Starting phenix.real_space_refine
on Sat May 10 15:48:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rl6_19332/05_2025/8rl6_19332.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rl6_19332/05_2025/8rl6_19332.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rl6_19332/05_2025/8rl6_19332.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rl6_19332/05_2025/8rl6_19332.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rl6_19332/05_2025/8rl6_19332.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rl6_19332/05_2025/8rl6_19332.cif"
  }
  resolution = 3.18
  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=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      20      5.16       5
     C    2083      2.51       5
     N     575      2.21       5
     O     597      1.98       5
     H    3217      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6493
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6492
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 436, 6492
          Classifications: {'peptide': 436}
          Link IDs: {'PTRANS': 17, 'TRANS': 418}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 131
          Unresolved non-hydrogen angles: 155
          Unresolved non-hydrogen dihedrals: 109
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 88
    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   5920  SG  CYS A 411      26.850  42.159  25.229  1.00 67.90           S
  ATOM   6155  SG  CYS A 427      24.363  42.143  28.158  1.00 94.76           S
  ATOM   6204  SG  CYS A 431      25.319  45.411  26.355  1.00 95.89           S
  ATOM   6243  SG  CYS A 434      23.526  42.902  24.196  1.00 70.28           S

  Time building chain proxies: 4.95, per 1000 atoms: 0.76
  Number of scatterers: 6493
  At special positions: 0
  Unit cell: (77.7, 81.9, 74.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      20     16.00
     O     597      8.00
     N     575      7.00
     C    2083      6.00
     H    3217      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 266 " - pdb=" SG  CYS A 272 " distance=2.03

  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: 1.81
  Conformation dependent library (CDL) restraints added in 650.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 411 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 431 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 434 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 427 "
      Number of angles added : 6


  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  826

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      56.0% alpha, 11.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 25
    Processing helix  chain 'A' and resid 31 through 44
    Processing helix  chain 'A' and resid 57 through 69
      removed outlier: 3.629A  pdb=" N   CYS A  61 " --> pdb=" O   GLY A  57 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   TYR A  62 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      Proline residue:  A  65  - end of helix
    Processing helix  chain 'A' and resid 79 through 93
    Processing helix  chain 'A' and resid 105 through 118
    Processing helix  chain 'A' and resid 129 through 134
    Processing helix  chain 'A' and resid 137 through 148
      removed outlier: 4.452A  pdb=" N   THR A 141 " --> pdb=" O   SER A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 163
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 4.039A  pdb=" N   GLY A 177 " --> pdb=" O   TYR A 173 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   ALA A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU A 179 " --> pdb=" O   ARG A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 207
    Processing helix  chain 'A' and resid 237 through 251
      removed outlier: 3.834A  pdb=" N   GLY A 251 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 283
      removed outlier: 3.596A  pdb=" N   GLU A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   GLN A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLY A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 307
    Processing helix  chain 'A' and resid 339 through 349
      removed outlier: 3.929A  pdb=" N   ARG A 349 " --> pdb=" O   GLN A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 385
    Processing helix  chain 'A' and resid 388 through 407
      removed outlier: 3.768A  pdb=" N   ILE A 396 " --> pdb=" O   ASP A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 421
    Processing helix  chain 'A' and resid 436 through 451
      removed outlier: 3.529A  pdb=" N   VAL A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 100
      removed outlier: 6.389A  pdb=" N   SER A  98 " --> pdb=" O   TYR A 127 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   THR A  73 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   ILE A 128 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   VAL A  75 " --> pdb=" O   ILE A 128 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   ILE A  72 " --> pdb=" O   TYR A 153 " (cutoff:3.500A)
      removed outlier: 7.880A  pdb=" N   VAL A 155 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ILE A  74 " --> pdb=" O   VAL A 155 " (cutoff:3.500A)
      removed outlier: 8.368A  pdb=" N   VAL A 189 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   LEU A 154 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   LEU A 191 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   VAL A 156 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ALA A 214 " --> pdb=" O   ASP A  47 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 231
      removed outlier: 5.801A  pdb=" N   PHE A 226 " --> pdb=" O   CYS A 359 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   LEU A 361 " --> pdb=" O   PHE A 226 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   ASP A 228 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 7.566A  pdb=" N   TYR A 363 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   GLN A 230 " --> pdb=" O   TYR A 363 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   VAL A 331 " --> pdb=" O   ARG A 360 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   TYR A 362 " --> pdb=" O   VAL A 331 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   HIS A 333 " --> pdb=" O   TYR A 362 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ILE A 263 " --> pdb=" O   ALA A 332 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   GLY A 262 " --> pdb=" O   ILE A 313 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   ALA A 315 " --> pdb=" O   GLY A 262 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   VAL A 264 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   TYR A 289 " --> pdb=" O   THR A 316 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    162 hydrogen bonds defined for protein.
    477 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: 2.68

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 3208
        1.03 -     1.23: 10
        1.23 -     1.42: 1369
        1.42 -     1.62: 1944
        1.62 -     1.81: 25
  Bond restraints: 6556
  Sorted by residual:
  bond pdb=" CG  LEU A 176 "
       pdb=" CD1 LEU A 176 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.35e+00
  bond pdb=" CB  CYS A 427 "
       pdb=" HB2 CYS A 427 "
    ideal  model  delta    sigma   weight residual
    0.970  0.954  0.016 2.00e-02 2.50e+03 6.46e-01
  bond pdb=" N   LEU A 176 "
       pdb=" CA  LEU A 176 "
    ideal  model  delta    sigma   weight residual
    1.457  1.467 -0.009 1.29e-02 6.01e+03 5.13e-01
  bond pdb=" CB  LEU A 183 "
       pdb=" CG  LEU A 183 "
    ideal  model  delta    sigma   weight residual
    1.530  1.543 -0.013 2.00e-02 2.50e+03 4.05e-01
  bond pdb=" CB  GLU A 407 "
       pdb=" CG  GLU A 407 "
    ideal  model  delta    sigma   weight residual
    1.520  1.502  0.018 3.00e-02 1.11e+03 3.68e-01
  ... (remaining 6551 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.01: 11079
        1.01 -     2.02: 717
        2.02 -     3.03: 34
        3.03 -     4.04: 12
        4.04 -     5.06: 9
  Bond angle restraints: 11851
  Sorted by residual:
  angle pdb=" CB  LEU A 279 "
        pdb=" CG  LEU A 279 "
        pdb=" CD1 LEU A 279 "
      ideal   model   delta    sigma   weight residual
     110.70  114.97   -4.27 3.00e+00 1.11e-01 2.03e+00
  angle pdb=" CA  LEU A 183 "
        pdb=" CB  LEU A 183 "
        pdb=" CG  LEU A 183 "
      ideal   model   delta    sigma   weight residual
     116.30  120.89   -4.59 3.50e+00 8.16e-02 1.72e+00
  angle pdb=" CB  LEU A 176 "
        pdb=" CG  LEU A 176 "
        pdb=" CD1 LEU A 176 "
      ideal   model   delta    sigma   weight residual
     110.70  114.51   -3.81 3.00e+00 1.11e-01 1.61e+00
  angle pdb=" CA  TYR A 173 "
        pdb=" CB  TYR A 173 "
        pdb=" CG  TYR A 173 "
      ideal   model   delta    sigma   weight residual
     113.90  111.64    2.26 1.80e+00 3.09e-01 1.57e+00
  angle pdb=" CB  MET A 132 "
        pdb=" CG  MET A 132 "
        pdb=" SD  MET A 132 "
      ideal   model   delta    sigma   weight residual
     112.70  116.43   -3.73 3.00e+00 1.11e-01 1.55e+00
  ... (remaining 11846 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.53: 2784
       15.53 -    31.06: 224
       31.06 -    46.59: 56
       46.59 -    62.11: 30
       62.11 -    77.64: 8
  Dihedral angle restraints: 3102
    sinusoidal: 1636
      harmonic: 1466
  Sorted by residual:
  dihedral pdb=" CB  CYS A 266 "
           pdb=" SG  CYS A 266 "
           pdb=" SG  CYS A 272 "
           pdb=" CB  CYS A 272 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.80   37.20     1      1.00e+01 1.00e-02 1.95e+01
  dihedral pdb=" CA  TYR A 363 "
           pdb=" C   TYR A 363 "
           pdb=" N   SER A 364 "
           pdb=" CA  SER A 364 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.55   16.45     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CG  ARG A 412 "
           pdb=" CD  ARG A 412 "
           pdb=" NE  ARG A 412 "
           pdb=" CZ  ARG A 412 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00  -49.78  -40.22     2      1.50e+01 4.44e-03 8.90e+00
  ... (remaining 3099 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 332
       0.024 -    0.047: 102
       0.047 -    0.071: 49
       0.071 -    0.094: 21
       0.094 -    0.118: 21
  Chirality restraints: 525
  Sorted by residual:
  chirality pdb=" CA  VAL A 314 "
            pdb=" N   VAL A 314 "
            pdb=" C   VAL A 314 "
            pdb=" CB  VAL A 314 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.47e-01
  chirality pdb=" CA  ILE A 128 "
            pdb=" N   ILE A 128 "
            pdb=" C   ILE A 128 "
            pdb=" CB  ILE A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.39e-01
  chirality pdb=" CA  ILE A  74 "
            pdb=" N   ILE A  74 "
            pdb=" C   ILE A  74 "
            pdb=" CB  ILE A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.38e-01
  ... (remaining 522 not shown)

  Planarity restraints: 996
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 363 "    0.013 2.00e-02 2.50e+03   9.54e-03 2.73e+00
        pdb=" CG  TYR A 363 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 363 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 363 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 363 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 363 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 363 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 363 "    0.000 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 363 "   -0.003 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 363 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 363 "    0.002 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 363 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 412 "   -0.128 9.50e-02 1.11e+02   4.29e-02 2.17e+00
        pdb=" NE  ARG A 412 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 412 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 412 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 412 "   -0.000 2.00e-02 2.50e+03
        pdb="HH11 ARG A 412 "    0.004 2.00e-02 2.50e+03
        pdb="HH12 ARG A 412 "   -0.000 2.00e-02 2.50e+03
        pdb="HH21 ARG A 412 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A 412 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 196 "   -0.019 5.00e-02 4.00e+02   2.91e-02 1.35e+00
        pdb=" N   PRO A 197 "    0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO A 197 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 197 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 993 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 600
        2.22 -     2.81: 14437
        2.81 -     3.41: 18983
        3.41 -     4.00: 24217
        4.00 -     4.60: 37030
  Nonbonded interactions: 95267
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 157 "
            pdb=" HH  TYR A 173 "
     model   vdw
     1.621 2.450
  nonbonded pdb=" H   ALA A 159 "
            pdb=" O   LEU A 191 "
     model   vdw
     1.652 2.450
  nonbonded pdb=" HE2 HIS A 333 "
            pdb=" OE1 GLU A 346 "
     model   vdw
     1.666 2.450
  nonbonded pdb=" O   ARG A 175 "
            pdb=" H   ALA A 178 "
     model   vdw
     1.681 2.450
  nonbonded pdb=" O   LEU A 382 "
            pdb=" H   GLY A 387 "
     model   vdw
     1.739 2.450
  ... (remaining 95262 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             6.500
  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:             0.130
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     22.840
  Find NCS groups from input model:        0.060
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5880
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   0.038   3344  Z= 0.113
  Angle     :  0.552  12.648   4537  Z= 0.254
  Chirality :  0.037   0.118    525
  Planarity :  0.004   0.056    580
  Dihedral  : 13.535  77.642   1194
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.86 (0.43), residues: 432
  helix:  2.14 (0.35), residues: 226
  sheet: -0.90 (0.62), residues: 74
  loop :  1.17 (0.61), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 334 
 HIS   0.003   0.001   HIS A 433 
 PHE   0.009   0.001   PHE A 216 
 TYR   0.027   0.002   TYR A 363 
 ARG   0.007   0.001   ARG A 349 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12246 (  162)
  hydrogen bonds       : angle       6.06628 (  477)
  metal coordination   : bond        0.01832 (    4)
  metal coordination   : angle       6.81760 (    6)
  SS BOND              : bond        0.00247 (    1)
  SS BOND              : angle       0.78293 (    2)
  covalent geometry    : bond        0.00243 ( 3339)
  covalent geometry    : angle       0.49378 ( 4529)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   68 is missing expected H atoms. Skipping.
Residue SER  259 is missing expected H atoms. Skipping.
Residue LYS  287 is missing expected H atoms. Skipping.
Residue LYS  309 is missing expected H atoms. Skipping.
Residue LYS  338 is missing expected H atoms. Skipping.
Residue LYS  389 is missing expected H atoms. Skipping.
Residue SER  391 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  397 is missing expected H atoms. Skipping.
Residue VAL  440 is missing expected H atoms. Skipping.
Evaluate side-chains
  81 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  359 CYS cc_start: 0.6830 (m) cc_final: 0.6624 (m)
REVERT: A  407 GLU cc_start: 0.6589 (mp0) cc_final: 0.6319 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2755
  time to fit residues: 28.1266
Evaluate side-chains
  78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0670
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 39 optimal weight:    0.2980
   overall best weight:    0.4718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.208597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.189253 restraints weight = 15765.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.4422 rms_B_bonded: 3.24
r_work: 0.4303 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.4303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6011
moved from start:          0.1420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3344  Z= 0.195
  Angle     :  0.594  11.080   4537  Z= 0.295
  Chirality :  0.039   0.135    525
  Planarity :  0.004   0.035    580
  Dihedral  :  3.991  15.028    469
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  7.81 %
    Favored  : 91.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.34 (0.42), residues: 432
  helix:  1.86 (0.35), residues: 229
  sheet: -1.80 (0.56), residues: 75
  loop :  1.10 (0.58), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 305 
 HIS   0.005   0.001   HIS A  89 
 PHE   0.015   0.002   PHE A  49 
 TYR   0.022   0.002   TYR A 363 
 ARG   0.004   0.001   ARG A 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04006 (  162)
  hydrogen bonds       : angle       5.03440 (  477)
  metal coordination   : bond        0.01253 (    4)
  metal coordination   : angle       6.26552 (    6)
  SS BOND              : bond        0.00381 (    1)
  SS BOND              : angle       0.40508 (    2)
  covalent geometry    : bond        0.00395 ( 3339)
  covalent geometry    : angle       0.54854 ( 4529)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   68 is missing expected H atoms. Skipping.
Residue SER  259 is missing expected H atoms. Skipping.
Residue LYS  287 is missing expected H atoms. Skipping.
Residue LYS  309 is missing expected H atoms. Skipping.
Residue LYS  338 is missing expected H atoms. Skipping.
Residue LYS  389 is missing expected H atoms. Skipping.
Residue SER  391 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  397 is missing expected H atoms. Skipping.
Residue VAL  440 is missing expected H atoms. Skipping.
Evaluate side-chains
  78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLN cc_start: 0.6686 (mm-40) cc_final: 0.6410 (mm-40)
REVERT: A  407 GLU cc_start: 0.6808 (mp0) cc_final: 0.6474 (mp0)
  outliers start: 2
  outliers final: 2
  residues processed: 77
  average time/residue: 0.2559
  time to fit residues: 24.8121
Evaluate side-chains
  77 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 ASN
Chi-restraints excluded: chain A residue  318 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 3 optimal weight:    0.3980
   chunk 38 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 20 optimal weight:    0.1980
   chunk 14 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 164 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.205219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.185204 restraints weight = 15685.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.4383 rms_B_bonded: 3.37
r_work: 0.4253 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.4253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6098
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3344  Z= 0.203
  Angle     :  0.600  10.456   4537  Z= 0.297
  Chirality :  0.038   0.135    525
  Planarity :  0.005   0.044    580
  Dihedral  :  4.270  17.491    469
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  8.71 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.87 (0.42), residues: 432
  helix:  1.52 (0.35), residues: 228
  sheet: -2.05 (0.55), residues: 74
  loop :  0.82 (0.57), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 305 
 HIS   0.006   0.002   HIS A  89 
 PHE   0.016   0.002   PHE A  49 
 TYR   0.035   0.002   TYR A 363 
 ARG   0.005   0.001   ARG A 442 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  162)
  hydrogen bonds       : angle       5.02006 (  477)
  metal coordination   : bond        0.01284 (    4)
  metal coordination   : angle       6.51219 (    6)
  SS BOND              : bond        0.00579 (    1)
  SS BOND              : angle       0.45935 (    2)
  covalent geometry    : bond        0.00418 ( 3339)
  covalent geometry    : angle       0.55211 ( 4529)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   68 is missing expected H atoms. Skipping.
Residue SER  259 is missing expected H atoms. Skipping.
Residue LYS  287 is missing expected H atoms. Skipping.
Residue LYS  309 is missing expected H atoms. Skipping.
Residue LYS  338 is missing expected H atoms. Skipping.
Residue LYS  389 is missing expected H atoms. Skipping.
Residue SER  391 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  397 is missing expected H atoms. Skipping.
Residue VAL  440 is missing expected H atoms. Skipping.
Evaluate side-chains
  79 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLN cc_start: 0.6669 (mm-40) cc_final: 0.6420 (mm-40)
REVERT: A  346 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7078 (mt-10)
  outliers start: 6
  outliers final: 5
  residues processed: 77
  average time/residue: 0.2351
  time to fit residues: 23.5508
Evaluate side-chains
  75 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  285 ASN
Chi-restraints excluded: chain A residue  318 SER
Chi-restraints excluded: chain A residue  364 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 34 optimal weight:    0.4980
   chunk 28 optimal weight:    0.0040
   chunk 11 optimal weight:    0.1980
   chunk 31 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.2792

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.206745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.186407 restraints weight = 15855.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.4390 rms_B_bonded: 3.37
r_work: 0.4266 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.4266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6066
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3344  Z= 0.136
  Angle     :  0.534   8.710   4537  Z= 0.257
  Chirality :  0.037   0.128    525
  Planarity :  0.004   0.036    580
  Dihedral  :  4.033  16.122    469
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 11.11 %
    Favored  : 87.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.01 (0.42), residues: 432
  helix:  1.61 (0.35), residues: 228
  sheet: -1.97 (0.56), residues: 75
  loop :  0.95 (0.58), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 305 
 HIS   0.007   0.001   HIS A 290 
 PHE   0.012   0.001   PHE A 204 
 TYR   0.016   0.001   TYR A 363 
 ARG   0.004   0.000   ARG A 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03329 (  162)
  hydrogen bonds       : angle       4.70582 (  477)
  metal coordination   : bond        0.01008 (    4)
  metal coordination   : angle       5.32884 (    6)
  SS BOND              : bond        0.00426 (    1)
  SS BOND              : angle       0.55742 (    2)
  covalent geometry    : bond        0.00288 ( 3339)
  covalent geometry    : angle       0.49740 ( 4529)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   68 is missing expected H atoms. Skipping.
Residue SER  259 is missing expected H atoms. Skipping.
Residue LYS  287 is missing expected H atoms. Skipping.
Residue LYS  309 is missing expected H atoms. Skipping.
Residue LYS  338 is missing expected H atoms. Skipping.
Residue LYS  389 is missing expected H atoms. Skipping.
Residue SER  391 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  397 is missing expected H atoms. Skipping.
Residue VAL  440 is missing expected H atoms. Skipping.
Evaluate side-chains
  77 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLN cc_start: 0.6594 (mm-40) cc_final: 0.6372 (mm-40)
REVERT: A  346 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6932 (mt-10)
  outliers start: 3
  outliers final: 2
  residues processed: 74
  average time/residue: 0.2200
  time to fit residues: 21.5312
Evaluate side-chains
  78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ILE
Chi-restraints excluded: chain A residue  285 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0980
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4538 r_free = 0.4538 target = 0.201967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.181559 restraints weight = 15747.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.4320 rms_B_bonded: 3.37
r_work: 0.4191 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6199
moved from start:          0.3389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   3344  Z= 0.255
  Angle     :  0.638  10.886   4537  Z= 0.326
  Chirality :  0.039   0.127    525
  Planarity :  0.005   0.052    580
  Dihedral  :  4.594  16.399    469
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 15.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 12.31 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.39 (0.42), residues: 432
  helix:  1.06 (0.36), residues: 225
  sheet: -2.15 (0.60), residues: 66
  loop :  0.48 (0.56), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 305 
 HIS   0.009   0.003   HIS A 208 
 PHE   0.019   0.002   PHE A  49 
 TYR   0.013   0.002   TYR A 363 
 ARG   0.005   0.001   ARG A 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04204 (  162)
  hydrogen bonds       : angle       5.08326 (  477)
  metal coordination   : bond        0.01472 (    4)
  metal coordination   : angle       6.08746 (    6)
  SS BOND              : bond        0.00542 (    1)
  SS BOND              : angle       0.93720 (    2)
  covalent geometry    : bond        0.00523 ( 3339)
  covalent geometry    : angle       0.59817 ( 4529)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   68 is missing expected H atoms. Skipping.
Residue SER  259 is missing expected H atoms. Skipping.
Residue LYS  287 is missing expected H atoms. Skipping.
Residue LYS  309 is missing expected H atoms. Skipping.
Residue LYS  338 is missing expected H atoms. Skipping.
Residue LYS  389 is missing expected H atoms. Skipping.
Residue SER  391 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  397 is missing expected H atoms. Skipping.
Residue VAL  440 is missing expected H atoms. Skipping.
Evaluate side-chains
  78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 GLN cc_start: 0.6632 (mm-40) cc_final: 0.6419 (mm-40)
REVERT: A  151 LEU cc_start: 0.7910 (tp) cc_final: 0.7647 (tt)
REVERT: A  345 GLN cc_start: 0.7239 (mm110) cc_final: 0.6480 (mm110)
REVERT: A  346 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6898 (mt-10)
  outliers start: 5
  outliers final: 4
  residues processed: 76
  average time/residue: 0.2314
  time to fit residues: 23.2106
Evaluate side-chains
  76 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue  285 ASN
Chi-restraints excluded: chain A residue  364 SER
Chi-restraints excluded: chain A residue  444 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 3 optimal weight:    0.1980
   chunk 26 optimal weight:    0.0980
   chunk 17 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0970
   chunk 13 optimal weight:    0.1980
   chunk 25 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.2578

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4565 r_free = 0.4565 target = 0.204700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.184168 restraints weight = 15487.853|
|-----------------------------------------------------------------------------|
r_work (start): 0.4350 rms_B_bonded: 3.41
r_work: 0.4223 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6136
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3344  Z= 0.134
  Angle     :  0.563   9.542   4537  Z= 0.268
  Chirality :  0.037   0.123    525
  Planarity :  0.004   0.038    580
  Dihedral  :  4.278  16.418    469
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.61 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.61 (0.42), residues: 432
  helix:  1.22 (0.35), residues: 227
  sheet: -2.05 (0.61), residues: 66
  loop :  0.60 (0.57), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 305 
 HIS   0.004   0.001   HIS A 290 
 PHE   0.013   0.001   PHE A 204 
 TYR   0.013   0.001   TYR A 363 
 ARG   0.003   0.000   ARG A 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03390 (  162)
  hydrogen bonds       : angle       4.69565 (  477)
  metal coordination   : bond        0.01073 (    4)
  metal coordination   : angle       6.56615 (    6)
  SS BOND              : bond        0.00335 (    1)
  SS BOND              : angle       0.87616 (    2)
  covalent geometry    : bond        0.00283 ( 3339)
  covalent geometry    : angle       0.50976 ( 4529)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   68 is missing expected H atoms. Skipping.
Residue SER  259 is missing expected H atoms. Skipping.
Residue LYS  287 is missing expected H atoms. Skipping.
Residue LYS  309 is missing expected H atoms. Skipping.
Residue LYS  338 is missing expected H atoms. Skipping.
Residue LYS  389 is missing expected H atoms. Skipping.
Residue SER  391 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  397 is missing expected H atoms. Skipping.
Residue VAL  440 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 PHE cc_start: 0.7349 (m-80) cc_final: 0.7145 (m-80)
REVERT: A  139 GLN cc_start: 0.6652 (mm-40) cc_final: 0.6435 (mm-40)
REVERT: A  151 LEU cc_start: 0.7897 (tp) cc_final: 0.7653 (tt)
REVERT: A  180 ARG cc_start: 0.6584 (tpt90) cc_final: 0.5902 (tpt90)
REVERT: A  189 VAL cc_start: 0.8339 (t) cc_final: 0.7820 (m)
REVERT: A  204 PHE cc_start: 0.7883 (m-80) cc_final: 0.7679 (m-80)
REVERT: A  345 GLN cc_start: 0.7172 (mm110) cc_final: 0.6415 (mm110)
REVERT: A  346 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6748 (mt-10)
  outliers start: 4
  outliers final: 4
  residues processed: 74
  average time/residue: 0.2660
  time to fit residues: 25.1457
Evaluate side-chains
  76 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  285 ASN
Chi-restraints excluded: chain A residue  444 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   chunk 9 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0970
   chunk 8 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 36 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.201295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.180709 restraints weight = 15252.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.4322 rms_B_bonded: 3.36
r_work: 0.4205 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6182
moved from start:          0.3800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3344  Z= 0.203
  Angle     :  0.608   9.147   4537  Z= 0.299
  Chirality :  0.038   0.123    525
  Planarity :  0.005   0.038    580
  Dihedral  :  4.449  16.081    469
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.21 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.50 (0.43), residues: 432
  helix:  1.16 (0.35), residues: 225
  sheet: -2.12 (0.57), residues: 75
  loop :  0.74 (0.62), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 305 
 HIS   0.007   0.002   HIS A 208 
 PHE   0.015   0.002   PHE A 204 
 TYR   0.014   0.002   TYR A 363 
 ARG   0.004   0.000   ARG A 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03734 (  162)
  hydrogen bonds       : angle       4.87273 (  477)
  metal coordination   : bond        0.01579 (    4)
  metal coordination   : angle       6.87671 (    6)
  SS BOND              : bond        0.00466 (    1)
  SS BOND              : angle       1.04919 (    2)
  covalent geometry    : bond        0.00417 ( 3339)
  covalent geometry    : angle       0.55377 ( 4529)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   68 is missing expected H atoms. Skipping.
Residue SER  259 is missing expected H atoms. Skipping.
Residue LYS  287 is missing expected H atoms. Skipping.
Residue LYS  309 is missing expected H atoms. Skipping.
Residue LYS  338 is missing expected H atoms. Skipping.
Residue LYS  389 is missing expected H atoms. Skipping.
Residue SER  391 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  397 is missing expected H atoms. Skipping.
Residue VAL  440 is missing expected H atoms. Skipping.
Evaluate side-chains
  79 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 PHE cc_start: 0.7391 (m-80) cc_final: 0.7180 (m-80)
REVERT: A   72 ILE cc_start: 0.7987 (pt) cc_final: 0.7396 (mp)
REVERT: A  151 LEU cc_start: 0.8005 (tp) cc_final: 0.7777 (tt)
REVERT: A  164 GLN cc_start: 0.7917 (mt0) cc_final: 0.7707 (mt0)
REVERT: A  248 LYS cc_start: 0.7924 (tppt) cc_final: 0.7598 (mmmt)
REVERT: A  345 GLN cc_start: 0.7205 (mm110) cc_final: 0.6518 (mm110)
REVERT: A  346 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7083 (mt-10)
  outliers start: 5
  outliers final: 5
  residues processed: 77
  average time/residue: 0.2661
  time to fit residues: 26.4418
Evaluate side-chains
  79 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  285 ASN
Chi-restraints excluded: chain A residue  444 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0970
   chunk 24 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0770
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.3536

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

Flipped N/Q/H residues before XYZ refinement:
A 185 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.202187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.181601 restraints weight = 15202.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.4332 rms_B_bonded: 3.34
r_work: 0.4214 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.4214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6159
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3344  Z= 0.155
  Angle     :  0.566   8.096   4537  Z= 0.275
  Chirality :  0.037   0.126    525
  Planarity :  0.004   0.037    580
  Dihedral  :  4.349  16.292    469
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.71 %
    Favored  : 83.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.55 (0.43), residues: 432
  helix:  1.19 (0.35), residues: 227
  sheet: -2.05 (0.57), residues: 75
  loop :  0.75 (0.64), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 305 
 HIS   0.004   0.001   HIS A 290 
 PHE   0.017   0.002   PHE A 204 
 TYR   0.011   0.002   TYR A 363 
 ARG   0.003   0.000   ARG A 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03413 (  162)
  hydrogen bonds       : angle       4.68643 (  477)
  metal coordination   : bond        0.01214 (    4)
  metal coordination   : angle       6.04471 (    6)
  SS BOND              : bond        0.00370 (    1)
  SS BOND              : angle       0.99635 (    2)
  covalent geometry    : bond        0.00321 ( 3339)
  covalent geometry    : angle       0.52136 ( 4529)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   68 is missing expected H atoms. Skipping.
Residue SER  259 is missing expected H atoms. Skipping.
Residue LYS  287 is missing expected H atoms. Skipping.
Residue LYS  309 is missing expected H atoms. Skipping.
Residue LYS  338 is missing expected H atoms. Skipping.
Residue LYS  389 is missing expected H atoms. Skipping.
Residue SER  391 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  397 is missing expected H atoms. Skipping.
Residue VAL  440 is missing expected H atoms. Skipping.
Evaluate side-chains
  81 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 74
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 PHE cc_start: 0.7426 (m-80) cc_final: 0.7206 (m-80)
REVERT: A   72 ILE cc_start: 0.7949 (pt) cc_final: 0.7346 (mp)
REVERT: A  151 LEU cc_start: 0.7964 (tp) cc_final: 0.7726 (tt)
REVERT: A  248 LYS cc_start: 0.7909 (tppt) cc_final: 0.7665 (tppt)
REVERT: A  345 GLN cc_start: 0.7167 (mm110) cc_final: 0.6477 (mm110)
REVERT: A  346 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6722 (mt-10)
  outliers start: 7
  outliers final: 5
  residues processed: 79
  average time/residue: 0.2521
  time to fit residues: 25.3712
Evaluate side-chains
  78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  163 SER
Chi-restraints excluded: chain A residue  185 HIS
Chi-restraints excluded: chain A residue  202 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0670
   chunk 16 optimal weight:    0.0980
   chunk 41 optimal weight:    0.6980
   chunk 2 optimal weight:    0.3980
   chunk 7 optimal weight:    0.4980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.3318

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.202565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.181884 restraints weight = 15257.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.4337 rms_B_bonded: 3.38
r_work: 0.4216 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.4216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6162
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3344  Z= 0.152
  Angle     :  0.569   7.843   4537  Z= 0.278
  Chirality :  0.037   0.128    525
  Planarity :  0.004   0.038    580
  Dihedral  :  4.312  15.753    469
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 15.92 %
    Favored  : 82.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.56 (0.43), residues: 432
  helix:  1.20 (0.35), residues: 227
  sheet: -2.00 (0.57), residues: 75
  loop :  0.71 (0.63), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 305 
 HIS   0.003   0.001   HIS A 185 
 PHE   0.019   0.001   PHE A 204 
 TYR   0.020   0.002   TYR A 363 
 ARG   0.003   0.000   ARG A 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03386 (  162)
  hydrogen bonds       : angle       4.67883 (  477)
  metal coordination   : bond        0.01198 (    4)
  metal coordination   : angle       5.96176 (    6)
  SS BOND              : bond        0.00392 (    1)
  SS BOND              : angle       1.03526 (    2)
  covalent geometry    : bond        0.00318 ( 3339)
  covalent geometry    : angle       0.52656 ( 4529)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   68 is missing expected H atoms. Skipping.
Residue SER  259 is missing expected H atoms. Skipping.
Residue LYS  287 is missing expected H atoms. Skipping.
Residue LYS  309 is missing expected H atoms. Skipping.
Residue LYS  338 is missing expected H atoms. Skipping.
Residue LYS  389 is missing expected H atoms. Skipping.
Residue SER  391 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  397 is missing expected H atoms. Skipping.
Residue VAL  440 is missing expected H atoms. Skipping.
Evaluate side-chains
  76 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 72
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 PHE cc_start: 0.7434 (m-80) cc_final: 0.7215 (m-80)
REVERT: A   72 ILE cc_start: 0.7928 (pt) cc_final: 0.7375 (mp)
REVERT: A  204 PHE cc_start: 0.7905 (m-80) cc_final: 0.7577 (m-80)
REVERT: A  248 LYS cc_start: 0.7893 (tppt) cc_final: 0.7650 (tppt)
REVERT: A  345 GLN cc_start: 0.7174 (mm110) cc_final: 0.6487 (mm110)
REVERT: A  346 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6720 (mt-10)
  outliers start: 4
  outliers final: 4
  residues processed: 76
  average time/residue: 0.2604
  time to fit residues: 25.2348
Evaluate side-chains
  75 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  405 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 15 optimal weight:    0.0070
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 41 optimal weight:    0.1980
   chunk 12 optimal weight:    0.0030
   chunk 0 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0980
   chunk 11 optimal weight:    0.4980
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.1608

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.204381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.183577 restraints weight = 15282.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.4357 rms_B_bonded: 3.41
r_work: 0.4238 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.4238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6113
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3344  Z= 0.109
  Angle     :  0.549   7.261   4537  Z= 0.258
  Chirality :  0.037   0.127    525
  Planarity :  0.004   0.038    580
  Dihedral  :  4.122  17.300    469
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 16.52 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.84 (0.43), residues: 432
  helix:  1.35 (0.35), residues: 227
  sheet: -1.84 (0.62), residues: 66
  loop :  0.76 (0.62), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 305 
 HIS   0.007   0.001   HIS A 185 
 PHE   0.017   0.001   PHE A 204 
 TYR   0.011   0.001   TYR A 363 
 ARG   0.003   0.000   ARG A 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03027 (  162)
  hydrogen bonds       : angle       4.47469 (  477)
  metal coordination   : bond        0.01084 (    4)
  metal coordination   : angle       5.66525 (    6)
  SS BOND              : bond        0.00291 (    1)
  SS BOND              : angle       1.01730 (    2)
  covalent geometry    : bond        0.00238 ( 3339)
  covalent geometry    : angle       0.50888 ( 4529)

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

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

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  864 Ramachandran restraints generated.
    432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS   22 is missing expected H atoms. Skipping.
Residue LEU   68 is missing expected H atoms. Skipping.
Residue SER  259 is missing expected H atoms. Skipping.
Residue LYS  287 is missing expected H atoms. Skipping.
Residue LYS  309 is missing expected H atoms. Skipping.
Residue LYS  338 is missing expected H atoms. Skipping.
Residue LYS  389 is missing expected H atoms. Skipping.
Residue SER  391 is missing expected H atoms. Skipping.
Residue LYS  393 is missing expected H atoms. Skipping.
Residue MET  397 is missing expected H atoms. Skipping.
Residue VAL  440 is missing expected H atoms. Skipping.
Evaluate side-chains
  75 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 PHE cc_start: 0.7397 (m-80) cc_final: 0.7181 (m-80)
REVERT: A  180 ARG cc_start: 0.6533 (tpt90) cc_final: 0.5806 (tpt90)
REVERT: A  204 PHE cc_start: 0.7927 (m-80) cc_final: 0.7605 (m-80)
REVERT: A  248 LYS cc_start: 0.7847 (tppt) cc_final: 0.7606 (tppt)
REVERT: A  346 GLU cc_start: 0.7424 (mt-10) cc_final: 0.6783 (mt-10)
  outliers start: 4
  outliers final: 4
  residues processed: 75
  average time/residue: 0.2540
  time to fit residues: 24.2056
Evaluate side-chains
  75 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   77 SER
Chi-restraints excluded: chain A residue  202 ASP
Chi-restraints excluded: chain A residue  405 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 21 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0980
   chunk 40 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A  89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.200914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.179922 restraints weight = 15418.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.4313 rms_B_bonded: 3.44
r_work: 0.4189 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6214
moved from start:          0.4370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3344  Z= 0.210
  Angle     :  0.613   8.079   4537  Z= 0.307
  Chirality :  0.038   0.132    525
  Planarity :  0.004   0.038    580
  Dihedral  :  4.436  16.069    469
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.12 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.69 (0.43), residues: 432
  helix:  1.16 (0.35), residues: 225
  sheet: -1.88 (0.57), residues: 76
  loop :  1.08 (0.65), residues: 131

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 305 
 HIS   0.005   0.002   HIS A 208 
 PHE   0.019   0.002   PHE A 204 
 TYR   0.013   0.002   TYR A 363 
 ARG   0.004   0.001   ARG A 329 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03689 (  162)
  hydrogen bonds       : angle       4.78062 (  477)
  metal coordination   : bond        0.01321 (    4)
  metal coordination   : angle       6.10544 (    6)
  SS BOND              : bond        0.00467 (    1)
  SS BOND              : angle       1.12195 (    2)
  covalent geometry    : bond        0.00430 ( 3339)
  covalent geometry    : angle       0.57154 ( 4529)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4882.44 seconds
wall clock time: 84 minutes 28.88 seconds (5068.88 seconds total)