Starting phenix.real_space_refine
on Thu Feb 13 02:51:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zla_14778/02_2025/7zla_14778.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zla_14778/02_2025/7zla_14778.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.99
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zla_14778/02_2025/7zla_14778.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zla_14778/02_2025/7zla_14778.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zla_14778/02_2025/7zla_14778.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zla_14778/02_2025/7zla_14778.cif"
  }
  resolution = 3.99
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      94      5.49       5
     S      18      5.16       5
     C    5227      2.51       5
     N    1497      2.21       5
     O    1788      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8624
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2995
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2995
          Classifications: {'peptide': 364}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 347}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 3743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 458, 3743
          Classifications: {'peptide': 458}
          Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 435}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 935
          Classifications: {'DNA': 46}
          Link IDs: {'rna3p': 45}
    Chain: "D"
      Number of atoms: 951
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 951
          Classifications: {'DNA': 46}
          Link IDs: {'rna3p': 45}
  Time building chain proxies: 5.31, per 1000 atoms: 0.62
  Number of scatterers: 8624
  At special positions: 0
  Unit cell: (83.566, 112.014, 131.572, 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      18     16.00
     P      94     15.00
     O    1788      8.00
     N    1497      7.00
     C    5227      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: 7.99
  Conformation dependent library (CDL) restraints added in 807.9 milliseconds
  

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1556

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 5 sheets defined
      43.6% alpha, 8.9% beta
      32 base pairs and 70 stacking pairs defined.
    Time for finding SS restraints: 3.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.734A  pdb=" N   TRP A 124 " --> pdb=" O   PRO A 120 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   TYR A 127 " --> pdb=" O   GLN A 123 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   MET A 132 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 141
      removed outlier: 3.574A  pdb=" N   LEU A 140 " --> pdb=" O   HIS A 137 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU A 141 " --> pdb=" O   ARG A 138 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 137 through 141'
    Processing helix  chain 'A' and resid 148 through 164
      removed outlier: 3.818A  pdb=" N   ILE A 155 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY A 164 " --> pdb=" O   HIS A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 172
    Processing helix  chain 'A' and resid 178 through 190
      removed outlier: 4.408A  pdb=" N   GLN A 184 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   LEU A 185 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 234
      removed outlier: 3.696A  pdb=" N   VAL A 232 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 268
      removed outlier: 3.900A  pdb=" N   ARG A 258 " --> pdb=" O   SER A 254 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   HIS A 268 " --> pdb=" O   TRP A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 296
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 3.999A  pdb=" N   VAL A 315 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ARG A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 312 through 316'
    Processing helix  chain 'A' and resid 323 through 334
      removed outlier: 3.895A  pdb=" N   HIS A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 329 " --> pdb=" O   PRO A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 353
      removed outlier: 3.871A  pdb=" N   GLN A 347 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   VAL A 348 " --> pdb=" O   ILE A 344 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   LEU A 349 " --> pdb=" O   ASP A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 382
      removed outlier: 4.008A  pdb=" N   ARG A 364 " --> pdb=" O   LYS A 360 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LYS A 367 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   LYS A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ARG A 382 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 418
      removed outlier: 3.880A  pdb=" N   ALA A 418 " --> pdb=" O   LYS A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 449
      No H-bonds generated for 'chain 'A' and resid 447 through 449'
    Processing helix  chain 'A' and resid 450 through 463
      removed outlier: 3.820A  pdb=" N   ALA A 456 " --> pdb=" O   GLU A 452 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   TRP A 462 " --> pdb=" O   VAL A 458 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY A 463 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 30
      removed outlier: 4.026A  pdb=" N   ALA B  22 " --> pdb=" O   GLU B  18 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LYS B  25 " --> pdb=" O   TYR B  21 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   THR B  26 " --> pdb=" O   ALA B  22 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B  27 " --> pdb=" O   HIS B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 50
    Processing helix  chain 'B' and resid 52 through 62
      removed outlier: 3.677A  pdb=" N   VAL B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   ALA B  58 " --> pdb=" O   ASN B  54 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLN B  62 " --> pdb=" O   ALA B  58 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 130
      removed outlier: 3.760A  pdb=" N   GLN B 130 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 163
      removed outlier: 3.642A  pdb=" N   HIS B 161 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 172
    Processing helix  chain 'B' and resid 178 through 190
      removed outlier: 4.080A  pdb=" N   GLN B 184 " --> pdb=" O   THR B 180 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   LEU B 185 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 209
      removed outlier: 3.680A  pdb=" N   LEU B 209 " --> pdb=" O   MET B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 233
    Processing helix  chain 'B' and resid 254 through 268
      removed outlier: 4.139A  pdb=" N   HIS B 268 " --> pdb=" O   TRP B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 295
    Processing helix  chain 'B' and resid 323 through 334
    Processing helix  chain 'B' and resid 342 through 355
      removed outlier: 4.145A  pdb=" N   ALA B 351 " --> pdb=" O   GLN B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 382
      removed outlier: 3.699A  pdb=" N   LYS B 360 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ARG B 382 " --> pdb=" O   SER B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 418
      removed outlier: 4.146A  pdb=" N   LEU B 411 " --> pdb=" O   ASP B 407 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU B 416 " --> pdb=" O   VAL B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 449
      No H-bonds generated for 'chain 'B' and resid 447 through 449'
    Processing helix  chain 'B' and resid 450 through 462
      removed outlier: 3.762A  pdb=" N   TRP B 462 " --> pdb=" O   VAL B 458 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175
      removed outlier: 6.559A  pdb=" N   ILE A 273 " --> pdb=" O   ILE A 302 " (cutoff:3.500A)
      removed outlier: 7.387A  pdb=" N   LEU A 304 " --> pdb=" O   ILE A 273 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   GLU A 275 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   ALA A 306 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   VAL A 239 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   ASP A 276 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   THR A 241 " --> pdb=" O   ASP A 276 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   TYR A 195 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 390
      removed outlier: 4.074A  pdb=" N   VAL A 399 " --> pdb=" O   ILE A 390 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 69 through 72
      removed outlier: 4.223A  pdb=" N   ILE B  72 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   GLY B  76 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 175
      removed outlier: 3.558A  pdb=" N   GLY B 305 " --> pdb=" O   TYR B 319 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   TYR B 303 " --> pdb=" O   VAL B 321 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   ILE B 273 " --> pdb=" O   ILE B 302 " (cutoff:3.500A)
      removed outlier: 7.378A  pdb=" N   LEU B 304 " --> pdb=" O   ILE B 273 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   GLU B 275 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 8.542A  pdb=" N   ALA B 306 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   VAL B 239 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   ASP B 276 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   THR B 241 " --> pdb=" O   ASP B 276 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   VAL B 194 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
      removed outlier: 7.682A  pdb=" N   TYR B 240 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   GLY B 196 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 387 through 390
      removed outlier: 3.583A  pdb=" N   LEU B 388 " --> pdb=" O   VAL B 401 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ILE B 390 " --> pdb=" O   VAL B 399 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   VAL B 399 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   TYR B 423 " --> pdb=" O   VAL B 440 " (cutoff:3.500A)

    225 hydrogen bonds defined for protein.
    636 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      77 hydrogen bonds
      154 hydrogen bond angles
      0 basepair planarities
      32 basepair parallelities
      70 stacking parallelities
  Total time for adding SS restraints: 2.92

  Time building geometry restraints manager: 2.72 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: 1965
        1.33 -     1.45: 2321
        1.45 -     1.57: 4516
        1.57 -     1.69: 184
        1.69 -     1.81: 32
  Bond restraints: 9018
  Sorted by residual:
  bond pdb=" OP4 LLP A 309 "
       pdb=" P   LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.726  1.547  0.179 2.00e-02 2.50e+03 7.99e+01
  bond pdb=" OP4 LLP B 309 "
       pdb=" P   LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.726  1.548  0.178 2.00e-02 2.50e+03 7.89e+01
  bond pdb=" NZ  LLP A 309 "
       pdb=" C4' LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.273  1.437 -0.164 2.00e-02 2.50e+03 6.75e+01
  bond pdb=" NZ  LLP B 309 "
       pdb=" C4' LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.273  1.434 -0.161 2.00e-02 2.50e+03 6.47e+01
  bond pdb=" C4  LLP B 309 "
       pdb=" C4' LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.464  1.617 -0.153 2.00e-02 2.50e+03 5.87e+01
  ... (remaining 9013 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.10: 12155
        2.10 -     4.20: 405
        4.20 -     6.30: 40
        6.30 -     8.40: 8
        8.40 -    10.50: 5
  Bond angle restraints: 12613
  Sorted by residual:
  angle pdb=" N   LYS A 367 "
        pdb=" CA  LYS A 367 "
        pdb=" C   LYS A 367 "
      ideal   model   delta    sigma   weight residual
     111.14  104.92    6.22 1.08e+00 8.57e-01 3.32e+01
  angle pdb=" C   TYR A 278 "
        pdb=" CA  TYR A 278 "
        pdb=" CB  TYR A 278 "
      ideal   model   delta    sigma   weight residual
     117.23  111.22    6.01 1.36e+00 5.41e-01 1.95e+01
  angle pdb=" NZ  LLP B 309 "
        pdb=" C4' LLP B 309 "
        pdb=" C4  LLP B 309 "
      ideal   model   delta    sigma   weight residual
     120.09  109.59   10.50 3.00e+00 1.11e-01 1.22e+01
  angle pdb=" N   LYS A 367 "
        pdb=" CA  LYS A 367 "
        pdb=" CB  LYS A 367 "
      ideal   model   delta    sigma   weight residual
     110.07  105.23    4.84 1.45e+00 4.76e-01 1.11e+01
  angle pdb=" NZ  LLP A 309 "
        pdb=" C4' LLP A 309 "
        pdb=" C4  LLP A 309 "
      ideal   model   delta    sigma   weight residual
     120.09  110.13    9.96 3.00e+00 1.11e-01 1.10e+01
  ... (remaining 12608 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.58: 4581
       29.58 -    59.16: 551
       59.16 -    88.73: 33
       88.73 -   118.31: 1
      118.31 -   147.89: 4
  Dihedral angle restraints: 5170
    sinusoidal: 2742
      harmonic: 2428
  Sorted by residual:
  dihedral pdb=" CA  HIS B 137 "
           pdb=" C   HIS B 137 "
           pdb=" N   ARG B 138 "
           pdb=" CA  ARG B 138 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.80  -26.20     0      5.00e+00 4.00e-02 2.75e+01
  dihedral pdb=" CA  HIS B 298 "
           pdb=" C   HIS B 298 "
           pdb=" N   ASN B 299 "
           pdb=" CA  ASN B 299 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.90   24.10     0      5.00e+00 4.00e-02 2.32e+01
  dihedral pdb=" CA  ASP A 199 "
           pdb=" C   ASP A 199 "
           pdb=" N   PRO A 200 "
           pdb=" CA  PRO A 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.89   23.11     0      5.00e+00 4.00e-02 2.14e+01
  ... (remaining 5167 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 963
       0.045 -    0.090: 316
       0.090 -    0.136: 91
       0.136 -    0.181: 10
       0.181 -    0.226: 3
  Chirality restraints: 1383
  Sorted by residual:
  chirality pdb=" CB  ILE A 231 "
            pdb=" CA  ILE A 231 "
            pdb=" CG1 ILE A 231 "
            pdb=" CG2 ILE A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  LYS A 367 "
            pdb=" N   LYS A 367 "
            pdb=" C   LYS A 367 "
            pdb=" CB  LYS A 367 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ARG B 382 "
            pdb=" N   ARG B 382 "
            pdb=" C   ARG B 382 "
            pdb=" CB  ARG B 382 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1380 not shown)

  Planarity restraints: 1288
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP A 309 "    0.166 2.00e-02 2.50e+03   2.96e-01 8.75e+02
        pdb=" NZ  LLP A 309 "   -0.409 2.00e-02 2.50e+03
        pdb=" C4  LLP A 309 "   -0.128 2.00e-02 2.50e+03
        pdb=" C4' LLP A 309 "    0.372 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 378 "   -0.015 2.00e-02 2.50e+03   2.87e-02 8.23e+00
        pdb=" C   SER B 378 "    0.050 2.00e-02 2.50e+03
        pdb=" O   SER B 378 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   LEU B 379 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 370 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.75e+00
        pdb=" C   ARG B 370 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ARG B 370 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ARG B 371 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1285 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 894
        2.74 -     3.28: 8477
        3.28 -     3.82: 14524
        3.82 -     4.36: 16726
        4.36 -     4.90: 26038
  Nonbonded interactions: 66659
  Sorted by model distance:
  nonbonded pdb=" O   MET A 132 "
            pdb=" NH2 ARG B 125 "
     model   vdw
     2.198 3.120
  nonbonded pdb=" OE1 GLU B 148 "
            pdb=" NE2 GLN B 347 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OH  TYR B 127 "
            pdb=" OE1 GLN B 355 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   LYS A 386 "
            pdb=" NZ  LYS A 403 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OD2 ASP A 115 "
            pdb=" NZ  LYS A 372 "
     model   vdw
     2.216 3.120
  ... (remaining 66654 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:             0.940
  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:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     24.370
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6704
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      :  0.007   0.179   9018  Z= 0.454
  Angle     :  0.860  10.499  12613  Z= 0.483
  Chirality :  0.048   0.226   1383
  Planarity :  0.010   0.296   1288
  Dihedral  : 21.723 147.890   3614
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 18.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.55 %
    Favored  : 99.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.94 (0.28), residues: 812
  helix: -1.06 (0.29), residues: 306
  sheet: -0.84 (0.50), residues: 85
  loop : -1.51 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A 264 
 HIS   0.008   0.002   HIS B 338 
 PHE   0.020   0.003   PHE B 247 
 TYR   0.025   0.002   TYR A 212 
 ARG   0.006   0.001   ARG B 382 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
REVERT: A  365 MET cc_start: 0.6770 (mmm) cc_final: 0.6561 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 89
  average time/residue: 0.1908
  time to fit residues: 24.5225
Evaluate side-chains
  57 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    7.9990
   chunk 67 optimal weight:    2.9990
   chunk 37 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 45 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   chunk 69 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 80 optimal weight:    0.3980
   overall best weight:    3.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 263 HIS
** A 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 145 HIS
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.128070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.104449 restraints weight = 24037.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.106523 restraints weight = 14335.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.108034 restraints weight = 9792.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6678
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9018  Z= 0.309
  Angle     :  0.735   9.221  12613  Z= 0.400
  Chirality :  0.046   0.158   1383
  Planarity :  0.006   0.053   1288
  Dihedral  : 24.753 148.186   1965
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  9.34 %
    Favored  : 89.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.71 (0.28), residues: 812
  helix: -0.85 (0.28), residues: 308
  sheet: -0.55 (0.50), residues: 97
  loop : -1.46 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 264 
 HIS   0.007   0.001   HIS B 338 
 PHE   0.025   0.003   PHE A 352 
 TYR   0.016   0.002   TYR B  17 
 ARG   0.004   0.001   ARG B  74 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.835 
Fit side-chains
   revert: symmetry clash
REVERT: A  202 TYR cc_start: 0.6527 (t80) cc_final: 0.6325 (t80)
REVERT: B  110 HIS cc_start: 0.8842 (t-90) cc_final: 0.8241 (t70)
REVERT: B  320 MET cc_start: 0.5992 (tmm) cc_final: 0.5767 (tmm)
  outliers start: 10
  outliers final: 6
  residues processed: 72
  average time/residue: 0.1853
  time to fit residues: 19.5568
Evaluate side-chains
  59 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  234 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 73 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 42 optimal weight:    0.0370
   chunk 53 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 76 optimal weight:    6.9990
   overall best weight:    2.6064

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 GLN
A 328 HIS
B 214 ASN
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.129284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.105161 restraints weight = 24517.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.107284 restraints weight = 14704.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.108803 restraints weight = 10055.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6634
moved from start:          0.1721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9018  Z= 0.237
  Angle     :  0.654   8.785  12613  Z= 0.357
  Chirality :  0.044   0.159   1383
  Planarity :  0.005   0.052   1288
  Dihedral  : 24.713 148.122   1965
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.32 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.39 (0.29), residues: 812
  helix: -0.45 (0.30), residues: 312
  sheet: -0.15 (0.51), residues: 99
  loop : -1.47 (0.30), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 264 
 HIS   0.006   0.001   HIS B 338 
 PHE   0.021   0.002   PHE A 352 
 TYR   0.016   0.002   TYR B  17 
 ARG   0.003   0.001   ARG B  74 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
REVERT: B  110 HIS cc_start: 0.8841 (t-90) cc_final: 0.8614 (t-90)
REVERT: B  406 MET cc_start: 0.4293 (tmm) cc_final: 0.4061 (tmm)
  outliers start: 21
  outliers final: 11
  residues processed: 80
  average time/residue: 0.1967
  time to fit residues: 22.7062
Evaluate side-chains
  71 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  341 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 31 optimal weight:    0.0870
   chunk 58 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 0 optimal weight:    9.9990
   chunk 5 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 41 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.9764

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 GLN
A 338 HIS
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.130582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.106656 restraints weight = 24150.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.108819 restraints weight = 14421.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.110325 restraints weight = 9801.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6604
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9018  Z= 0.201
  Angle     :  0.612   8.928  12613  Z= 0.336
  Chirality :  0.042   0.156   1383
  Planarity :  0.005   0.053   1288
  Dihedral  : 24.584 148.474   1965
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 15.25 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.10 (0.29), residues: 812
  helix: -0.15 (0.31), residues: 312
  sheet:  0.22 (0.50), residues: 105
  loop : -1.47 (0.30), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 264 
 HIS   0.004   0.001   HIS B 338 
 PHE   0.013   0.002   PHE A 352 
 TYR   0.016   0.001   TYR B  17 
 ARG   0.003   0.000   ARG B  74 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
REVERT: A  183 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6139 (mt0)
REVERT: B  110 HIS cc_start: 0.8816 (t-90) cc_final: 0.8452 (t-90)
REVERT: B  202 TYR cc_start: 0.5869 (OUTLIER) cc_final: 0.4542 (t80)
REVERT: B  308 SER cc_start: 0.7738 (t) cc_final: 0.7344 (p)
REVERT: B  320 MET cc_start: 0.6146 (tmm) cc_final: 0.5904 (tmm)
REVERT: B  406 MET cc_start: 0.4631 (OUTLIER) cc_final: 0.3852 (tmm)
  outliers start: 23
  outliers final: 11
  residues processed: 84
  average time/residue: 0.1779
  time to fit residues: 21.8912
Evaluate side-chains
  75 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  367 LYS
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  406 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 78 optimal weight:    8.9990
   chunk 37 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 60 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 73 optimal weight:    0.1980
   chunk 29 optimal weight:    0.4980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 GLN
** B 293 GLN ** 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 = 0.4249 r_free = 0.4249 target = 0.131619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.107379 restraints weight = 23801.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.109602 restraints weight = 14263.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.111161 restraints weight = 9678.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6562
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9018  Z= 0.175
  Angle     :  0.584   9.332  12613  Z= 0.321
  Chirality :  0.041   0.169   1383
  Planarity :  0.005   0.051   1288
  Dihedral  : 24.482 148.693   1965
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.03 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -0.82 (0.30), residues: 812
  helix:  0.13 (0.31), residues: 312
  sheet:  0.31 (0.52), residues: 105
  loop : -1.33 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 264 
 HIS   0.006   0.001   HIS B 338 
 PHE   0.015   0.002   PHE B 109 
 TYR   0.014   0.001   TYR B  17 
 ARG   0.003   0.000   ARG A 364 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
REVERT: A  183 GLN cc_start: 0.6379 (OUTLIER) cc_final: 0.5952 (mt0)
REVERT: A  271 ARG cc_start: 0.6169 (mtm-85) cc_final: 0.5668 (mtm-85)
REVERT: B  110 HIS cc_start: 0.8830 (t-90) cc_final: 0.8489 (t-90)
REVERT: B  202 TYR cc_start: 0.5817 (OUTLIER) cc_final: 0.4529 (t80)
REVERT: B  268 HIS cc_start: 0.5660 (OUTLIER) cc_final: 0.5181 (t-90)
REVERT: B  320 MET cc_start: 0.6190 (tmm) cc_final: 0.5810 (tmm)
REVERT: B  406 MET cc_start: 0.4555 (OUTLIER) cc_final: 0.3921 (tmm)
  outliers start: 20
  outliers final: 12
  residues processed: 80
  average time/residue: 0.1894
  time to fit residues: 22.0371
Evaluate side-chains
  81 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  268 HIS
Chi-restraints excluded: chain B residue  406 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 48 optimal weight:    0.8980
   chunk 80 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 67 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 123 GLN
A 183 GLN
A 328 HIS
B 183 GLN
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.133267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.109743 restraints weight = 23905.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.111820 restraints weight = 14725.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.113322 restraints weight = 10185.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6506
moved from start:          0.2648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9018  Z= 0.160
  Angle     :  0.564   9.437  12613  Z= 0.308
  Chirality :  0.040   0.167   1383
  Planarity :  0.005   0.052   1288
  Dihedral  : 24.370 148.824   1965
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.31 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.76 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -0.65 (0.30), residues: 812
  helix:  0.27 (0.31), residues: 313
  sheet:  0.44 (0.51), residues: 105
  loop : -1.25 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 264 
 HIS   0.006   0.001   HIS B 338 
 PHE   0.029   0.002   PHE A 219 
 TYR   0.012   0.001   TYR B  17 
 ARG   0.003   0.000   ARG A 364 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
REVERT: A  406 MET cc_start: 0.5413 (mmp) cc_final: 0.5047 (mmp)
REVERT: B  110 HIS cc_start: 0.8831 (t-90) cc_final: 0.8522 (t-90)
REVERT: B  148 GLU cc_start: 0.6339 (mm-30) cc_final: 0.6088 (mt-10)
REVERT: B  202 TYR cc_start: 0.5757 (OUTLIER) cc_final: 0.4512 (t80)
REVERT: B  268 HIS cc_start: 0.5687 (OUTLIER) cc_final: 0.5243 (t-90)
REVERT: B  320 MET cc_start: 0.5948 (tmm) cc_final: 0.5566 (tmm)
  outliers start: 24
  outliers final: 14
  residues processed: 87
  average time/residue: 0.1947
  time to fit residues: 24.4019
Evaluate side-chains
  79 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue   11 ASP
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  268 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0970
   chunk 72 optimal weight:    0.9990
   chunk 73 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 GLN
** B 293 GLN ** 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 = 0.4276 r_free = 0.4276 target = 0.133255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.109492 restraints weight = 23701.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.111622 restraints weight = 14557.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.113163 restraints weight = 10013.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6533
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9018  Z= 0.166
  Angle     :  0.570   9.511  12613  Z= 0.308
  Chirality :  0.040   0.174   1383
  Planarity :  0.005   0.051   1288
  Dihedral  : 24.271 148.708   1965
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.43 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 18.13 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -0.57 (0.30), residues: 812
  helix:  0.38 (0.31), residues: 312
  sheet:  0.51 (0.51), residues: 105
  loop : -1.24 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 264 
 HIS   0.005   0.001   HIS B 338 
 PHE   0.021   0.002   PHE A 219 
 TYR   0.011   0.001   TYR B  21 
 ARG   0.004   0.000   ARG A 271 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 69
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: B  110 HIS cc_start: 0.8802 (t-90) cc_final: 0.8544 (t-90)
REVERT: B  202 TYR cc_start: 0.5753 (OUTLIER) cc_final: 0.4511 (t80)
REVERT: B  268 HIS cc_start: 0.5659 (OUTLIER) cc_final: 0.5277 (t-90)
REVERT: B  320 MET cc_start: 0.5980 (tmm) cc_final: 0.5568 (tmm)
  outliers start: 20
  outliers final: 14
  residues processed: 82
  average time/residue: 0.2016
  time to fit residues: 23.9327
Evaluate side-chains
  83 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.926 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  268 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   chunk 71 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 GLN
A 328 HIS
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.131944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.107947 restraints weight = 24533.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.110188 restraints weight = 14680.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.111709 restraints weight = 9974.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6580
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9018  Z= 0.201
  Angle     :  0.596   9.508  12613  Z= 0.322
  Chirality :  0.042   0.189   1383
  Planarity :  0.005   0.052   1288
  Dihedral  : 24.283 148.325   1965
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.30 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 18.13 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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 (0.30), residues: 812
  helix:  0.21 (0.31), residues: 313
  sheet:  0.35 (0.50), residues: 106
  loop : -1.25 (0.32), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 264 
 HIS   0.006   0.001   HIS B 338 
 PHE   0.019   0.002   PHE A 219 
 TYR   0.015   0.001   TYR A 337 
 ARG   0.003   0.000   ARG A 271 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 64
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 PHE cc_start: 0.7137 (m-80) cc_final: 0.6733 (m-80)
REVERT: B  110 HIS cc_start: 0.8856 (t-90) cc_final: 0.8565 (t-90)
REVERT: B  202 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.4615 (t80)
  outliers start: 25
  outliers final: 18
  residues processed: 83
  average time/residue: 0.1756
  time to fit residues: 21.4959
Evaluate side-chains
  81 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  400 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 52 optimal weight:    9.9990
   chunk 45 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 31 optimal weight:    6.9990
   chunk 81 optimal weight:   10.0000
   chunk 69 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9990
   chunk 84 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 GLN
B   9 ASN
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.126659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.103229 restraints weight = 24748.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.105214 restraints weight = 15059.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.106727 restraints weight = 10412.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6746
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   9018  Z= 0.363
  Angle     :  0.778  10.255  12613  Z= 0.417
  Chirality :  0.048   0.226   1383
  Planarity :  0.006   0.050   1288
  Dihedral  : 24.763 146.783   1965
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 18.68 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -1.44 (0.29), residues: 812
  helix: -0.56 (0.29), residues: 312
  sheet: -0.25 (0.53), residues: 100
  loop : -1.42 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP A 264 
 HIS   0.012   0.002   HIS B 338 
 PHE   0.027   0.004   PHE B 352 
 TYR   0.025   0.002   TYR B  17 
 ARG   0.006   0.001   ARG A 271 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 63
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A  320 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6539 (ttp)
REVERT: B  320 MET cc_start: 0.6107 (tmm) cc_final: 0.5887 (tmm)
REVERT: B  393 ARG cc_start: 0.5899 (pmt170) cc_final: 0.5540 (ptt-90)
  outliers start: 27
  outliers final: 21
  residues processed: 85
  average time/residue: 0.2068
  time to fit residues: 24.9670
Evaluate side-chains
  80 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.839 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 ILE
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  198 GLU
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  341 VAL
Chi-restraints excluded: chain B residue  400 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 18 optimal weight:    0.0170
   chunk 54 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 41 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 67 optimal weight:    6.9990
   overall best weight:    1.1220

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 HIS
** B 293 GLN ** 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 = 0.4260 r_free = 0.4260 target = 0.132006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.108848 restraints weight = 24107.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.110970 restraints weight = 14758.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.112471 restraints weight = 10182.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6566
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9018  Z= 0.172
  Angle     :  0.604  10.328  12613  Z= 0.326
  Chirality :  0.042   0.196   1383
  Planarity :  0.005   0.053   1288
  Dihedral  : 24.413 147.935   1965
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.47 %
    Favored  : 77.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -0.89 (0.30), residues: 812
  helix:  0.15 (0.31), residues: 308
  sheet:  0.31 (0.54), residues: 93
  loop : -1.39 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 264 
 HIS   0.006   0.001   HIS B 338 
 PHE   0.019   0.002   PHE A 219 
 TYR   0.014   0.001   TYR B  21 
 ARG   0.008   0.000   ARG A 271 

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

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

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1624 Ramachandran restraints generated.
    812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.798 
Fit side-chains
REVERT: B  202 TYR cc_start: 0.5908 (OUTLIER) cc_final: 0.4526 (t80)
REVERT: B  308 SER cc_start: 0.7595 (t) cc_final: 0.7318 (p)
  outliers start: 17
  outliers final: 14
  residues processed: 78
  average time/residue: 0.1969
  time to fit residues: 21.9629
Evaluate side-chains
  77 residues out of total 728 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  262 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  308 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  403 LYS
Chi-restraints excluded: chain B residue  110 HIS
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  226 ILE
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  400 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 84 optimal weight:   10.0000
   chunk 72 optimal weight:    0.6980
   chunk 6 optimal weight:   10.0000
   chunk 47 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0570
   chunk 62 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.6500

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.134273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.109973 restraints weight = 23772.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.112386 restraints weight = 13929.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.114202 restraints weight = 9319.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6469
moved from start:          0.3515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9018  Z= 0.165
  Angle     :  0.600  13.186  12613  Z= 0.318
  Chirality :  0.040   0.182   1383
  Planarity :  0.005   0.051   1288
  Dihedral  : 24.172 149.821   1965
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.05 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 21.29 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.89 %
    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: -0.62 (0.30), residues: 812
  helix:  0.48 (0.32), residues: 310
  sheet:  0.35 (0.53), residues: 95
  loop : -1.30 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP A 264 
 HIS   0.011   0.001   HIS B 110 
 PHE   0.020   0.001   PHE B 109 
 TYR   0.012   0.001   TYR B  21 
 ARG   0.007   0.000   ARG A 271 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2697.41 seconds
wall clock time: 49 minutes 15.71 seconds (2955.71 seconds total)