Starting phenix.real_space_refine
on Wed Mar 12 06:18:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uz2_20950/03_2025/6uz2_20950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uz2_20950/03_2025/6uz2_20950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uz2_20950/03_2025/6uz2_20950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uz2_20950/03_2025/6uz2_20950.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uz2_20950/03_2025/6uz2_20950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uz2_20950/03_2025/6uz2_20950.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    4640      2.51       5
     N    1328      2.21       5
     O    1380      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7392
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 3694
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 210}
          Link IDs: {'PTRANS': 13, 'TRANS': 556}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 749
          Unresolved non-hydrogen angles: 959
          Unresolved non-hydrogen dihedrals: 588
          Unresolved non-hydrogen chiralities: 79
          Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 13, 'ASP:plan': 17, 'PHE:plan': 6, 'GLU:plan': 21, 'ARG:plan': 21}
          Unresolved non-hydrogen planarities: 434
    Chain: "B"
      Number of atoms: 3698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 3698
          Classifications: {'peptide': 570}
          Incomplete info: {'truncation_to_alanine': 209}
          Link IDs: {'PTRANS': 13, 'TRANS': 556}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 745
          Unresolved non-hydrogen angles: 954
          Unresolved non-hydrogen dihedrals: 585
          Unresolved non-hydrogen chiralities: 79
          Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 13, 'ASP:plan': 17, 'PHE:plan': 6, 'GLU:plan': 20, 'ARG:plan': 21}
          Unresolved non-hydrogen planarities: 430
  Time building chain proxies: 4.92, per 1000 atoms: 0.67
  Number of scatterers: 7392
  At special positions: 0
  Unit cell: (72, 96, 131, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1380      8.00
     N    1328      7.00
     C    4640      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: 1.99
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 5 sheets defined
      71.8% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 21
      Proline residue:  A  18  - end of helix
    Processing helix  chain 'A' and resid 24 through 47
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 3.574A  pdb=" N   ASP A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 59
    Processing helix  chain 'A' and resid 62 through 109
      removed outlier: 3.712A  pdb=" N   TRP A  66 " --> pdb=" O   SER A  62 " (cutoff:3.500A)
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 113 through 118
    Processing helix  chain 'A' and resid 120 through 164
      removed outlier: 3.556A  pdb=" N   GLY A 155 " --> pdb=" O   ALA A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 196
      Proline residue:  A 176  - end of helix
      removed outlier: 3.755A  pdb=" N   MET A 196 " --> pdb=" O   ILE A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 221
      removed outlier: 5.028A  pdb=" N   LYS A 215 " --> pdb=" O   LEU A 211 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   GLU A 216 " --> pdb=" O   LYS A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 269
      removed outlier: 3.553A  pdb=" N   LYS A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   SER A 251 " --> pdb=" O   ALA A 247 " (cutoff:3.500A)
      removed outlier: 4.930A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.640A  pdb=" N   ALA A 262 " --> pdb=" O   ILE A 258 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   LEU A 263 " --> pdb=" O   ALA A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 276
    Processing helix  chain 'A' and resid 280 through 324
      Proline residue:  A 297  - end of helix
      removed outlier: 4.073A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ASN A 303 " --> pdb=" O   LYS A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 390
      removed outlier: 3.834A  pdb=" N   ALA A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 464
    Processing helix  chain 'A' and resid 468 through 472
      removed outlier: 3.687A  pdb=" N   ASP A 471 " --> pdb=" O   ASN A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 512 through 527
    Processing helix  chain 'A' and resid 538 through 545
      removed outlier: 4.118A  pdb=" N   ALA A 545 " --> pdb=" O   THR A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 566
    Processing helix  chain 'A' and resid 570 through 574
      removed outlier: 3.521A  pdb=" N   ALA A 573 " --> pdb=" O   GLY A 570 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 17
    Processing helix  chain 'B' and resid 18 through 22
      Proline residue:  B  22  - end of helix
    Processing helix  chain 'B' and resid 23 through 53
      removed outlier: 3.861A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 60 through 109
      Proline residue:  B  68  - end of helix
    Processing helix  chain 'B' and resid 112 through 118
    Processing helix  chain 'B' and resid 120 through 164
    Processing helix  chain 'B' and resid 164 through 213
      Proline residue:  B 176  - end of helix
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 222 through 275
      removed outlier: 4.767A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
      Proline residue:  B 273  - end of helix
    Processing helix  chain 'B' and resid 280 through 323
      removed outlier: 3.632A  pdb=" N   PHE B 288 " --> pdb=" O   ILE B 284 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 3.797A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE B 308 " --> pdb=" O   VAL B 304 " (cutoff:3.500A)
      removed outlier: 5.045A  pdb=" N   GLN B 309 " --> pdb=" O   ASN B 305 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ARG B 310 " --> pdb=" O   ALA B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 390
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'B' and resid 432 through 437
    Processing helix  chain 'B' and resid 446 through 457
    Processing helix  chain 'B' and resid 459 through 464
      removed outlier: 3.668A  pdb=" N   ASN B 464 " --> pdb=" O   MET B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 479
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 512 through 527
    Processing helix  chain 'B' and resid 540 through 545
      removed outlier: 3.677A  pdb=" N   LYS B 544 " --> pdb=" O   SER B 540 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   ALA B 545 " --> pdb=" O   THR B 541 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 540 through 545'
    Processing helix  chain 'B' and resid 561 through 567
    Processing helix  chain 'B' and resid 570 through 579
      removed outlier: 3.590A  pdb=" N   GLN B 574 " --> pdb=" O   GLY B 570 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 359 through 366
      removed outlier: 5.615A  pdb=" N   ARG A 360 " --> pdb=" O   PHE A 349 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   PHE A 349 " --> pdb=" O   ARG A 360 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   LEU A 364 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   ARG A 345 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
      removed outlier: 7.095A  pdb=" N   ILE A 366 " --> pdb=" O   GLU A 343 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   GLU A 343 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   VAL A 347 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   GLU A 397 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 371 through 374
    Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 422
      removed outlier: 5.311A  pdb=" N   ALA A 420 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 342 through 343
    Processing sheet with id=AA5, first strand: chain 'B' and resid 421 through 422
      removed outlier: 3.653A  pdb=" N   VAL B 422 " --> pdb=" O   ILE B 503 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    586 hydrogen bonds defined for protein.
    1734 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 2.33 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2498
        1.34 -     1.45: 996
        1.45 -     1.57: 3894
        1.57 -     1.69: 2
        1.69 -     1.81: 84
  Bond restraints: 7474
  Sorted by residual:
  bond pdb=" CG  ARG B 296 "
       pdb=" CD  ARG B 296 "
    ideal  model  delta    sigma   weight residual
    1.520  1.588 -0.068 3.00e-02 1.11e+03 5.18e+00
  bond pdb=" CG  ARG A 296 "
       pdb=" CD  ARG A 296 "
    ideal  model  delta    sigma   weight residual
    1.520  1.588 -0.068 3.00e-02 1.11e+03 5.15e+00
  bond pdb=" CB  TRP A  17 "
       pdb=" CG  TRP A  17 "
    ideal  model  delta    sigma   weight residual
    1.498  1.436  0.062 3.10e-02 1.04e+03 4.02e+00
  bond pdb=" CB  PHE A  13 "
       pdb=" CG  PHE A  13 "
    ideal  model  delta    sigma   weight residual
    1.502  1.459  0.043 2.30e-02 1.89e+03 3.52e+00
  bond pdb=" CB  TRP B  17 "
       pdb=" CG  TRP B  17 "
    ideal  model  delta    sigma   weight residual
    1.498  1.442  0.056 3.10e-02 1.04e+03 3.30e+00
  ... (remaining 7469 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 9918
        2.73 -     5.47: 230
        5.47 -     8.20: 31
        8.20 -    10.93: 8
       10.93 -    13.67: 8
  Bond angle restraints: 10195
  Sorted by residual:
  angle pdb=" N   HIS B 537 "
        pdb=" CA  HIS B 537 "
        pdb=" C   HIS B 537 "
      ideal   model   delta    sigma   weight residual
     112.59  100.04   12.55 1.22e+00 6.72e-01 1.06e+02
  angle pdb=" C   MET A 295 "
        pdb=" N   ARG A 296 "
        pdb=" CA  ARG A 296 "
      ideal   model   delta    sigma   weight residual
     119.83  112.91    6.92 1.11e+00 8.12e-01 3.88e+01
  angle pdb=" N   ALA B 536 "
        pdb=" CA  ALA B 536 "
        pdb=" C   ALA B 536 "
      ideal   model   delta    sigma   weight residual
     108.56  118.02   -9.46 1.74e+00 3.30e-01 2.95e+01
  angle pdb=" N   SER B 164 "
        pdb=" CA  SER B 164 "
        pdb=" C   SER B 164 "
      ideal   model   delta    sigma   weight residual
     107.93  116.15   -8.22 1.65e+00 3.67e-01 2.48e+01
  angle pdb=" N   TYR A 163 "
        pdb=" CA  TYR A 163 "
        pdb=" C   TYR A 163 "
      ideal   model   delta    sigma   weight residual
     111.36  116.32   -4.96 1.09e+00 8.42e-01 2.07e+01
  ... (remaining 10190 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.39: 3904
       13.39 -    26.77: 398
       26.77 -    40.16: 121
       40.16 -    53.54: 39
       53.54 -    66.93: 9
  Dihedral angle restraints: 4471
    sinusoidal: 1189
      harmonic: 3282
  Sorted by residual:
  dihedral pdb=" CA  GLU A 552 "
           pdb=" C   GLU A 552 "
           pdb=" N   ASP A 553 "
           pdb=" CA  ASP A 553 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.68   28.32     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" CA  ALA A 457 "
           pdb=" C   ALA A 457 "
           pdb=" N   TYR A 458 "
           pdb=" CA  TYR A 458 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.96   28.04     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" CA  LYS B 544 "
           pdb=" C   LYS B 544 "
           pdb=" N   ALA B 545 "
           pdb=" CA  ALA B 545 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.94   27.06     0      5.00e+00 4.00e-02 2.93e+01
  ... (remaining 4468 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 883
       0.048 -    0.096: 318
       0.096 -    0.143: 73
       0.143 -    0.191: 5
       0.191 -    0.239: 5
  Chirality restraints: 1284
  Sorted by residual:
  chirality pdb=" CA  VAL A 334 "
            pdb=" N   VAL A 334 "
            pdb=" C   VAL A 334 "
            pdb=" CB  VAL A 334 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CA  ALA B 536 "
            pdb=" N   ALA B 536 "
            pdb=" C   ALA B 536 "
            pdb=" CB  ALA B 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.25    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality pdb=" CA  TYR A 163 "
            pdb=" N   TYR A 163 "
            pdb=" C   TYR A 163 "
            pdb=" CB  TYR A 163 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 1281 not shown)

  Planarity restraints: 1327
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 262 "   -0.012 2.00e-02 2.50e+03   2.40e-02 5.77e+00
        pdb=" C   ALA B 262 "    0.042 2.00e-02 2.50e+03
        pdb=" O   ALA B 262 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LEU B 263 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 136 "   -0.011 2.00e-02 2.50e+03   2.31e-02 5.35e+00
        pdb=" C   ALA B 136 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ALA B 136 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   SER B 137 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 296 "    0.039 5.00e-02 4.00e+02   5.73e-02 5.26e+00
        pdb=" N   PRO B 297 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO B 297 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 297 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1324 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1320
        2.74 -     3.28: 8957
        3.28 -     3.82: 12479
        3.82 -     4.36: 13927
        4.36 -     4.90: 22048
  Nonbonded interactions: 58731
  Sorted by model distance:
  nonbonded pdb=" O   ARG A  78 "
            pdb=" OG1 THR A  81 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   GLN B 256 "
            pdb=" OG  SER B 260 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   PRO A 297 "
            pdb=" OG  SER A 300 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   ALA A 175 "
            pdb=" OG  SER A 179 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" O   VAL A 135 "
            pdb=" OG  SER A 139 "
     model   vdw
     2.208 3.040
  ... (remaining 58726 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 11 through 148 or (resid 149 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 150 through 580))
}

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:             1.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.630
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
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      :  0.009   0.068   7474  Z= 0.574
  Angle     :  1.131  13.667  10195  Z= 0.668
  Chirality :  0.051   0.239   1284
  Planarity :  0.005   0.057   1327
  Dihedral  : 13.781  66.927   2339
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 31.10
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 15.49 %
    Favored  : 84.33 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 12.70 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.29 (0.18), residues: 1136
  helix: -3.00 (0.14), residues: 715
  sheet: -3.18 (0.60), residues: 43
  loop : -4.28 (0.25), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A  91 
 HIS   0.009   0.002   HIS A 107 
 PHE   0.040   0.004   PHE A 308 
 TYR   0.010   0.002   TYR A  83 
 ARG   0.005   0.001   ARG A 296 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 246
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 LYS cc_start: 0.8540 (tptm) cc_final: 0.8238 (pttt)
REVERT: A  148 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7782 (tpp80)
REVERT: A  159 MET cc_start: 0.9199 (mmm) cc_final: 0.8523 (mmm)
REVERT: A  189 PHE cc_start: 0.8718 (m-10) cc_final: 0.8247 (m-80)
REVERT: A  190 ARG cc_start: 0.9025 (mtt180) cc_final: 0.8771 (mmp80)
REVERT: A  196 MET cc_start: 0.9023 (mmm) cc_final: 0.8645 (mmm)
REVERT: A  198 ASN cc_start: 0.9149 (m-40) cc_final: 0.8784 (p0)
REVERT: A  208 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8117 (mm-30)
REVERT: A  210 MET cc_start: 0.8939 (mmm) cc_final: 0.8543 (mtt)
REVERT: A  212 LYS cc_start: 0.9177 (mttt) cc_final: 0.8634 (mttm)
REVERT: A  230 PHE cc_start: 0.8652 (m-10) cc_final: 0.8355 (m-10)
REVERT: A  296 ARG cc_start: 0.5977 (mtt180) cc_final: 0.5146 (ttm170)
REVERT: B   98 MET cc_start: 0.9275 (ttm) cc_final: 0.8646 (tpp)
REVERT: B  171 LEU cc_start: 0.9173 (mt) cc_final: 0.8938 (mt)
REVERT: B  189 PHE cc_start: 0.8602 (m-10) cc_final: 0.8196 (t80)
REVERT: B  190 ARG cc_start: 0.9037 (mtt180) cc_final: 0.8715 (ptt180)
REVERT: B  191 ASN cc_start: 0.8431 (m-40) cc_final: 0.8061 (t0)
REVERT: B  196 MET cc_start: 0.8861 (mmm) cc_final: 0.8567 (tpp)
REVERT: B  210 MET cc_start: 0.8608 (tpt) cc_final: 0.8363 (tpt)
REVERT: B  296 ARG cc_start: 0.5595 (mtt180) cc_final: 0.4564 (ttm170)
REVERT: B  312 MET cc_start: 0.9242 (mmm) cc_final: 0.9026 (mmm)
  outliers start: 11
  outliers final: 5
  residues processed: 252
  average time/residue: 0.1869
  time to fit residues: 62.7869
Evaluate side-chains
  189 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 183
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:   20.0000
   chunk 86 optimal weight:    0.8980
   chunk 47 optimal weight:   20.0000
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 89 optimal weight:   20.0000
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0370
   chunk 66 optimal weight:    0.8980
   chunk 103 optimal weight:   30.0000
   overall best weight:    0.7260

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

Flipped N/Q/H residues before XYZ refinement:
A  37 ASN
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.109547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.085293 restraints weight = 23823.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.087622 restraints weight = 14491.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.089260 restraints weight = 10116.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.3111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7474  Z= 0.209
  Angle     :  0.696   9.042  10195  Z= 0.376
  Chirality :  0.045   0.159   1284
  Planarity :  0.004   0.051   1327
  Dihedral  :  5.425  24.252   1184
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.22
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.87 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.23), residues: 1136
  helix: -0.76 (0.17), residues: 742
  sheet: -3.15 (0.74), residues: 39
  loop : -3.35 (0.30), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  91 
 HIS   0.010   0.004   HIS A 214 
 PHE   0.039   0.003   PHE A 115 
 TYR   0.012   0.002   TYR A  87 
 ARG   0.006   0.001   ARG B  15 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 PHE cc_start: 0.8368 (m-80) cc_final: 0.7936 (m-80)
REVERT: A   60 ASP cc_start: 0.8827 (m-30) cc_final: 0.8586 (m-30)
REVERT: A   63 VAL cc_start: 0.9261 (p) cc_final: 0.8939 (m)
REVERT: A   98 MET cc_start: 0.8947 (tpp) cc_final: 0.8501 (tpp)
REVERT: A  118 LYS cc_start: 0.8157 (tptm) cc_final: 0.7846 (pttt)
REVERT: A  130 TYR cc_start: 0.8522 (t80) cc_final: 0.8311 (t80)
REVERT: A  131 ASP cc_start: 0.8732 (m-30) cc_final: 0.8404 (m-30)
REVERT: A  159 MET cc_start: 0.9366 (mmm) cc_final: 0.7945 (mmm)
REVERT: A  171 LEU cc_start: 0.9006 (mt) cc_final: 0.8758 (mt)
REVERT: A  190 ARG cc_start: 0.8862 (mtt180) cc_final: 0.8658 (mmp80)
REVERT: A  196 MET cc_start: 0.8818 (mmm) cc_final: 0.8461 (tpp)
REVERT: A  198 ASN cc_start: 0.9177 (m-40) cc_final: 0.8797 (p0)
REVERT: A  208 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8510 (mm-30)
REVERT: A  212 LYS cc_start: 0.9072 (mttt) cc_final: 0.8716 (tppt)
REVERT: A  216 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8890 (pt0)
REVERT: A  250 ILE cc_start: 0.9597 (mt) cc_final: 0.9360 (tp)
REVERT: A  312 MET cc_start: 0.9108 (mmm) cc_final: 0.8521 (mmm)
REVERT: B   36 LEU cc_start: 0.9234 (mt) cc_final: 0.8793 (tt)
REVERT: B   37 ASN cc_start: 0.9151 (t0) cc_final: 0.8910 (t0)
REVERT: B   54 ASP cc_start: 0.8525 (m-30) cc_final: 0.7786 (m-30)
REVERT: B   98 MET cc_start: 0.9357 (ttm) cc_final: 0.8583 (tpp)
REVERT: B  125 LEU cc_start: 0.8672 (mt) cc_final: 0.7341 (mt)
REVERT: B  159 MET cc_start: 0.9091 (mmm) cc_final: 0.8741 (mmm)
REVERT: B  171 LEU cc_start: 0.9185 (mt) cc_final: 0.8958 (mt)
REVERT: B  190 ARG cc_start: 0.8983 (mtt180) cc_final: 0.8630 (ptt180)
REVERT: B  191 ASN cc_start: 0.8315 (m-40) cc_final: 0.8089 (t0)
REVERT: B  210 MET cc_start: 0.8627 (tpt) cc_final: 0.8274 (ttt)
REVERT: B  214 HIS cc_start: 0.7951 (p-80) cc_final: 0.7559 (p90)
REVERT: B  261 LEU cc_start: 0.9331 (mt) cc_final: 0.8935 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 0.1612
  time to fit residues: 59.0053
Evaluate side-chains
  205 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 96 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 42 optimal weight:   20.0000
   chunk 89 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 35 optimal weight:   20.0000
   chunk 84 optimal weight:    0.7980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 326 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.112081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.085408 restraints weight = 24106.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.087621 restraints weight = 15368.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.089206 restraints weight = 11039.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.3946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7474  Z= 0.240
  Angle     :  0.663   8.897  10195  Z= 0.352
  Chirality :  0.045   0.137   1284
  Planarity :  0.004   0.049   1327
  Dihedral  :  4.945  20.847   1184
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.43 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.36 (0.24), residues: 1136
  helix:  0.14 (0.18), residues: 747
  sheet: -2.55 (0.98), residues: 27
  loop : -2.97 (0.32), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  66 
 HIS   0.008   0.003   HIS A 214 
 PHE   0.022   0.002   PHE A 308 
 TYR   0.025   0.002   TYR A  87 
 ARG   0.004   0.001   ARG B 127 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.8589 (m-30) cc_final: 0.8386 (m-30)
REVERT: A   98 MET cc_start: 0.8929 (tpp) cc_final: 0.8402 (tpp)
REVERT: A  115 PHE cc_start: 0.7496 (m-80) cc_final: 0.7076 (m-80)
REVERT: A  118 LYS cc_start: 0.8091 (tptm) cc_final: 0.7824 (pttt)
REVERT: A  131 ASP cc_start: 0.8820 (m-30) cc_final: 0.8461 (m-30)
REVERT: A  159 MET cc_start: 0.9142 (mmm) cc_final: 0.8677 (mmm)
REVERT: A  196 MET cc_start: 0.8742 (mmm) cc_final: 0.8200 (tpp)
REVERT: A  198 ASN cc_start: 0.9235 (m-40) cc_final: 0.8842 (p0)
REVERT: A  208 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8518 (mm-30)
REVERT: A  212 LYS cc_start: 0.9058 (mttt) cc_final: 0.8741 (tppt)
REVERT: A  216 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8943 (pt0)
REVERT: A  230 PHE cc_start: 0.8198 (m-10) cc_final: 0.7943 (m-10)
REVERT: A  261 LEU cc_start: 0.9565 (mt) cc_final: 0.9360 (mt)
REVERT: A  296 ARG cc_start: 0.5265 (ttm170) cc_final: 0.4891 (ttm170)
REVERT: A  312 MET cc_start: 0.9209 (mmm) cc_final: 0.8774 (mmm)
REVERT: B   53 ASP cc_start: 0.8190 (p0) cc_final: 0.7976 (p0)
REVERT: B   75 MET cc_start: 0.9109 (mmt) cc_final: 0.8815 (mmm)
REVERT: B   98 MET cc_start: 0.9315 (ttm) cc_final: 0.8494 (tpp)
REVERT: B  105 PHE cc_start: 0.8372 (m-10) cc_final: 0.8058 (m-10)
REVERT: B  159 MET cc_start: 0.9004 (mmm) cc_final: 0.8022 (mmm)
REVERT: B  163 TYR cc_start: 0.8065 (m-80) cc_final: 0.6830 (m-80)
REVERT: B  190 ARG cc_start: 0.8978 (mtt180) cc_final: 0.8486 (ptt180)
REVERT: B  191 ASN cc_start: 0.8340 (m-40) cc_final: 0.7969 (t0)
REVERT: B  210 MET cc_start: 0.8416 (tpt) cc_final: 0.8115 (ttt)
REVERT: B  230 PHE cc_start: 0.8331 (m-10) cc_final: 0.7486 (m-10)
REVERT: B  290 SER cc_start: 0.9404 (p) cc_final: 0.9109 (p)
REVERT: B  320 THR cc_start: 0.9191 (p) cc_final: 0.8977 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.1480
  time to fit residues: 52.1356
Evaluate side-chains
  206 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 49 optimal weight:   40.0000
   chunk 78 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 92 optimal weight:   50.0000
   chunk 93 optimal weight:   30.0000
   chunk 94 optimal weight:    7.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 GLN ** 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 = 0.3851 r_free = 0.3851 target = 0.111863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.084505 restraints weight = 24107.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.086710 restraints weight = 15369.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.088200 restraints weight = 11014.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.4391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7474  Z= 0.279
  Angle     :  0.674   8.347  10195  Z= 0.359
  Chirality :  0.045   0.145   1284
  Planarity :  0.004   0.048   1327
  Dihedral  :  4.725  18.953   1184
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.34 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  4.36 %
    Favored  : 95.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.25), residues: 1136
  helix:  0.40 (0.18), residues: 758
  sheet: -2.50 (1.01), residues: 27
  loop : -2.74 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  66 
 HIS   0.006   0.002   HIS A 214 
 PHE   0.052   0.003   PHE A 105 
 TYR   0.017   0.002   TYR A 163 
 ARG   0.003   0.001   ARG A 190 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 243
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 VAL cc_start: 0.9363 (p) cc_final: 0.9015 (m)
REVERT: A   98 MET cc_start: 0.8916 (tpp) cc_final: 0.8609 (tpp)
REVERT: A  118 LYS cc_start: 0.8166 (tptm) cc_final: 0.7921 (pttt)
REVERT: A  131 ASP cc_start: 0.8700 (m-30) cc_final: 0.8461 (m-30)
REVERT: A  159 MET cc_start: 0.9076 (mmm) cc_final: 0.8844 (mmm)
REVERT: A  196 MET cc_start: 0.8651 (mmm) cc_final: 0.8244 (tpp)
REVERT: A  198 ASN cc_start: 0.9169 (m-40) cc_final: 0.8866 (p0)
REVERT: A  216 GLU cc_start: 0.9171 (mt-10) cc_final: 0.8937 (pt0)
REVERT: A  296 ARG cc_start: 0.6176 (ttm170) cc_final: 0.5757 (ttt180)
REVERT: A  312 MET cc_start: 0.9154 (mmm) cc_final: 0.8704 (mmm)
REVERT: B   36 LEU cc_start: 0.9229 (mt) cc_final: 0.8993 (tp)
REVERT: B   53 ASP cc_start: 0.8064 (p0) cc_final: 0.7731 (p0)
REVERT: B   75 MET cc_start: 0.9058 (mmt) cc_final: 0.8741 (mmm)
REVERT: B   98 MET cc_start: 0.9264 (ttm) cc_final: 0.8381 (tpp)
REVERT: B  159 MET cc_start: 0.8989 (mmm) cc_final: 0.8451 (mmm)
REVERT: B  163 TYR cc_start: 0.8891 (m-80) cc_final: 0.7770 (m-80)
REVERT: B  190 ARG cc_start: 0.9022 (mtt180) cc_final: 0.8478 (ptt180)
REVERT: B  191 ASN cc_start: 0.8251 (m-40) cc_final: 0.7915 (t0)
REVERT: B  240 GLN cc_start: 0.8864 (mt0) cc_final: 0.8469 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 243
  average time/residue: 0.1403
  time to fit residues: 49.1173
Evaluate side-chains
  185 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 33 optimal weight:   50.0000
   chunk 72 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 112 optimal weight:    4.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 GLN ** 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 = 0.3858 r_free = 0.3858 target = 0.111305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.088433 restraints weight = 23116.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.090491 restraints weight = 15280.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.092016 restraints weight = 11112.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.4967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7474  Z= 0.197
  Angle     :  0.605   7.489  10195  Z= 0.321
  Chirality :  0.043   0.134   1284
  Planarity :  0.004   0.043   1327
  Dihedral  :  4.469  18.375   1184
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.93 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.26), residues: 1136
  helix:  0.84 (0.19), residues: 767
  sheet: -2.58 (0.89), residues: 32
  loop : -2.61 (0.35), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  66 
 HIS   0.004   0.002   HIS A 214 
 PHE   0.030   0.002   PHE A 105 
 TYR   0.018   0.002   TYR A  87 
 ARG   0.003   0.000   ARG A 101 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.8844 (tpp) cc_final: 0.8176 (tpp)
REVERT: A  118 LYS cc_start: 0.7977 (tptm) cc_final: 0.7754 (ptmt)
REVERT: A  131 ASP cc_start: 0.8631 (m-30) cc_final: 0.8422 (m-30)
REVERT: A  191 ASN cc_start: 0.8347 (m-40) cc_final: 0.7778 (t0)
REVERT: A  192 ILE cc_start: 0.8983 (mt) cc_final: 0.8633 (mt)
REVERT: A  196 MET cc_start: 0.8658 (mmm) cc_final: 0.8273 (tpp)
REVERT: A  198 ASN cc_start: 0.9063 (m-40) cc_final: 0.8785 (p0)
REVERT: A  208 GLU cc_start: 0.8337 (tp30) cc_final: 0.8091 (tp30)
REVERT: A  212 LYS cc_start: 0.9058 (tptp) cc_final: 0.8600 (tppt)
REVERT: A  216 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8813 (pt0)
REVERT: A  288 PHE cc_start: 0.9148 (m-10) cc_final: 0.8820 (m-10)
REVERT: A  312 MET cc_start: 0.9019 (mmm) cc_final: 0.8480 (mmm)
REVERT: B   53 ASP cc_start: 0.7930 (p0) cc_final: 0.7571 (p0)
REVERT: B   75 MET cc_start: 0.8905 (mmt) cc_final: 0.8664 (mmm)
REVERT: B   98 MET cc_start: 0.9171 (ttm) cc_final: 0.8338 (tpp)
REVERT: B  105 PHE cc_start: 0.8123 (m-10) cc_final: 0.7718 (m-10)
REVERT: B  131 ASP cc_start: 0.8211 (m-30) cc_final: 0.7966 (m-30)
REVERT: B  149 GLU cc_start: 0.8461 (mp0) cc_final: 0.7807 (mp0)
REVERT: B  159 MET cc_start: 0.8766 (mmm) cc_final: 0.8406 (mmm)
REVERT: B  163 TYR cc_start: 0.8774 (m-80) cc_final: 0.8026 (m-80)
REVERT: B  190 ARG cc_start: 0.8965 (mtt180) cc_final: 0.8477 (ptt180)
REVERT: B  191 ASN cc_start: 0.8185 (m-40) cc_final: 0.7881 (t0)
REVERT: B  197 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8519 (tm-30)
REVERT: B  208 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8358 (mm-30)
REVERT: B  212 LYS cc_start: 0.8967 (mttt) cc_final: 0.8640 (tppt)
REVERT: B  261 LEU cc_start: 0.9237 (mt) cc_final: 0.8816 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1468
  time to fit residues: 50.1190
Evaluate side-chains
  199 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    0.0470
   chunk 7 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 45 optimal weight:   30.0000
   chunk 39 optimal weight:   30.0000
   chunk 43 optimal weight:    8.9990
   chunk 29 optimal weight:    0.8980
   chunk 97 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 96 optimal weight:    8.9990
   overall best weight:    1.0680

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 119 GLN ** 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 = 0.3872 r_free = 0.3872 target = 0.110301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.087252 restraints weight = 23135.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.089445 restraints weight = 14877.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.091064 restraints weight = 10581.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.5300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7474  Z= 0.203
  Angle     :  0.617   7.837  10195  Z= 0.325
  Chirality :  0.044   0.188   1284
  Planarity :  0.004   0.046   1327
  Dihedral  :  4.329  21.327   1184
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.84 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.26), residues: 1136
  helix:  0.94 (0.19), residues: 765
  sheet: -2.50 (0.89), residues: 32
  loop : -2.51 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  66 
 HIS   0.004   0.002   HIS A 214 
 PHE   0.033   0.002   PHE B 116 
 TYR   0.016   0.001   TYR A  87 
 ARG   0.002   0.000   ARG B 127 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.8352 (m-30) cc_final: 0.8130 (m-30)
REVERT: A   98 MET cc_start: 0.8925 (tpp) cc_final: 0.8536 (tpp)
REVERT: A  131 ASP cc_start: 0.8546 (m-30) cc_final: 0.8230 (m-30)
REVERT: A  171 LEU cc_start: 0.8820 (mt) cc_final: 0.8612 (mt)
REVERT: A  191 ASN cc_start: 0.8371 (m-40) cc_final: 0.7878 (t0)
REVERT: A  192 ILE cc_start: 0.8986 (mt) cc_final: 0.8598 (mt)
REVERT: A  196 MET cc_start: 0.8685 (mmm) cc_final: 0.8431 (tpp)
REVERT: A  198 ASN cc_start: 0.9083 (m-40) cc_final: 0.8813 (p0)
REVERT: A  208 GLU cc_start: 0.8436 (tp30) cc_final: 0.8166 (tp30)
REVERT: A  212 LYS cc_start: 0.9121 (tptp) cc_final: 0.8412 (tppt)
REVERT: A  216 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8922 (pt0)
REVERT: A  224 GLU cc_start: 0.9231 (mp0) cc_final: 0.9022 (mp0)
REVERT: A  312 MET cc_start: 0.9096 (mmm) cc_final: 0.8503 (mmm)
REVERT: B   53 ASP cc_start: 0.7799 (p0) cc_final: 0.7271 (p0)
REVERT: B   75 MET cc_start: 0.8941 (mmt) cc_final: 0.8663 (mmm)
REVERT: B   98 MET cc_start: 0.9287 (ttm) cc_final: 0.8264 (tpp)
REVERT: B  105 PHE cc_start: 0.8275 (m-10) cc_final: 0.7850 (m-10)
REVERT: B  131 ASP cc_start: 0.8284 (m-30) cc_final: 0.8042 (m-30)
REVERT: B  190 ARG cc_start: 0.8986 (mtt180) cc_final: 0.8445 (ptt180)
REVERT: B  191 ASN cc_start: 0.8236 (m-40) cc_final: 0.7953 (t0)
REVERT: B  197 GLN cc_start: 0.8903 (tm-30) cc_final: 0.8538 (tm-30)
REVERT: B  208 GLU cc_start: 0.8711 (mm-30) cc_final: 0.7877 (tp30)
REVERT: B  261 LEU cc_start: 0.9078 (mt) cc_final: 0.8848 (tp)
REVERT: B  288 PHE cc_start: 0.8884 (m-80) cc_final: 0.8663 (m-80)
REVERT: B  296 ARG cc_start: 0.5625 (ttm170) cc_final: 0.5136 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.1540
  time to fit residues: 54.5201
Evaluate side-chains
  202 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 98 optimal weight:   40.0000
   chunk 46 optimal weight:    0.4980
   chunk 62 optimal weight:    0.4980
   chunk 1 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 HIS
** B 119 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 = 0.3894 r_free = 0.3894 target = 0.111289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.087741 restraints weight = 23124.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.089984 restraints weight = 15139.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.091638 restraints weight = 10889.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.5737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7474  Z= 0.184
  Angle     :  0.618   7.794  10195  Z= 0.325
  Chirality :  0.044   0.165   1284
  Planarity :  0.003   0.038   1327
  Dihedral  :  4.115  18.407   1184
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.49 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.26), residues: 1136
  helix:  1.11 (0.19), residues: 768
  sheet: -2.36 (0.91), residues: 32
  loop : -2.42 (0.36), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B  91 
 HIS   0.006   0.002   HIS A 214 
 PHE   0.023   0.002   PHE A 189 
 TYR   0.022   0.002   TYR A  87 
 ARG   0.002   0.000   ARG B 101 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.8261 (m-30) cc_final: 0.8050 (m-30)
REVERT: A   98 MET cc_start: 0.9034 (tpp) cc_final: 0.8208 (tpp)
REVERT: A  131 ASP cc_start: 0.8544 (m-30) cc_final: 0.8265 (m-30)
REVERT: A  171 LEU cc_start: 0.8813 (mt) cc_final: 0.8547 (mt)
REVERT: A  191 ASN cc_start: 0.8377 (m-40) cc_final: 0.7880 (t0)
REVERT: A  192 ILE cc_start: 0.8948 (mt) cc_final: 0.8576 (mt)
REVERT: A  196 MET cc_start: 0.8616 (mmm) cc_final: 0.8396 (tpp)
REVERT: A  198 ASN cc_start: 0.9070 (m-40) cc_final: 0.8803 (p0)
REVERT: A  212 LYS cc_start: 0.9117 (tptp) cc_final: 0.8629 (tppt)
REVERT: A  216 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8841 (pt0)
REVERT: A  294 LEU cc_start: 0.9466 (tp) cc_final: 0.9264 (tp)
REVERT: A  296 ARG cc_start: 0.5245 (ttt180) cc_final: 0.4973 (ttt180)
REVERT: A  298 LEU cc_start: 0.9266 (mt) cc_final: 0.9000 (mt)
REVERT: A  312 MET cc_start: 0.9004 (mmm) cc_final: 0.8548 (mmm)
REVERT: B   53 ASP cc_start: 0.7831 (p0) cc_final: 0.7509 (p0)
REVERT: B   75 MET cc_start: 0.8967 (mmt) cc_final: 0.8695 (mmm)
REVERT: B   98 MET cc_start: 0.9281 (ttm) cc_final: 0.8263 (tpp)
REVERT: B  105 PHE cc_start: 0.8315 (m-10) cc_final: 0.7846 (m-10)
REVERT: B  130 TYR cc_start: 0.8639 (t80) cc_final: 0.8427 (t80)
REVERT: B  131 ASP cc_start: 0.8314 (m-30) cc_final: 0.8103 (m-30)
REVERT: B  149 GLU cc_start: 0.8644 (mp0) cc_final: 0.7867 (mp0)
REVERT: B  190 ARG cc_start: 0.8988 (mtt180) cc_final: 0.8449 (ptt180)
REVERT: B  191 ASN cc_start: 0.8265 (m-40) cc_final: 0.8001 (t0)
REVERT: B  200 MET cc_start: 0.8807 (ptm) cc_final: 0.8436 (ptt)
REVERT: B  208 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7924 (tp30)
REVERT: B  261 LEU cc_start: 0.9270 (mt) cc_final: 0.8831 (tp)
REVERT: B  288 PHE cc_start: 0.8964 (m-80) cc_final: 0.8686 (m-80)
REVERT: B  296 ARG cc_start: 0.5772 (ttm170) cc_final: 0.5431 (ttt90)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1435
  time to fit residues: 50.0430
Evaluate side-chains
  197 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 103 optimal weight:   20.0000
   chunk 59 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 93 optimal weight:   50.0000
   chunk 22 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 90 optimal weight:   30.0000
   chunk 0 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 HIS
B 119 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.113926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.087940 restraints weight = 23722.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.090320 restraints weight = 15185.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.091981 restraints weight = 10827.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.5939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7474  Z= 0.208
  Angle     :  0.650   8.372  10195  Z= 0.339
  Chirality :  0.044   0.168   1284
  Planarity :  0.003   0.036   1327
  Dihedral  :  4.151  25.037   1184
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.11 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.09 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.26), residues: 1136
  helix:  1.07 (0.19), residues: 769
  sheet: -2.28 (0.93), residues: 32
  loop : -2.34 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  91 
 HIS   0.005   0.001   HIS A 214 
 PHE   0.035   0.002   PHE B 116 
 TYR   0.020   0.002   TYR B  87 
 ARG   0.003   0.000   ARG B 127 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 241
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9160 (m-80) cc_final: 0.8598 (m-80)
REVERT: A   60 ASP cc_start: 0.8267 (m-30) cc_final: 0.7993 (m-30)
REVERT: A   98 MET cc_start: 0.9023 (tpp) cc_final: 0.8578 (tpp)
REVERT: A  131 ASP cc_start: 0.8546 (m-30) cc_final: 0.8251 (m-30)
REVERT: A  171 LEU cc_start: 0.8834 (mt) cc_final: 0.8566 (mt)
REVERT: A  191 ASN cc_start: 0.8346 (m-40) cc_final: 0.7927 (t0)
REVERT: A  192 ILE cc_start: 0.8959 (mt) cc_final: 0.8570 (mt)
REVERT: A  196 MET cc_start: 0.8704 (mmm) cc_final: 0.8204 (tpp)
REVERT: A  198 ASN cc_start: 0.9073 (m-40) cc_final: 0.8770 (p0)
REVERT: A  212 LYS cc_start: 0.9112 (tptp) cc_final: 0.8664 (tppt)
REVERT: A  216 GLU cc_start: 0.9310 (mt-10) cc_final: 0.8947 (pt0)
REVERT: A  294 LEU cc_start: 0.9408 (tp) cc_final: 0.9192 (tp)
REVERT: A  296 ARG cc_start: 0.5277 (ttt180) cc_final: 0.5018 (ttt180)
REVERT: A  298 LEU cc_start: 0.9284 (mt) cc_final: 0.9045 (mt)
REVERT: A  312 MET cc_start: 0.9163 (mmm) cc_final: 0.8625 (mmm)
REVERT: B   53 ASP cc_start: 0.7933 (p0) cc_final: 0.7542 (p0)
REVERT: B   75 MET cc_start: 0.8927 (mmt) cc_final: 0.8662 (mmm)
REVERT: B   98 MET cc_start: 0.9270 (ttm) cc_final: 0.8392 (tpp)
REVERT: B  105 PHE cc_start: 0.8224 (m-10) cc_final: 0.7706 (m-10)
REVERT: B  131 ASP cc_start: 0.8354 (m-30) cc_final: 0.8077 (m-30)
REVERT: B  190 ARG cc_start: 0.8997 (mtt180) cc_final: 0.8515 (ptt180)
REVERT: B  191 ASN cc_start: 0.8288 (m-40) cc_final: 0.8009 (t0)
REVERT: B  197 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8472 (tm-30)
REVERT: B  200 MET cc_start: 0.8761 (ptm) cc_final: 0.8354 (ptt)
REVERT: B  261 LEU cc_start: 0.9261 (mt) cc_final: 0.8834 (tp)
REVERT: B  295 MET cc_start: 0.8200 (tmm) cc_final: 0.7943 (tmm)
REVERT: B  296 ARG cc_start: 0.5814 (ttm170) cc_final: 0.5400 (ttt90)
  outliers start: 1
  outliers final: 0
  residues processed: 242
  average time/residue: 0.1376
  time to fit residues: 48.2559
Evaluate side-chains
  197 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 37 optimal weight:    0.0870
   chunk 109 optimal weight:    8.9990
   chunk 73 optimal weight:    2.9990
   chunk 106 optimal weight:    8.9990
   chunk 105 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0770
   chunk 84 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 89 optimal weight:   30.0000
   chunk 40 optimal weight:    7.9990
   chunk 77 optimal weight:    0.0070
   overall best weight:    0.8338

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

Flipped N/Q/H residues before XYZ refinement:
B 107 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.112252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.088409 restraints weight = 23264.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.090739 restraints weight = 15414.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.092385 restraints weight = 11104.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.6180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7474  Z= 0.194
  Angle     :  0.648   8.500  10195  Z= 0.336
  Chirality :  0.044   0.172   1284
  Planarity :  0.003   0.039   1327
  Dihedral  :  4.062  25.021   1184
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.26), residues: 1136
  helix:  1.11 (0.19), residues: 774
  sheet: -2.75 (0.90), residues: 30
  loop : -2.30 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A  91 
 HIS   0.010   0.002   HIS A 214 
 PHE   0.032   0.002   PHE B 116 
 TYR   0.019   0.001   TYR A  87 
 ARG   0.004   0.000   ARG A 296 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9232 (m-80) cc_final: 0.8657 (m-80)
REVERT: A   98 MET cc_start: 0.9028 (tpp) cc_final: 0.8558 (tpp)
REVERT: A  131 ASP cc_start: 0.8555 (m-30) cc_final: 0.8278 (m-30)
REVERT: A  171 LEU cc_start: 0.8831 (mt) cc_final: 0.8551 (mt)
REVERT: A  191 ASN cc_start: 0.8356 (m-40) cc_final: 0.7941 (t0)
REVERT: A  192 ILE cc_start: 0.8932 (mt) cc_final: 0.8585 (mt)
REVERT: A  198 ASN cc_start: 0.9085 (m-40) cc_final: 0.8726 (p0)
REVERT: A  212 LYS cc_start: 0.9146 (tptp) cc_final: 0.8414 (tppt)
REVERT: A  216 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8858 (pt0)
REVERT: A  294 LEU cc_start: 0.9427 (tp) cc_final: 0.9220 (tp)
REVERT: A  296 ARG cc_start: 0.5227 (ttt180) cc_final: 0.4912 (ttt180)
REVERT: A  298 LEU cc_start: 0.9329 (mt) cc_final: 0.9065 (mt)
REVERT: A  312 MET cc_start: 0.9112 (mmm) cc_final: 0.8571 (mmm)
REVERT: A  323 ASP cc_start: 0.9165 (m-30) cc_final: 0.8793 (m-30)
REVERT: B   53 ASP cc_start: 0.7786 (p0) cc_final: 0.7397 (p0)
REVERT: B   75 MET cc_start: 0.8991 (mmt) cc_final: 0.8734 (mmm)
REVERT: B   98 MET cc_start: 0.9282 (ttm) cc_final: 0.8409 (tpp)
REVERT: B  105 PHE cc_start: 0.8149 (m-10) cc_final: 0.7734 (m-10)
REVERT: B  111 MET cc_start: 0.7423 (ttt) cc_final: 0.7208 (tmm)
REVERT: B  131 ASP cc_start: 0.8425 (m-30) cc_final: 0.8158 (m-30)
REVERT: B  190 ARG cc_start: 0.9012 (mtt180) cc_final: 0.8540 (ptt180)
REVERT: B  191 ASN cc_start: 0.8316 (m-40) cc_final: 0.8060 (t0)
REVERT: B  197 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8506 (tm-30)
REVERT: B  200 MET cc_start: 0.8726 (ptm) cc_final: 0.8377 (ptt)
REVERT: B  229 ARG cc_start: 0.9205 (ttm110) cc_final: 0.8874 (tpp80)
REVERT: B  261 LEU cc_start: 0.9282 (mt) cc_final: 0.8850 (tt)
REVERT: B  288 PHE cc_start: 0.9000 (m-80) cc_final: 0.8739 (m-80)
REVERT: B  295 MET cc_start: 0.8195 (tmm) cc_final: 0.7932 (tmm)
REVERT: B  296 ARG cc_start: 0.5856 (ttm170) cc_final: 0.5423 (ttt90)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.1445
  time to fit residues: 50.4815
Evaluate side-chains
  199 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 100 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 81 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 67 optimal weight:    9.9990
   chunk 36 optimal weight:   50.0000
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 107 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.112724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.090117 restraints weight = 22928.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.092339 restraints weight = 15038.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.093979 restraints weight = 10815.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.6379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7474  Z= 0.196
  Angle     :  0.654   8.562  10195  Z= 0.337
  Chirality :  0.044   0.170   1284
  Planarity :  0.003   0.038   1327
  Dihedral  :  4.025  21.355   1184
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.26), residues: 1136
  helix:  1.13 (0.19), residues: 776
  sheet: -2.66 (0.91), residues: 30
  loop : -2.31 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  91 
 HIS   0.012   0.003   HIS A 214 
 PHE   0.029   0.002   PHE B 116 
 TYR   0.014   0.001   TYR B  87 
 ARG   0.002   0.000   ARG B 229 

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

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

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2272 Ramachandran restraints generated.
    1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9182 (m-80) cc_final: 0.8560 (m-10)
REVERT: A   60 ASP cc_start: 0.8099 (m-30) cc_final: 0.7848 (m-30)
REVERT: A   98 MET cc_start: 0.8983 (tpp) cc_final: 0.8522 (tpp)
REVERT: A  131 ASP cc_start: 0.8527 (m-30) cc_final: 0.8224 (m-30)
REVERT: A  171 LEU cc_start: 0.8789 (mt) cc_final: 0.8530 (mt)
REVERT: A  191 ASN cc_start: 0.8304 (m-40) cc_final: 0.7905 (t0)
REVERT: A  192 ILE cc_start: 0.8869 (mt) cc_final: 0.8487 (mt)
REVERT: A  198 ASN cc_start: 0.9003 (m-40) cc_final: 0.8679 (p0)
REVERT: A  216 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8837 (pt0)
REVERT: A  288 PHE cc_start: 0.8691 (m-10) cc_final: 0.8453 (m-80)
REVERT: A  296 ARG cc_start: 0.5175 (ttt180) cc_final: 0.4889 (ttt180)
REVERT: A  312 MET cc_start: 0.9092 (mmm) cc_final: 0.8585 (mmm)
REVERT: B   53 ASP cc_start: 0.7745 (p0) cc_final: 0.7322 (p0)
REVERT: B   75 MET cc_start: 0.8995 (mmt) cc_final: 0.8710 (mmm)
REVERT: B   98 MET cc_start: 0.9259 (ttm) cc_final: 0.8396 (tpp)
REVERT: B  105 PHE cc_start: 0.8089 (m-10) cc_final: 0.7600 (m-10)
REVERT: B  131 ASP cc_start: 0.8408 (m-30) cc_final: 0.8101 (m-30)
REVERT: B  149 GLU cc_start: 0.8551 (mp0) cc_final: 0.8226 (mp0)
REVERT: B  190 ARG cc_start: 0.9009 (mtt180) cc_final: 0.8537 (ptt180)
REVERT: B  191 ASN cc_start: 0.8261 (m-40) cc_final: 0.8013 (t0)
REVERT: B  200 MET cc_start: 0.8749 (ptm) cc_final: 0.8477 (ptt)
REVERT: B  218 LEU cc_start: 0.9364 (mp) cc_final: 0.8948 (mp)
REVERT: B  228 LYS cc_start: 0.9319 (mttt) cc_final: 0.8996 (tttt)
REVERT: B  261 LEU cc_start: 0.9263 (mt) cc_final: 0.8822 (tt)
REVERT: B  288 PHE cc_start: 0.8937 (m-80) cc_final: 0.8724 (m-80)
REVERT: B  295 MET cc_start: 0.8093 (tmm) cc_final: 0.7843 (tmm)
REVERT: B  296 ARG cc_start: 0.5737 (ttm170) cc_final: 0.5447 (ttt90)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.1408
  time to fit residues: 49.5536
Evaluate side-chains
  197 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 45 optimal weight:   40.0000
   chunk 26 optimal weight:    0.0870
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 110 optimal weight:    0.3980
   chunk 63 optimal weight:    0.0870
   chunk 88 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 113 optimal weight:   30.0000
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.4736

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 107 HIS
B 214 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.114089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.091165 restraints weight = 22768.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.093492 restraints weight = 15054.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.095172 restraints weight = 10873.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.6598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7474  Z= 0.190
  Angle     :  0.654   8.851  10195  Z= 0.334
  Chirality :  0.044   0.216   1284
  Planarity :  0.003   0.039   1327
  Dihedral  :  3.938  18.726   1184
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.49 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.26), residues: 1136
  helix:  1.18 (0.19), residues: 778
  sheet: -2.62 (0.91), residues: 30
  loop : -2.20 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  91 
 HIS   0.009   0.003   HIS A 214 
 PHE   0.024   0.002   PHE B 116 
 TYR   0.011   0.001   TYR A  87 
 ARG   0.003   0.000   ARG A 103 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2447.42 seconds
wall clock time: 43 minutes 1.13 seconds (2581.13 seconds total)