Starting phenix.real_space_refine
on Thu Jun  5 02:22:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bzo_16344/06_2025/8bzo_16344.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bzo_16344/06_2025/8bzo_16344.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bzo_16344/06_2025/8bzo_16344.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bzo_16344/06_2025/8bzo_16344.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bzo_16344/06_2025/8bzo_16344.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bzo_16344/06_2025/8bzo_16344.cif"
  }
  resolution = 3.5
  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=  -0.001 sd=   0.029
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
     P       1      5.49       5
     S      17      5.16       5
     C    3134      2.51       5
     N     821      2.21       5
     O     861      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4834
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 284, 2212
          Classifications: {'peptide': 284}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 19, 'TRANS': 264}
          Unresolved non-hydrogen bonds: 79
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 4, 'TPO:plan-1': 1, 'ARG:plan': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "B"
      Number of atoms: 2029
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 2029
          Classifications: {'peptide': 258}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 243}
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 34
    Chain: "C"
      Number of atoms: 593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 593
          Classifications: {'peptide': 72}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 7, 'TRANS': 64}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 23
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 3.73, per 1000 atoms: 0.77
  Number of scatterers: 4834
  At special positions: 0
  Unit cell: (81.32, 93.09, 80.25, 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)
     S      17     16.00
     P       1     15.00
     O     861      8.00
     N     821      7.00
     C    3134      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: 1.25
  Conformation dependent library (CDL) restraints added in 601.4 milliseconds
  

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1176

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 3 sheets defined
      48.9% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.913A  pdb=" N   GLU A  51 " --> pdb=" O   THR A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 94
    Processing helix  chain 'A' and resid 100 through 121
      removed outlier: 3.701A  pdb=" N   LEU A 111 " --> pdb=" O   TYR A 107 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   GLN A 113 " --> pdb=" O   PHE A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 169
    Processing helix  chain 'A' and resid 170 through 176
      removed outlier: 3.710A  pdb=" N   LEU A 175 " --> pdb=" O   PRO A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 199
      removed outlier: 3.917A  pdb=" N   ILE A 186 " --> pdb=" O   THR A 182 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL A 197 " --> pdb=" O   PHE A 193 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   THR A 198 " --> pdb=" O   ALA A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 220
      removed outlier: 3.716A  pdb=" N   ARG A 217 " --> pdb=" O   PHE A 213 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   THR A 218 " --> pdb=" O   ARG A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 252
      removed outlier: 3.629A  pdb=" N   VAL A 251 " --> pdb=" O   ASP A 247 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 247 through 252'
    Processing helix  chain 'A' and resid 258 through 267
      removed outlier: 4.154A  pdb=" N   LEU A 262 " --> pdb=" O   ASP A 258 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LEU A 263 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER A 264 " --> pdb=" O   ARG A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 281
      removed outlier: 3.586A  pdb=" N   LEU A 281 " --> pdb=" O   ALA A 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 190
    Processing helix  chain 'B' and resid 207 through 224
      removed outlier: 3.730A  pdb=" N   ILE B 213 " --> pdb=" O   SER B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 228 through 243
      removed outlier: 4.159A  pdb=" N   LEU B 232 " --> pdb=" O   GLN B 228 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   HIS B 233 " --> pdb=" O   ASN B 229 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ASN B 237 " --> pdb=" O   HIS B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 269
      removed outlier: 4.033A  pdb=" N   PHE B 267 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 282
    Processing helix  chain 'B' and resid 287 through 292
      removed outlier: 3.655A  pdb=" N   LEU B 292 " --> pdb=" O   LYS B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 302
      removed outlier: 4.178A  pdb=" N   LYS B 300 " --> pdb=" O   HIS B 296 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 320
      removed outlier: 3.900A  pdb=" N   LEU B 315 " --> pdb=" O   VAL B 311 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   GLN B 317 " --> pdb=" O   GLN B 313 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   LEU B 320 " --> pdb=" O   THR B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 343
      removed outlier: 3.674A  pdb=" N   SER B 340 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   LEU B 341 " --> pdb=" O   GLY B 337 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ILE B 342 " --> pdb=" O   GLU B 338 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   ASP B 343 " --> pdb=" O   LEU B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 351 through 368
      removed outlier: 3.599A  pdb=" N   GLY B 357 " --> pdb=" O   SER B 353 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   TYR B 365 " --> pdb=" O   HIS B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 378
      removed outlier: 3.944A  pdb=" N   ARG B 378 " --> pdb=" O   SER B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 401
      removed outlier: 3.808A  pdb=" N   GLN B 396 " --> pdb=" O   MET B 392 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   THR B 397 " --> pdb=" O   ASP B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 404
      No H-bonds generated for 'chain 'B' and resid 402 through 404'
    Processing helix  chain 'B' and resid 408 through 415
      removed outlier: 3.997A  pdb=" N   ASN B 415 " --> pdb=" O   GLU B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 419
    Processing helix  chain 'B' and resid 420 through 424
      removed outlier: 3.672A  pdb=" N   LEU B 423 " --> pdb=" O   GLY B 420 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 37 through 52
      removed outlier: 3.540A  pdb=" N   HIS C  48 " --> pdb=" O   ASP C  44 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   MET C  52 " --> pdb=" O   HIS C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 90
      removed outlier: 3.506A  pdb=" N   TYR C  88 " --> pdb=" O   PRO C  85 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ARG C  90 " --> pdb=" O   PHE C  87 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 22
      removed outlier: 4.549A  pdb=" N   VAL A  18 " --> pdb=" O   VAL C  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 36
      removed outlier: 7.022A  pdb=" N   GLU A  81 " --> pdb=" O   LEU A  66 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   LEU A  66 " --> pdb=" O   GLU A  81 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 86

    173 hydrogen bonds defined for protein.
    495 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 1.49 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: 982
        1.33 -     1.45: 1144
        1.45 -     1.57: 2811
        1.57 -     1.69: 1
        1.69 -     1.82: 27
  Bond restraints: 4965
  Sorted by residual:
  bond pdb=" OG1 TPO A 160 "
       pdb=" P   TPO A 160 "
    ideal  model  delta    sigma   weight residual
    1.717  1.627  0.090 2.00e-02 2.50e+03 2.01e+01
  bond pdb=" N   VAL B 311 "
       pdb=" CA  VAL B 311 "
    ideal  model  delta    sigma   weight residual
    1.462  1.513 -0.051 1.17e-02 7.31e+03 1.89e+01
  bond pdb=" N   ARG A 122 "
       pdb=" CA  ARG A 122 "
    ideal  model  delta    sigma   weight residual
    1.459  1.502 -0.043 1.15e-02 7.56e+03 1.39e+01
  bond pdb=" CA  SER B 386 "
       pdb=" CB  SER B 386 "
    ideal  model  delta    sigma   weight residual
    1.531  1.470  0.060 1.69e-02 3.50e+03 1.28e+01
  bond pdb=" CB  TPO A 160 "
       pdb=" OG1 TPO A 160 "
    ideal  model  delta    sigma   weight residual
    1.406  1.472 -0.066 2.00e-02 2.50e+03 1.08e+01
  ... (remaining 4960 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 6493
        1.72 -     3.44: 224
        3.44 -     5.15: 35
        5.15 -     6.87: 10
        6.87 -     8.59: 3
  Bond angle restraints: 6765
  Sorted by residual:
  angle pdb=" N   HIS C  23 "
        pdb=" CA  HIS C  23 "
        pdb=" C   HIS C  23 "
      ideal   model   delta    sigma   weight residual
     109.64  101.51    8.13 1.27e+00 6.20e-01 4.09e+01
  angle pdb=" N   ILE B 377 "
        pdb=" CA  ILE B 377 "
        pdb=" C   ILE B 377 "
      ideal   model   delta    sigma   weight residual
     112.90  107.27    5.63 9.60e-01 1.09e+00 3.44e+01
  angle pdb=" N   LEU B 384 "
        pdb=" CA  LEU B 384 "
        pdb=" C   LEU B 384 "
      ideal   model   delta    sigma   weight residual
     113.18  107.93    5.25 1.21e+00 6.83e-01 1.88e+01
  angle pdb=" C   GLU A 195 "
        pdb=" CA  GLU A 195 "
        pdb=" CB  GLU A 195 "
      ideal   model   delta    sigma   weight residual
     109.67  101.08    8.59 2.01e+00 2.48e-01 1.83e+01
  angle pdb=" C   LEU A  78 "
        pdb=" N   VAL A  79 "
        pdb=" CA  VAL A  79 "
      ideal   model   delta    sigma   weight residual
     122.43  127.45   -5.02 1.26e+00 6.30e-01 1.59e+01
  ... (remaining 6760 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.13: 2520
       16.13 -    32.26: 319
       32.26 -    48.38: 111
       48.38 -    64.51: 15
       64.51 -    80.64: 7
  Dihedral angle restraints: 2972
    sinusoidal: 1156
      harmonic: 1816
  Sorted by residual:
  dihedral pdb=" C   GLU A 195 "
           pdb=" N   GLU A 195 "
           pdb=" CA  GLU A 195 "
           pdb=" CB  GLU A 195 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.61  -10.99     0      2.50e+00 1.60e-01 1.93e+01
  dihedral pdb=" CA  HIS C  23 "
           pdb=" C   HIS C  23 "
           pdb=" N   PRO C  24 "
           pdb=" CA  PRO C  24 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.68  -21.32     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  LEU A  83 "
           pdb=" C   LEU A  83 "
           pdb=" N   HIS A  84 "
           pdb=" CA  HIS A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.19  -17.81     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 2969 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 559
       0.046 -    0.093: 165
       0.093 -    0.139: 30
       0.139 -    0.185: 4
       0.185 -    0.231: 3
  Chirality restraints: 761
  Sorted by residual:
  chirality pdb=" CA  GLU A 195 "
            pdb=" N   GLU A 195 "
            pdb=" C   GLU A 195 "
            pdb=" CB  GLU A 195 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  LYS C  47 "
            pdb=" N   LYS C  47 "
            pdb=" C   LYS C  47 "
            pdb=" CB  LYS C  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  ARG B 378 "
            pdb=" N   ARG B 378 "
            pdb=" C   ARG B 378 "
            pdb=" CB  ARG B 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.08e+00
  ... (remaining 758 not shown)

  Planarity restraints: 860
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 199 "    0.014 2.00e-02 2.50e+03   2.84e-02 8.09e+00
        pdb=" C   TYR B 199 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   TYR B 199 "    0.018 2.00e-02 2.50e+03
        pdb=" N   MET B 200 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 353 "   -0.012 2.00e-02 2.50e+03   2.46e-02 6.05e+00
        pdb=" C   SER B 353 "    0.043 2.00e-02 2.50e+03
        pdb=" O   SER B 353 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL B 354 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A  60 "   -0.032 5.00e-02 4.00e+02   4.77e-02 3.64e+00
        pdb=" N   PRO A  61 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A  61 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A  61 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 857 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 942
        2.77 -     3.30: 4554
        3.30 -     3.83: 7541
        3.83 -     4.37: 8874
        4.37 -     4.90: 15177
  Nonbonded interactions: 37088
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  68 "
            pdb=" NE1 TRP C  60 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" OG1 THR A 137 "
            pdb=" OE2 GLU A 138 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   GLU A  42 "
            pdb=" NZ  LYS B 266 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OG  SER B 331 "
            pdb=" O   TYR B 418 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" NZ  LYS A 278 "
            pdb=" O   ASP B 177 "
     model   vdw
     2.267 3.120
  ... (remaining 37083 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.930
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.400
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7341
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      :  0.005   0.090   4965  Z= 0.294
  Angle     :  0.733   8.588   6765  Z= 0.428
  Chirality :  0.046   0.231    761
  Planarity :  0.005   0.048    860
  Dihedral  : 16.406  80.641   1796
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.62 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 24.21 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -1.51 (0.34), residues: 605
  helix: -0.73 (0.33), residues: 270
  sheet: -0.06 (1.14), residues: 25
  loop : -1.27 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 167 
 HIS   0.010   0.001   HIS B 361 
 PHE   0.012   0.002   PHE A  80 
 TYR   0.015   0.001   TYR B 199 
 ARG   0.007   0.001   ARG A 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21881 (  173)
  hydrogen bonds       : angle       7.02491 (  495)
  covalent geometry    : bond        0.00531 ( 4965)
  covalent geometry    : angle       0.73347 ( 6765)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.622 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 97
  average time/residue: 0.2423
  time to fit residues: 29.0675
Evaluate side-chains
  87 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  395 HIS
Chi-restraints excluded: chain C residue   66 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0270
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
B 179 HIS
B 296 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.190025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.166733 restraints weight = 6328.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.170692 restraints weight = 4189.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.173439 restraints weight = 3125.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.1046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4965  Z= 0.138
  Angle     :  0.598   7.281   6765  Z= 0.307
  Chirality :  0.041   0.134    761
  Planarity :  0.005   0.048    860
  Dihedral  :  5.071  43.019    672
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.46 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 23.02 %
    Favored  : 74.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.95 (0.35), residues: 605
  helix: -0.15 (0.33), residues: 277
  sheet:  1.14 (1.41), residues: 15
  loop : -1.12 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 372 
 HIS   0.006   0.001   HIS B 361 
 PHE   0.010   0.001   PHE A  80 
 TYR   0.010   0.001   TYR C  88 
 ARG   0.006   0.001   ARG C  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04407 (  173)
  hydrogen bonds       : angle       4.87245 (  495)
  covalent geometry    : bond        0.00322 ( 4965)
  covalent geometry    : angle       0.59765 ( 6765)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
  outliers start: 13
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2113
  time to fit residues: 28.8969
Evaluate side-chains
  95 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  395 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0050
   chunk 35 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.9196

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

Flipped N/Q/H residues before XYZ refinement:
A  71 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.185285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.161784 restraints weight = 6340.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.165622 restraints weight = 4240.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.168277 restraints weight = 3198.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4965  Z= 0.170
  Angle     :  0.614   7.448   6765  Z= 0.311
  Chirality :  0.042   0.131    761
  Planarity :  0.005   0.046    860
  Dihedral  :  4.966  39.298    670
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.63 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 23.41 %
    Favored  : 72.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.95 (0.35), residues: 605
  helix: -0.07 (0.33), residues: 277
  sheet: -0.18 (1.13), residues: 25
  loop : -1.16 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 372 
 HIS   0.005   0.001   HIS B 296 
 PHE   0.014   0.002   PHE A  80 
 TYR   0.016   0.001   TYR B 199 
 ARG   0.005   0.001   ARG C  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04202 (  173)
  hydrogen bonds       : angle       4.59975 (  495)
  covalent geometry    : bond        0.00412 ( 4965)
  covalent geometry    : angle       0.61400 ( 6765)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
REVERT: A  195 GLU cc_start: 0.8424 (tm-30) cc_final: 0.8203 (tm-30)
  outliers start: 20
  outliers final: 12
  residues processed: 107
  average time/residue: 0.2556
  time to fit residues: 34.9771
Evaluate side-chains
  103 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  243 TRP
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  377 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0570
   chunk 14 optimal weight:    0.0970
   chunk 15 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
A  71 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.181097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.154214 restraints weight = 6544.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.158480 restraints weight = 4299.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.161488 restraints weight = 3199.340|
|-----------------------------------------------------------------------------|
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4965  Z= 0.112
  Angle     :  0.555   6.827   6765  Z= 0.282
  Chirality :  0.040   0.135    761
  Planarity :  0.005   0.045    860
  Dihedral  :  4.435  30.523    668
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.30 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 24.21 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.63 (0.36), residues: 605
  helix:  0.13 (0.34), residues: 279
  sheet:  1.06 (1.43), residues: 15
  loop : -0.96 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 372 
 HIS   0.005   0.001   HIS B 296 
 PHE   0.008   0.001   PHE A  80 
 TYR   0.012   0.001   TYR B 199 
 ARG   0.006   0.000   ARG C  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03163 (  173)
  hydrogen bonds       : angle       4.27148 (  495)
  covalent geometry    : bond        0.00265 ( 4965)
  covalent geometry    : angle       0.55545 ( 6765)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A   71 HIS cc_start: 0.7700 (t70) cc_final: 0.7022 (t70)
REVERT: A  195 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8182 (tm-30)
REVERT: A  265 GLN cc_start: 0.7960 (mp10) cc_final: 0.6828 (mp10)
  outliers start: 17
  outliers final: 8
  residues processed: 112
  average time/residue: 0.1785
  time to fit residues: 27.3471
Evaluate side-chains
  100 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  391 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** B 296 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 = 0.4003 r_free = 0.4003 target = 0.179288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.153242 restraints weight = 6669.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.157291 restraints weight = 4336.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.160243 restraints weight = 3244.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4965  Z= 0.159
  Angle     :  0.594   8.819   6765  Z= 0.299
  Chirality :  0.042   0.149    761
  Planarity :  0.005   0.044    860
  Dihedral  :  4.528  26.961    668
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.46 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.21 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.71 (0.35), residues: 605
  helix:  0.09 (0.33), residues: 279
  sheet:  0.91 (1.40), residues: 15
  loop : -1.02 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 372 
 HIS   0.012   0.001   HIS B 296 
 PHE   0.012   0.001   PHE C  62 
 TYR   0.013   0.001   TYR B 199 
 ARG   0.006   0.000   ARG C  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03677 (  173)
  hydrogen bonds       : angle       4.35368 (  495)
  covalent geometry    : bond        0.00383 ( 4965)
  covalent geometry    : angle       0.59380 ( 6765)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 21
  outliers final: 14
  residues processed: 111
  average time/residue: 0.1513
  time to fit residues: 22.0622
Evaluate side-chains
  105 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  158 THR
Chi-restraints excluded: chain A residue  243 TRP
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  386 SER
Chi-restraints excluded: chain C residue   70 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0370
   chunk 10 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 21 optimal weight:    0.2980
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
** B 296 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 = 0.4048 r_free = 0.4048 target = 0.183424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.157566 restraints weight = 6688.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.161861 restraints weight = 4325.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.164900 restraints weight = 3186.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4965  Z= 0.132
  Angle     :  0.579   8.219   6765  Z= 0.291
  Chirality :  0.041   0.150    761
  Planarity :  0.005   0.047    860
  Dihedral  :  4.405  25.129    668
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 23.81 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.59 (0.36), residues: 605
  helix:  0.20 (0.34), residues: 279
  sheet:  0.96 (1.39), residues: 15
  loop : -0.98 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 372 
 HIS   0.010   0.001   HIS B 296 
 PHE   0.009   0.001   PHE A  80 
 TYR   0.011   0.001   TYR B 199 
 ARG   0.007   0.000   ARG C  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03276 (  173)
  hydrogen bonds       : angle       4.23370 (  495)
  covalent geometry    : bond        0.00314 ( 4965)
  covalent geometry    : angle       0.57894 ( 6765)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
REVERT: C   77 GLN cc_start: 0.7401 (mt0) cc_final: 0.7175 (mt0)
  outliers start: 25
  outliers final: 18
  residues processed: 113
  average time/residue: 0.1400
  time to fit residues: 21.1214
Evaluate side-chains
  107 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  243 TRP
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  392 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 296 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 = 0.4092 r_free = 0.4092 target = 0.187211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.164360 restraints weight = 6250.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.168076 restraints weight = 4138.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.170699 restraints weight = 3100.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4965  Z= 0.169
  Angle     :  0.601   7.900   6765  Z= 0.302
  Chirality :  0.042   0.145    761
  Planarity :  0.005   0.046    860
  Dihedral  :  4.557  22.782    668
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 24.60 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 (0.35), residues: 605
  helix:  0.10 (0.33), residues: 280
  sheet:  0.71 (1.35), residues: 15
  loop : -0.99 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 167 
 HIS   0.009   0.001   HIS B 296 
 PHE   0.013   0.002   PHE C  62 
 TYR   0.016   0.001   TYR B 199 
 ARG   0.006   0.000   ARG C  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03745 (  173)
  hydrogen bonds       : angle       4.38842 (  495)
  covalent geometry    : bond        0.00407 ( 4965)
  covalent geometry    : angle       0.60118 ( 6765)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   77 GLN cc_start: 0.7317 (mt0) cc_final: 0.7105 (mt0)
  outliers start: 23
  outliers final: 19
  residues processed: 111
  average time/residue: 0.1652
  time to fit residues: 24.0802
Evaluate side-chains
  107 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  243 TRP
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain C residue   70 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0170
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 ASN
** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.188643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.165561 restraints weight = 6403.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.169462 restraints weight = 4194.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.171917 restraints weight = 3119.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.1867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4965  Z= 0.138
  Angle     :  0.580   7.429   6765  Z= 0.293
  Chirality :  0.042   0.142    761
  Planarity :  0.005   0.047    860
  Dihedral  :  4.470  22.305    668
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 24.21 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 (0.36), residues: 605
  helix:  0.20 (0.33), residues: 280
  sheet:  0.93 (1.39), residues: 15
  loop : -0.94 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 167 
 HIS   0.008   0.001   HIS B 296 
 PHE   0.010   0.001   PHE C  62 
 TYR   0.013   0.001   TYR B 199 
 ARG   0.007   0.000   ARG C  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03351 (  173)
  hydrogen bonds       : angle       4.26559 (  495)
  covalent geometry    : bond        0.00333 ( 4965)
  covalent geometry    : angle       0.58008 ( 6765)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
REVERT: C   77 GLN cc_start: 0.7331 (mt0) cc_final: 0.7124 (mt0)
  outliers start: 25
  outliers final: 22
  residues processed: 106
  average time/residue: 0.1505
  time to fit residues: 20.9144
Evaluate side-chains
  107 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  243 TRP
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain C residue   70 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 14 optimal weight:    0.0060
   chunk 19 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 42 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 ASN
** B 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.189069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.166075 restraints weight = 6279.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.169995 restraints weight = 4138.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.172662 restraints weight = 3067.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4965  Z= 0.133
  Angle     :  0.568   7.154   6765  Z= 0.288
  Chirality :  0.041   0.139    761
  Planarity :  0.005   0.045    860
  Dihedral  :  4.379  22.229    668
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 24.40 %
    Favored  : 71.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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 (0.36), residues: 605
  helix:  0.25 (0.33), residues: 280
  sheet:  0.97 (1.40), residues: 15
  loop : -0.90 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 167 
 HIS   0.008   0.001   HIS B 296 
 PHE   0.010   0.001   PHE C  62 
 TYR   0.014   0.001   TYR B 199 
 ARG   0.007   0.001   ARG C  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03235 (  173)
  hydrogen bonds       : angle       4.22451 (  495)
  covalent geometry    : bond        0.00320 ( 4965)
  covalent geometry    : angle       0.56802 ( 6765)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.608 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  265 GLN cc_start: 0.8144 (mp10) cc_final: 0.7905 (mp10)
REVERT: C   77 GLN cc_start: 0.7466 (mt0) cc_final: 0.7261 (mt0)
  outliers start: 23
  outliers final: 21
  residues processed: 106
  average time/residue: 0.1454
  time to fit residues: 20.5346
Evaluate side-chains
  105 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 84
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  243 TRP
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  316 THR
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain C residue   70 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 2 optimal weight:    0.4980
   chunk 20 optimal weight:    0.3980
   chunk 28 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 21 optimal weight:    0.1980
   chunk 54 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.190695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.167600 restraints weight = 6354.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.171532 restraints weight = 4163.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.174083 restraints weight = 3099.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.2043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4965  Z= 0.116
  Angle     :  0.552   7.138   6765  Z= 0.280
  Chirality :  0.041   0.138    761
  Planarity :  0.005   0.046    860
  Dihedral  :  4.230  21.659    668
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 25.20 %
    Favored  : 70.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.37 (0.36), residues: 605
  helix:  0.37 (0.34), residues: 280
  sheet:  1.12 (1.44), residues: 15
  loop : -0.85 (0.37), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 372 
 HIS   0.008   0.001   HIS C  48 
 PHE   0.009   0.001   PHE A 152 
 TYR   0.010   0.001   TYR B 238 
 ARG   0.007   0.000   ARG C  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02964 (  173)
  hydrogen bonds       : angle       4.11690 (  495)
  covalent geometry    : bond        0.00276 ( 4965)
  covalent geometry    : angle       0.55196 ( 6765)

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

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

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1210 Ramachandran restraints generated.
    605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.606 
Fit side-chains
   revert: symmetry clash
REVERT: A  243 TRP cc_start: 0.7209 (OUTLIER) cc_final: 0.6348 (m-90)
  outliers start: 20
  outliers final: 19
  residues processed: 100
  average time/residue: 0.1507
  time to fit residues: 20.2506
Evaluate side-chains
  104 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   55 LEU
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue   76 LEU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  137 THR
Chi-restraints excluded: chain A residue  243 TRP
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  290 THR
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  207 THR
Chi-restraints excluded: chain B residue  248 VAL
Chi-restraints excluded: chain B residue  291 VAL
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  392 MET
Chi-restraints excluded: chain C residue   70 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 43 optimal weight:    0.2980
   chunk 21 optimal weight:    0.0570
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0370
   chunk 29 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.3176

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

Flipped N/Q/H residues before XYZ refinement:
A  71 HIS
B 229 ASN
B 296 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.192486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.169529 restraints weight = 6321.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.173571 restraints weight = 4128.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.176413 restraints weight = 3023.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.2123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4965  Z= 0.106
  Angle     :  0.545   6.935   6765  Z= 0.277
  Chirality :  0.041   0.136    761
  Planarity :  0.005   0.045    860
  Dihedral  :  4.122  20.966    668
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 25.79 %
    Favored  : 70.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.27 (0.36), residues: 605
  helix:  0.50 (0.34), residues: 279
  sheet: -0.34 (1.23), residues: 21
  loop : -0.75 (0.38), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 217 
 HIS   0.007   0.001   HIS C  48 
 PHE   0.008   0.001   PHE A 152 
 TYR   0.011   0.001   TYR B 238 
 ARG   0.007   0.000   ARG C  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02786 (  173)
  hydrogen bonds       : angle       4.00895 (  495)
  covalent geometry    : bond        0.00250 ( 4965)
  covalent geometry    : angle       0.54520 ( 6765)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2249.63 seconds
wall clock time: 41 minutes 52.70 seconds (2512.70 seconds total)