Starting phenix.real_space_refine
on Sat Jul 26 00:03:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lre_23496/07_2025/7lre_23496.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lre_23496/07_2025/7lre_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_23496/07_2025/7lre_23496.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lre_23496/07_2025/7lre_23496.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lre_23496/07_2025/7lre_23496.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lre_23496/07_2025/7lre_23496.cif"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.81, per 1000 atoms: 0.96
  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: 1.84
  Conformation dependent library (CDL) restraints added in 980.3 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: 0.89
  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: 2.36

  Time building geometry restraints manager: 2.19 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: 0.04
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:             2.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.590
  Find NCS groups from input model:        0.130
  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:             0.010
  Load rotamer database and sin/cos tables:13.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.630
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  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
 TRP   0.003   0.001   TRP B 110 
 HIS   0.001   0.000   HIS A 274 
 PHE   0.012   0.001   PHE A 145 
 TYR   0.006   0.001   TYR A 236 
 ARG   0.001   0.000   ARG B 309 

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

*********************** 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  : 0.940 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 42
  average time/residue: 1.4218
  time to fit residues: 63.8909
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  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 40 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0370
   chunk 58 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    1.4066

-------------------------------------------------------------------------------
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 = 0.3016 r_free = 0.3016 target = 0.041983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.031737 restraints weight = 33100.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.2642 rms_B_bonded: 3.71
r_work: 0.2487 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8884
moved from start:          0.0808

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= 0.176
  Angle     :  0.447   6.259  11118  Z= 0.238
  Chirality :  0.038   0.134   1232
  Planarity :  0.003   0.028   1400
  Dihedral  :  3.570  14.841   1094
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  2.42 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.26), residues: 992
  helix:  3.15 (0.28), residues: 366
  sheet:  1.83 (0.39), residues: 164
  loop :  0.03 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 322 
 HIS   0.004   0.001   HIS B 274 
 PHE   0.019   0.001   PHE B 145 
 TYR   0.007   0.001   TYR B 293 
 ARG   0.002   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03190 (  372)
  hydrogen bonds       : angle       3.83075 ( 1050)
  metal coordination   : bond        0.01476 (    8)
  metal coordination   : angle       2.14696 (    6)
  covalent geometry    : bond        0.00387 ( 8282)
  covalent geometry    : angle       0.44434 (11112)

*********************** 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
  42 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.914 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9597 (mpp) cc_final: 0.9304 (mpp)
REVERT: B  414 MET cc_start: 0.9595 (mpp) cc_final: 0.9306 (mpp)
  outliers start: 10
  outliers final: 0
  residues processed: 34
  average time/residue: 1.4873
  time to fit residues: 54.4546
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  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0050
   chunk 66 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 93 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.9600

-------------------------------------------------------------------------------
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 = 0.2985 r_free = 0.2985 target = 0.040884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.030712 restraints weight = 33895.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.2607 rms_B_bonded: 3.71
r_work: 0.2453 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.2453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8904
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8290  Z= 0.230
  Angle     :  0.471   7.663  11118  Z= 0.249
  Chirality :  0.039   0.132   1232
  Planarity :  0.003   0.037   1400
  Dihedral  :  3.726  14.684   1094
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  3.08 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.27), residues: 992
  helix:  3.20 (0.28), residues: 366
  sheet:  1.72 (0.39), residues: 164
  loop :  0.02 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 322 
 HIS   0.004   0.001   HIS A 274 
 PHE   0.018   0.001   PHE B 145 
 TYR   0.006   0.001   TYR B 293 
 ARG   0.002   0.000   ARG B 526 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03112 (  372)
  hydrogen bonds       : angle       3.78966 ( 1050)
  metal coordination   : bond        0.01990 (    8)
  metal coordination   : angle       1.67696 (    6)
  covalent geometry    : bond        0.00510 ( 8282)
  covalent geometry    : angle       0.46959 (11112)

*********************** 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
  38 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.937 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9677 (mpp) cc_final: 0.9345 (mpp)
REVERT: B  414 MET cc_start: 0.9678 (mpp) cc_final: 0.9348 (mpp)
  outliers start: 6
  outliers final: 0
  residues processed: 34
  average time/residue: 1.4061
  time to fit residues: 51.4857
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  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    0.2980
   chunk 13 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 90 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.2994 r_free = 0.2994 target = 0.041335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.031140 restraints weight = 33250.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.2621 rms_B_bonded: 3.73
r_work: 0.2454 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8912
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8290  Z= 0.169
  Angle     :  0.425   8.081  11118  Z= 0.228
  Chirality :  0.038   0.133   1232
  Planarity :  0.003   0.032   1400
  Dihedral  :  3.694  15.465   1094
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.81 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.27), residues: 992
  helix:  3.28 (0.28), residues: 364
  sheet:  1.68 (0.39), residues: 164
  loop :  0.03 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP A 337 
 HIS   0.004   0.001   HIS B 274 
 PHE   0.017   0.001   PHE A 145 
 TYR   0.005   0.001   TYR B 529 
 ARG   0.002   0.000   ARG A 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02809 (  372)
  hydrogen bonds       : angle       3.72469 ( 1050)
  metal coordination   : bond        0.01641 (    8)
  metal coordination   : angle       1.47204 (    6)
  covalent geometry    : bond        0.00375 ( 8282)
  covalent geometry    : angle       0.42401 (11112)

*********************** 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: 6
    poor density    : 32
  time to evaluate  : 1.177 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9668 (mpp) cc_final: 0.9409 (mpp)
REVERT: B  414 MET cc_start: 0.9670 (mpp) cc_final: 0.9414 (mpp)
  outliers start: 6
  outliers final: 0
  residues processed: 34
  average time/residue: 1.6010
  time to fit residues: 58.3981
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  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0870
   chunk 96 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   overall best weight:    1.3162

-------------------------------------------------------------------------------
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 = 0.2993 r_free = 0.2993 target = 0.041107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.030989 restraints weight = 33239.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.2624 rms_B_bonded: 3.70
r_work: 0.2460 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8903
moved from start:          0.1371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   8290  Z= 0.161
  Angle     :  0.427   9.483  11118  Z= 0.227
  Chirality :  0.038   0.133   1232
  Planarity :  0.003   0.030   1400
  Dihedral  :  3.677  15.813   1094
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.61 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  3.30 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.27), residues: 992
  helix:  3.27 (0.28), residues: 364
  sheet:  1.57 (0.39), residues: 168
  loop :  0.05 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 337 
 HIS   0.004   0.001   HIS B 274 
 PHE   0.011   0.001   PHE B 145 
 TYR   0.005   0.001   TYR B 529 
 ARG   0.002   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02705 (  372)
  hydrogen bonds       : angle       3.72109 ( 1050)
  metal coordination   : bond        0.01382 (    8)
  metal coordination   : angle       0.69885 (    6)
  covalent geometry    : bond        0.00359 ( 8282)
  covalent geometry    : angle       0.42663 (11112)

*********************** 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
  40 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 1.192 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9691 (mpp) cc_final: 0.9467 (mpp)
REVERT: B  414 MET cc_start: 0.9692 (mpp) cc_final: 0.9471 (mpp)
  outliers start: 8
  outliers final: 0
  residues processed: 34
  average time/residue: 1.4985
  time to fit residues: 54.7144
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  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0570
   chunk 96 optimal weight:    3.9990
   overall best weight:    1.7704

-------------------------------------------------------------------------------
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 = 0.2986 r_free = 0.2986 target = 0.040904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.030726 restraints weight = 33402.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.2611 rms_B_bonded: 3.72
r_work: 0.2453 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8913
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8290  Z= 0.209
  Angle     :  0.465  10.411  11118  Z= 0.243
  Chirality :  0.039   0.133   1232
  Planarity :  0.003   0.033   1400
  Dihedral  :  3.722  15.415   1094
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  2.02 %
    Favored  : 97.78 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.27), residues: 992
  helix:  3.25 (0.28), residues: 364
  sheet:  1.66 (0.39), residues: 164
  loop :  0.06 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 337 
 HIS   0.004   0.001   HIS B 274 
 PHE   0.019   0.001   PHE A 145 
 TYR   0.006   0.001   TYR A 529 
 ARG   0.002   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02879 (  372)
  hydrogen bonds       : angle       3.75383 ( 1050)
  metal coordination   : bond        0.02004 (    8)
  metal coordination   : angle       1.00534 (    6)
  covalent geometry    : bond        0.00464 ( 8282)
  covalent geometry    : angle       0.46438 (11112)

*********************** 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  : 0.765 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9706 (mpp) cc_final: 0.9380 (mpp)
REVERT: B  414 MET cc_start: 0.9711 (mpp) cc_final: 0.9389 (mpp)
  outliers start: 8
  outliers final: 2
  residues processed: 36
  average time/residue: 1.3960
  time to fit residues: 54.0083
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  : 1.002 
-------------------------------------------------------------------------------
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 49 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0770
   chunk 90 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 82 optimal weight:    0.8980
   chunk 96 optimal weight:    0.5980
   chunk 2 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.3015 r_free = 0.3015 target = 0.041756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.031594 restraints weight = 33202.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.2642 rms_B_bonded: 3.73
r_work: 0.2486 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.2486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8887
moved from start:          0.1489

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= 0.096
  Angle     :  0.424  10.566  11118  Z= 0.221
  Chirality :  0.037   0.132   1232
  Planarity :  0.002   0.023   1400
  Dihedral  :  3.586  16.805   1094
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.61 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  3.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.27), residues: 992
  helix:  3.26 (0.28), residues: 364
  sheet:  1.58 (0.39), residues: 168
  loop :  0.06 (0.27), residues: 460

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02499 (  372)
  hydrogen bonds       : angle       3.63793 ( 1050)
  metal coordination   : bond        0.00842 (    8)
  metal coordination   : angle       1.51247 (    6)
  covalent geometry    : bond        0.00211 ( 8282)
  covalent geometry    : angle       0.42243 (11112)

*********************** 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
  37 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 32
  time to evaluate  : 1.316 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9700 (mpp) cc_final: 0.9450 (mpp)
REVERT: B  414 MET cc_start: 0.9704 (mpp) cc_final: 0.9457 (mpp)
  outliers start: 5
  outliers final: 2
  residues processed: 36
  average time/residue: 2.0866
  time to fit residues: 81.0349
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  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain B residue  136 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 20 optimal weight:    0.3980
   chunk 80 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 48 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 15 optimal weight:    0.3980
   chunk 74 optimal weight:    1.9990
   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 = 0.3011 r_free = 0.3011 target = 0.041553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.031468 restraints weight = 33564.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.2641 rms_B_bonded: 3.70
r_work: 0.2476 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8907
moved from start:          0.1537

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= 0.122
  Angle     :  0.429  11.317  11118  Z= 0.223
  Chirality :  0.038   0.132   1232
  Planarity :  0.002   0.025   1400
  Dihedral  :  3.543  16.445   1094
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.81 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  3.85 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.27), residues: 992
  helix:  3.25 (0.28), residues: 364
  sheet:  1.55 (0.39), residues: 168
  loop :  0.07 (0.27), residues: 460

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02528 (  372)
  hydrogen bonds       : angle       3.66637 ( 1050)
  metal coordination   : bond        0.01179 (    8)
  metal coordination   : angle       1.41469 (    6)
  covalent geometry    : bond        0.00273 ( 8282)
  covalent geometry    : angle       0.42754 (11112)

*********************** 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
  39 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 1.179 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9707 (mpp) cc_final: 0.9432 (mpp)
REVERT: B  414 MET cc_start: 0.9712 (mpp) cc_final: 0.9440 (mpp)
  outliers start: 7
  outliers final: 2
  residues processed: 36
  average time/residue: 2.5860
  time to fit residues: 100.8481
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  : 0.973 
-------------------------------------------------------------------------------
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 58 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0370
   chunk 92 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 41 optimal weight:    0.3980
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.7660

-------------------------------------------------------------------------------
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 = 0.041782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.031565 restraints weight = 33733.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.2646 rms_B_bonded: 3.79
r_work: 0.2479 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
moved from start:          0.1571

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= 0.107
  Angle     :  0.428  11.907  11118  Z= 0.220
  Chirality :  0.038   0.131   1232
  Planarity :  0.002   0.023   1400
  Dihedral  :  3.501  16.395   1094
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.61 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  4.19 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.27), residues: 992
  helix:  3.20 (0.28), residues: 366
  sheet:  1.58 (0.39), residues: 168
  loop :  0.06 (0.27), residues: 458

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

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02409 (  372)
  hydrogen bonds       : angle       3.64146 ( 1050)
  metal coordination   : bond        0.01001 (    8)
  metal coordination   : angle       1.46863 (    6)
  covalent geometry    : bond        0.00239 ( 8282)
  covalent geometry    : angle       0.42652 (11112)

*********************** 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  : 1.369 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9710 (mpp) cc_final: 0.9432 (mpp)
REVERT: B  414 MET cc_start: 0.9716 (mpp) cc_final: 0.9443 (mpp)
  outliers start: 4
  outliers final: 2
  residues processed: 36
  average time/residue: 1.7549
  time to fit residues: 68.4330
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  : 1.005 
-------------------------------------------------------------------------------
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 94 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.3017 r_free = 0.3017 target = 0.041680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.031547 restraints weight = 33220.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.2646 rms_B_bonded: 3.71
r_work: 0.2483 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8905
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8290  Z= 0.117
  Angle     :  0.434  12.433  11118  Z= 0.222
  Chirality :  0.038   0.131   1232
  Planarity :  0.002   0.024   1400
  Dihedral  :  3.496  16.332   1094
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.41 %
    Favored  : 98.39 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.27 (0.27), residues: 992
  helix:  3.21 (0.28), residues: 366
  sheet:  1.59 (0.39), residues: 168
  loop :  0.05 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 337 
 HIS   0.003   0.001   HIS A 323 
 PHE   0.016   0.001   PHE A 145 
 TYR   0.004   0.001   TYR A 487 
 ARG   0.002   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02453 (  372)
  hydrogen bonds       : angle       3.64180 ( 1050)
  metal coordination   : bond        0.01125 (    8)
  metal coordination   : angle       1.41819 (    6)
  covalent geometry    : bond        0.00262 ( 8282)
  covalent geometry    : angle       0.43287 (11112)

********************** 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
  36 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 32
  time to evaluate  : 0.998 
Fit side-chains
REVERT: A  414 MET cc_start: 0.9712 (mpp) cc_final: 0.9413 (mpp)
REVERT: B  414 MET cc_start: 0.9712 (mpp) cc_final: 0.9414 (mpp)
  outliers start: 4
  outliers final: 2
  residues processed: 36
  average time/residue: 1.3675
  time to fit residues: 53.0534
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  : 0.904 
-------------------------------------------------------------------------------
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 40 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 27 optimal weight:    0.2980
   chunk 89 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 86 optimal weight:    0.6980
   chunk 71 optimal weight:    0.4980
   chunk 78 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3031 r_free = 0.3031 target = 0.041926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.031912 restraints weight = 33470.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.2657 rms_B_bonded: 3.65
r_work: 0.2501 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
moved from start:          0.1625

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= 0.090
  Angle     :  0.423  12.479  11118  Z= 0.215
  Chirality :  0.037   0.131   1232
  Planarity :  0.002   0.023   1400
  Dihedral  :  3.438  16.414   1094
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  1.51 %
    Favored  : 98.29 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.27), residues: 992
  helix:  3.22 (0.28), residues: 366
  sheet:  1.62 (0.39), residues: 168
  loop :  0.05 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 337 
 HIS   0.003   0.001   HIS B 274 
 PHE   0.015   0.001   PHE A 145 
 TYR   0.005   0.001   TYR A 487 
 ARG   0.002   0.000   ARG B 155 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02306 (  372)
  hydrogen bonds       : angle       3.60810 ( 1050)
  metal coordination   : bond        0.00806 (    8)
  metal coordination   : angle       1.63245 (    6)
  covalent geometry    : bond        0.00199 ( 8282)
  covalent geometry    : angle       0.42109 (11112)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4378.22 seconds
wall clock time: 77 minutes 31.26 seconds (4651.26 seconds total)