues before XYZ refinement:
A 323 HIS
B 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.042203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.032045 restraints weight = 33568.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.2662 rms_B_bonded: 3.74
r_work: 0.2500 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8886
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8290  Z= 0.079
  Angle     :  0.426  11.416  11118  Z= 0.220
  Chirality :  0.037   0.135   1232
  Planarity :  0.002   0.024   1400
  Dihedral  :  3.536  17.047   1094
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.41 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  3.52 %
    Favored  : 95.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.35 (0.27), residues: 992
  helix:  3.23 (0.28), residues: 364
  sheet:  1.74 (0.40), residues: 164
  loop :  0.13 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 155 
 TYR   0.006   0.001   TYR A 487 
 PHE   0.015   0.001   PHE A 145 
 TRP   0.003   0.001   TRP B 337 
 HIS   0.003   0.001   HIS A 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00171 ( 8282)
  covalent geometry    : angle       0.42496 (11112)
  hydrogen bonds       : bond        0.02368 (  372)
  hydrogen bonds       : angle       3.61270 ( 1050)
  metal coordination   : bond        0.00495 (    8)
  metal coordination   : angle       1.60974 (    6)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9688 (mpp) cc_final: 0.9438 (mpp)
REVERT: B  414 MET cc_start: 0.9683 (mpp) cc_final: 0.9435 (mpp)
  outliers start: 8
  outliers final: 0
  residues processed: 34
  average time/residue: 0.6777
  time to fit residues: 24.6611
Evaluate side-chains
  32 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 32
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 68 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 18 optimal weight:    0.2980
   chunk 54 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 323 HIS
B 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.041933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.031789 restraints weight = 33250.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.2651 rms_B_bonded: 3.71
r_work: 0.2491 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   8290  Z= 0.115
  Angle     :  0.429  11.183  11118  Z= 0.222
  Chirality :  0.037   0.133   1232
  Planarity :  0.002   0.024   1400
  Dihedral  :  3.501  16.310   1094
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.41 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  4.07 %
    Favored  : 95.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.38 (0.27), residues: 992
  helix:  3.27 (0.28), residues: 364
  sheet:  1.71 (0.40), residues: 164
  loop :  0.15 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 155 
 TYR   0.004   0.001   TYR B 518 
 PHE   0.016   0.001   PHE A 145 
 TRP   0.002   0.000   TRP B 337 
 HIS   0.003   0.001   HIS A 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 8282)
  covalent geometry    : angle       0.42826 (11112)
  hydrogen bonds       : bond        0.02446 (  372)
  hydrogen bonds       : angle       3.58269 ( 1050)
  metal coordination   : bond        0.01066 (    8)
  metal coordination   : angle       1.42606 (    6)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.336 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9700 (mpp) cc_final: 0.9433 (mpp)
REVERT: B  414 MET cc_start: 0.9695 (mpp) cc_final: 0.9430 (mpp)
  outliers start: 6
  outliers final: 2
  residues processed: 36
  average time/residue: 0.6096
  time to fit residues: 23.4464
Evaluate side-chains
  34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 323 HIS
B 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.041275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.031062 restraints weight = 33300.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.2627 rms_B_bonded: 3.73
r_work: 0.2461 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.2461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8905
moved from start:          0.1525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8290  Z= 0.182
  Angle     :  0.472  12.235  11118  Z= 0.242
  Chirality :  0.038   0.131   1232
  Planarity :  0.003   0.031   1400
  Dihedral  :  3.626  15.603   1094
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.81 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  4.41 %
    Favored  : 95.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.37 (0.27), residues: 992
  helix:  3.25 (0.28), residues: 366
  sheet:  1.66 (0.39), residues: 164
  loop :  0.17 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 155 
 TYR   0.005   0.001   TYR B 293 
 PHE   0.017   0.001   PHE A 145 
 TRP   0.002   0.001   TRP A 322 
 HIS   0.003   0.001   HIS A 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 8282)
  covalent geometry    : angle       0.47201 (11112)
  hydrogen bonds       : bond        0.02692 (  372)
  hydrogen bonds       : angle       3.63094 ( 1050)
  metal coordination   : bond        0.01709 (    8)
  metal coordination   : angle       0.86166 (    6)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9699 (mpp) cc_final: 0.9436 (mpp)
REVERT: B  414 MET cc_start: 0.9701 (mpp) cc_final: 0.9440 (mpp)
  outliers start: 4
  outliers final: 2
  residues processed: 36
  average time/residue: 0.6046
  time to fit residues: 23.3542
Evaluate side-chains
  34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 56 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 323 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.041532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.031416 restraints weight = 33329.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.2637 rms_B_bonded: 3.70
r_work: 0.2477 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8904
moved from start:          0.1544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8290  Z= 0.137
  Angle     :  0.451  12.354  11118  Z= 0.231
  Chirality :  0.038   0.132   1232
  Planarity :  0.002   0.027   1400
  Dihedral  :  3.587  16.121   1094
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.81 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  4.52 %
    Favored  : 95.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.32 (0.27), residues: 992
  helix:  3.23 (0.28), residues: 364
  sheet:  1.66 (0.40), residues: 164
  loop :  0.12 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 155 
 TYR   0.004   0.001   TYR A 529 
 PHE   0.016   0.001   PHE A 145 
 TRP   0.002   0.000   TRP B 337 
 HIS   0.003   0.001   HIS B 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 8282)
  covalent geometry    : angle       0.45020 (11112)
  hydrogen bonds       : bond        0.02552 (  372)
  hydrogen bonds       : angle       3.61492 ( 1050)
  metal coordination   : bond        0.01237 (    8)
  metal coordination   : angle       1.14710 (    6)

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

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

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1984 Ramachandran restraints generated.
    992 Oldfield, 0 Emsley, 992 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 32
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9698 (mpp) cc_final: 0.9387 (mpp)
REVERT: B  414 MET cc_start: 0.9698 (mpp) cc_final: 0.9390 (mpp)
  outliers start: 3
  outliers final: 2
  residues processed: 35
  average time/residue: 0.6176
  time to fit residues: 23.0861
Evaluate side-chains
  34 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 32
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.6980
   chunk 58 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 42 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 323 HIS
B 323 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.041411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.031238 restraints weight = 33226.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.2631 rms_B_bonded: 3.71
r_work: 0.2476 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.2476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8897
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   8290  Z= 0.158
  Angle     :  0.459  12.372  11118  Z= 0.235
  Chirality :  0.038   0.132   1232
  Planarity :  0.002   0.028   1400
  Dihedral  :  3.601  15.971   1094
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.02 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  4.41 %
    Favored  : 95.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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:  2.32 (0.27), residues: 992
  helix:  3.21 (0.28), residues: 366
  sheet:  1.63 (0.39), residues: 164
  loop :  0.13 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 155 
 TYR   0.005   0.001   TYR A 529 
 PHE   0.017   0.001   PHE A 145 
 TRP   0.002   0.000   TRP A 337 
 HIS   0.004   0.001   HIS A 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8282)
  covalent geometry    : angle       0.45857 (11112)
  hydrogen bonds       : bond        0.02594 (  372)
  hydrogen bonds       : angle       3.62067 ( 1050)
  metal coordination   : bond        0.01433 (    8)
  metal coordination   : angle       1.09386 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1990.73 seconds
wall clock time: 34 minutes 46.55 seconds (2086.55 seconds total)