Starting phenix.real_space_refine
on Wed Feb 12 06:19:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uz2_20950/02_2025/6uz2_20950.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uz2_20950/02_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_20950/02_2025/6uz2_20950.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uz2_20950/02_2025/6uz2_20950.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uz2_20950/02_2025/6uz2_20950.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uz2_20950/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.93, 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: 2.16
  Conformation dependent library (CDL) restraints added in 1.2 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: 0.75
  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: 2.47

  Time building geometry restraints manager: 2.46 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:             1.410
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.130
  Find NCS groups from input model:        0.290
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.970
-------------------------------------------------------------------------------
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  : 0.816 
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: 0.1905
  time to fit residues: 63.6726
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  : 0.867 
-------------------------------------------------------------------------------
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 = 0.3855 r_free = 0.3855 target = 0.109667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.085511 restraints weight = 23930.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.087692 restraints weight = 14867.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.089299 restraints weight = 10554.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
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  : 0.842 
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: 0.8354 (m-80) cc_final: 0.7946 (m-80)
REVERT: A   60 ASP cc_start: 0.8818 (m-30) cc_final: 0.8577 (m-30)
REVERT: A   63 VAL cc_start: 0.9251 (p) cc_final: 0.8925 (m)
REVERT: A   98 MET cc_start: 0.8892 (tpp) cc_final: 0.8438 (tpp)
REVERT: A  118 LYS cc_start: 0.8147 (tptm) cc_final: 0.7853 (pttt)
REVERT: A  130 TYR cc_start: 0.8515 (t80) cc_final: 0.8301 (t80)
REVERT: A  131 ASP cc_start: 0.8698 (m-30) cc_final: 0.8372 (m-30)
REVERT: A  159 MET cc_start: 0.9333 (mmm) cc_final: 0.7892 (mmm)
REVERT: A  171 LEU cc_start: 0.9001 (mt) cc_final: 0.8758 (mt)
REVERT: A  196 MET cc_start: 0.8780 (mmm) cc_final: 0.8470 (tpp)
REVERT: A  198 ASN cc_start: 0.9167 (m-40) cc_final: 0.8790 (p0)
REVERT: A  208 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8502 (mm-30)
REVERT: A  212 LYS cc_start: 0.9070 (mttt) cc_final: 0.8700 (tppt)
REVERT: A  216 GLU cc_start: 0.9137 (mt-10) cc_final: 0.8868 (pt0)
REVERT: A  250 ILE cc_start: 0.9586 (mt) cc_final: 0.9351 (tp)
REVERT: A  312 MET cc_start: 0.9083 (mmm) cc_final: 0.8484 (mmm)
REVERT: B   36 LEU cc_start: 0.9249 (mt) cc_final: 0.8801 (tt)
REVERT: B   37 ASN cc_start: 0.9137 (t0) cc_final: 0.8907 (t0)
REVERT: B   54 ASP cc_start: 0.8499 (m-30) cc_final: 0.7736 (m-30)
REVERT: B   98 MET cc_start: 0.9321 (ttm) cc_final: 0.8562 (tpp)
REVERT: B  125 LEU cc_start: 0.8670 (mt) cc_final: 0.7303 (mt)
REVERT: B  159 MET cc_start: 0.9050 (mmm) cc_final: 0.8712 (mmm)
REVERT: B  171 LEU cc_start: 0.9181 (mt) cc_final: 0.8958 (mt)
REVERT: B  190 ARG cc_start: 0.8981 (mtt180) cc_final: 0.8630 (ptt180)
REVERT: B  191 ASN cc_start: 0.8301 (m-40) cc_final: 0.8077 (t0)
REVERT: B  210 MET cc_start: 0.8580 (tpt) cc_final: 0.8260 (ttt)
REVERT: B  214 HIS cc_start: 0.7916 (p-80) cc_final: 0.7533 (p90)
REVERT: B  261 LEU cc_start: 0.9321 (mt) cc_final: 0.8919 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 0.1615
  time to fit residues: 58.9459
Evaluate side-chains
  204 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 7 optimal weight:    2.9990
   chunk 42 optimal weight:   20.0000
   chunk 89 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 35 optimal weight:   30.0000
   chunk 84 optimal weight:    0.6980
   overall best weight:    1.3384

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.111007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.086969 restraints weight = 24058.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.089209 restraints weight = 15118.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.090864 restraints weight = 10718.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.4050

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= 0.220
  Angle     :  0.649   8.272  10195  Z= 0.344
  Chirality :  0.045   0.139   1284
  Planarity :  0.004   0.047   1327
  Dihedral  :  4.905  20.799   1184
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.16 %
    Favored  : 93.75 %
  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: -1.28 (0.24), residues: 1136
  helix:  0.19 (0.18), residues: 751
  sheet: -2.56 (0.98), residues: 27
  loop : -2.93 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  66 
 HIS   0.010   0.003   HIS A 214 
 PHE   0.022   0.002   PHE B 116 
 TYR   0.025   0.002   TYR A  87 
 ARG   0.004   0.001   ARG B 238 

*********************** 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
  249 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.799 
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: 0.8601 (m-30) cc_final: 0.8392 (m-30)
REVERT: A   98 MET cc_start: 0.8965 (tpp) cc_final: 0.8454 (tpp)
REVERT: A  118 LYS cc_start: 0.8071 (tptm) cc_final: 0.7797 (pttt)
REVERT: A  131 ASP cc_start: 0.8815 (m-30) cc_final: 0.8450 (m-30)
REVERT: A  159 MET cc_start: 0.9201 (mmm) cc_final: 0.8706 (mmm)
REVERT: A  196 MET cc_start: 0.8706 (mmm) cc_final: 0.8312 (tpp)
REVERT: A  198 ASN cc_start: 0.9226 (m-40) cc_final: 0.8837 (p0)
REVERT: A  208 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8550 (mm-30)
REVERT: A  212 LYS cc_start: 0.9053 (mttt) cc_final: 0.8619 (tppt)
REVERT: A  216 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8932 (pt0)
REVERT: A  261 LEU cc_start: 0.9545 (mt) cc_final: 0.9321 (mt)
REVERT: A  312 MET cc_start: 0.9187 (mmm) cc_final: 0.8798 (mmm)
REVERT: B   75 MET cc_start: 0.9133 (mmt) cc_final: 0.8839 (mmm)
REVERT: B   98 MET cc_start: 0.9330 (ttm) cc_final: 0.8520 (tpp)
REVERT: B  105 PHE cc_start: 0.8364 (m-10) cc_final: 0.8111 (m-10)
REVERT: B  159 MET cc_start: 0.9003 (mmm) cc_final: 0.7897 (mmm)
REVERT: B  163 TYR cc_start: 0.7658 (m-80) cc_final: 0.6626 (m-80)
REVERT: B  190 ARG cc_start: 0.8959 (mtt180) cc_final: 0.8472 (ptt180)
REVERT: B  191 ASN cc_start: 0.8316 (m-40) cc_final: 0.7964 (t0)
REVERT: B  210 MET cc_start: 0.8409 (tpt) cc_final: 0.8090 (ttt)
REVERT: B  230 PHE cc_start: 0.8277 (m-10) cc_final: 0.7260 (m-10)
REVERT: B  261 LEU cc_start: 0.9352 (mt) cc_final: 0.8949 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1567
  time to fit residues: 54.6752
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  : 0.781 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 92 optimal weight:   50.0000
   chunk 93 optimal weight:   30.0000
   chunk 94 optimal weight:    8.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.115569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.088404 restraints weight = 23653.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.090668 restraints weight = 15175.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.092238 restraints weight = 10876.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.4694

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= 0.202
  Angle     :  0.618   7.564  10195  Z= 0.329
  Chirality :  0.044   0.150   1284
  Planarity :  0.004   0.042   1327
  Dihedral  :  4.546  18.379   1184
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.81 %
    Favored  : 94.10 %
  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: -0.64 (0.26), residues: 1136
  helix:  0.66 (0.19), residues: 757
  sheet: -2.44 (0.99), residues: 27
  loop : -2.67 (0.34), residues: 352

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   0.038   0.002   PHE A 105 
 TYR   0.018   0.002   TYR A 163 
 ARG   0.003   0.001   ARG B 238 

*********************** 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
  253 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 252
  time to evaluate  : 0.815 
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   63 VAL cc_start: 0.9331 (p) cc_final: 0.9048 (m)
REVERT: A   98 MET cc_start: 0.8930 (tpp) cc_final: 0.8242 (tpp)
REVERT: A  105 PHE cc_start: 0.8384 (m-80) cc_final: 0.7624 (m-80)
REVERT: A  117 ASP cc_start: 0.8083 (m-30) cc_final: 0.7525 (t0)
REVERT: A  118 LYS cc_start: 0.7965 (tptm) cc_final: 0.7549 (ptmt)
REVERT: A  131 ASP cc_start: 0.8713 (m-30) cc_final: 0.8493 (m-30)
REVERT: A  159 MET cc_start: 0.9014 (mmm) cc_final: 0.8626 (mmm)
REVERT: A  196 MET cc_start: 0.8665 (mmm) cc_final: 0.8142 (tpp)
REVERT: A  198 ASN cc_start: 0.9132 (m-40) cc_final: 0.8853 (p0)
REVERT: A  210 MET cc_start: 0.8289 (ttt) cc_final: 0.7838 (mmp)
REVERT: A  216 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8898 (pt0)
REVERT: A  296 ARG cc_start: 0.6396 (ttm170) cc_final: 0.5974 (ttm170)
REVERT: A  312 MET cc_start: 0.9149 (mmm) cc_final: 0.8583 (mmm)
REVERT: B   53 ASP cc_start: 0.8088 (p0) cc_final: 0.7839 (p0)
REVERT: B   75 MET cc_start: 0.8967 (mmt) cc_final: 0.8690 (mmm)
REVERT: B   98 MET cc_start: 0.9224 (ttm) cc_final: 0.8288 (tpp)
REVERT: B  105 PHE cc_start: 0.8427 (m-10) cc_final: 0.7947 (m-10)
REVERT: B  111 MET cc_start: 0.7809 (ttm) cc_final: 0.7514 (ttp)
REVERT: B  125 LEU cc_start: 0.9456 (tt) cc_final: 0.9042 (tt)
REVERT: B  131 ASP cc_start: 0.8417 (m-30) cc_final: 0.8152 (m-30)
REVERT: B  149 GLU cc_start: 0.8631 (mp0) cc_final: 0.7997 (mp0)
REVERT: B  159 MET cc_start: 0.8896 (mmm) cc_final: 0.7915 (mmm)
REVERT: B  163 TYR cc_start: 0.8000 (m-80) cc_final: 0.6783 (m-80)
REVERT: B  190 ARG cc_start: 0.8917 (mtt180) cc_final: 0.8408 (ptt180)
REVERT: B  191 ASN cc_start: 0.8225 (m-40) cc_final: 0.7903 (t0)
REVERT: B  257 LEU cc_start: 0.9511 (pp) cc_final: 0.9175 (pp)
REVERT: B  261 LEU cc_start: 0.9284 (mt) cc_final: 0.8885 (tp)
REVERT: B  290 SER cc_start: 0.9326 (p) cc_final: 0.9126 (p)
  outliers start: 1
  outliers final: 0
  residues processed: 252
  average time/residue: 0.1384
  time to fit residues: 50.0884
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  : 0.830 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 113 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   chunk 33 optimal weight:   10.0000
   chunk 72 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 8 optimal weight:    0.0670
   chunk 112 optimal weight:    8.9990
   overall best weight:    0.7118

-------------------------------------------------------------------------------
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 326 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.112643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.089423 restraints weight = 22752.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.091631 restraints weight = 14827.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.093240 restraints weight = 10696.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3578
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.5203

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= 0.190
  Angle     :  0.617   7.618  10195  Z= 0.328
  Chirality :  0.044   0.168   1284
  Planarity :  0.004   0.044   1327
  Dihedral  :  4.361  18.024   1184
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.84 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.26), residues: 1136
  helix:  0.84 (0.19), residues: 774
  sheet: -2.51 (0.90), residues: 32
  loop : -2.62 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  91 
 HIS   0.011   0.003   HIS A 214 
 PHE   0.027   0.002   PHE A 161 
 TYR   0.020   0.002   TYR A 163 
 ARG   0.003   0.000   ARG B 127 

*********************** 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
  248 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.8318 (m-30) cc_final: 0.8115 (m-30)
REVERT: A   63 VAL cc_start: 0.9293 (p) cc_final: 0.8972 (m)
REVERT: A   98 MET cc_start: 0.8939 (tpp) cc_final: 0.8234 (tpp)
REVERT: A  105 PHE cc_start: 0.8363 (m-80) cc_final: 0.7806 (m-10)
REVERT: A  117 ASP cc_start: 0.7958 (m-30) cc_final: 0.7419 (t0)
REVERT: A  191 ASN cc_start: 0.8540 (m-40) cc_final: 0.7935 (t0)
REVERT: A  192 ILE cc_start: 0.8958 (mt) cc_final: 0.8721 (mt)
REVERT: A  196 MET cc_start: 0.8468 (mmm) cc_final: 0.8158 (tpp)
REVERT: A  198 ASN cc_start: 0.9131 (m-40) cc_final: 0.8794 (p0)
REVERT: A  208 GLU cc_start: 0.8405 (tp30) cc_final: 0.8160 (tp30)
REVERT: A  212 LYS cc_start: 0.9120 (tptt) cc_final: 0.8894 (tppt)
REVERT: A  216 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8864 (pt0)
REVERT: A  288 PHE cc_start: 0.9168 (m-10) cc_final: 0.8941 (m-10)
REVERT: A  296 ARG cc_start: 0.6473 (ttm170) cc_final: 0.6008 (ttt180)
REVERT: A  312 MET cc_start: 0.9148 (mmm) cc_final: 0.8601 (mmm)
REVERT: B   53 ASP cc_start: 0.7799 (p0) cc_final: 0.7431 (p0)
REVERT: B   75 MET cc_start: 0.8936 (mmt) cc_final: 0.8730 (mmm)
REVERT: B   98 MET cc_start: 0.9228 (ttm) cc_final: 0.8272 (tpp)
REVERT: B  105 PHE cc_start: 0.8363 (m-10) cc_final: 0.7718 (m-10)
REVERT: B  159 MET cc_start: 0.8834 (mmm) cc_final: 0.8136 (mmm)
REVERT: B  160 MET cc_start: 0.9004 (mmm) cc_final: 0.8800 (mmm)
REVERT: B  163 TYR cc_start: 0.8026 (m-80) cc_final: 0.7210 (m-80)
REVERT: B  190 ARG cc_start: 0.8921 (mtt180) cc_final: 0.8404 (ptt180)
REVERT: B  191 ASN cc_start: 0.8173 (m-40) cc_final: 0.7879 (t0)
REVERT: B  212 LYS cc_start: 0.8891 (mttt) cc_final: 0.8596 (tppt)
REVERT: B  257 LEU cc_start: 0.9511 (pp) cc_final: 0.9201 (pp)
REVERT: B  261 LEU cc_start: 0.9213 (mt) cc_final: 0.8813 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.1478
  time to fit residues: 52.3530
Evaluate side-chains
  204 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 7 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   chunk 39 optimal weight:   30.0000
   chunk 43 optimal weight:   20.0000
   chunk 29 optimal weight:    0.7980
   chunk 97 optimal weight:    5.9990
   chunk 1 optimal weight:    0.1980
   chunk 96 optimal weight:   20.0000
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.116863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.090428 restraints weight = 23079.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.092665 restraints weight = 15184.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.094292 restraints weight = 11051.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.5631

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= 0.185
  Angle     :  0.608   7.898  10195  Z= 0.321
  Chirality :  0.044   0.186   1284
  Planarity :  0.003   0.038   1327
  Dihedral  :  4.190  25.139   1184
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.16
  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: -0.11 (0.26), residues: 1136
  helix:  1.02 (0.19), residues: 767
  sheet: -2.40 (0.91), residues: 32
  loop : -2.43 (0.36), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  66 
 HIS   0.010   0.003   HIS A 214 
 PHE   0.024   0.002   PHE A 161 
 TYR   0.024   0.001   TYR B  87 
 ARG   0.002   0.000   ARG B 101 

*********************** 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  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 VAL cc_start: 0.9233 (p) cc_final: 0.8920 (m)
REVERT: A   98 MET cc_start: 0.8861 (tpp) cc_final: 0.8086 (tpp)
REVERT: A  108 MET cc_start: 0.9137 (mtp) cc_final: 0.8926 (mtm)
REVERT: A  117 ASP cc_start: 0.7946 (m-30) cc_final: 0.7420 (t0)
REVERT: A  131 ASP cc_start: 0.8383 (m-30) cc_final: 0.8107 (m-30)
REVERT: A  191 ASN cc_start: 0.8515 (m-40) cc_final: 0.7941 (t0)
REVERT: A  198 ASN cc_start: 0.9127 (m-40) cc_final: 0.8774 (p0)
REVERT: A  210 MET cc_start: 0.7797 (tpt) cc_final: 0.7285 (tpt)
REVERT: A  216 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8830 (pt0)
REVERT: A  224 GLU cc_start: 0.9207 (mp0) cc_final: 0.9002 (mp0)
REVERT: A  295 MET cc_start: 0.8719 (tpp) cc_final: 0.8301 (tmm)
REVERT: A  296 ARG cc_start: 0.6260 (ttm170) cc_final: 0.5921 (ttt180)
REVERT: A  298 LEU cc_start: 0.9239 (mt) cc_final: 0.9004 (mt)
REVERT: A  312 MET cc_start: 0.9083 (mmm) cc_final: 0.8617 (mmm)
REVERT: B   53 ASP cc_start: 0.7775 (p0) cc_final: 0.7318 (p0)
REVERT: B   75 MET cc_start: 0.8835 (mmt) cc_final: 0.8611 (mmm)
REVERT: B   98 MET cc_start: 0.9126 (ttm) cc_final: 0.8209 (tpp)
REVERT: B  105 PHE cc_start: 0.8192 (m-10) cc_final: 0.7726 (m-10)
REVERT: B  149 GLU cc_start: 0.8544 (mp0) cc_final: 0.7756 (mp0)
REVERT: B  159 MET cc_start: 0.8710 (mmm) cc_final: 0.8354 (mmm)
REVERT: B  163 TYR cc_start: 0.8105 (m-80) cc_final: 0.7564 (m-80)
REVERT: B  190 ARG cc_start: 0.8899 (mtt180) cc_final: 0.8372 (ptt180)
REVERT: B  191 ASN cc_start: 0.8169 (m-40) cc_final: 0.7896 (t0)
REVERT: B  208 GLU cc_start: 0.8294 (tp30) cc_final: 0.7983 (tp30)
REVERT: B  257 LEU cc_start: 0.9462 (pp) cc_final: 0.9167 (pp)
REVERT: B  261 LEU cc_start: 0.9166 (mt) cc_final: 0.8802 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.1575
  time to fit residues: 55.3437
Evaluate side-chains
  207 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 5 optimal weight:    0.2980
   chunk 85 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 98 optimal weight:   30.0000
   chunk 46 optimal weight:   40.0000
   chunk 62 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.117257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.090815 restraints weight = 22866.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.093094 restraints weight = 15089.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.094691 restraints weight = 10932.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.5855

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= 0.193
  Angle     :  0.628   8.041  10195  Z= 0.326
  Chirality :  0.044   0.180   1284
  Planarity :  0.004   0.040   1327
  Dihedral  :  4.089  26.270   1184
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.58 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    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:  0.03 (0.26), residues: 1136
  helix:  1.11 (0.19), residues: 767
  sheet: -2.32 (0.93), residues: 32
  loop : -2.35 (0.36), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  91 
 HIS   0.006   0.002   HIS A 214 
 PHE   0.037   0.002   PHE B 116 
 TYR   0.016   0.001   TYR B  87 
 ARG   0.002   0.000   ARG A 229 

*********************** 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
  240 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   63 VAL cc_start: 0.9172 (p) cc_final: 0.8897 (m)
REVERT: A   98 MET cc_start: 0.8915 (tpp) cc_final: 0.8162 (tpp)
REVERT: A  117 ASP cc_start: 0.8060 (m-30) cc_final: 0.7472 (t0)
REVERT: A  131 ASP cc_start: 0.8498 (m-30) cc_final: 0.8156 (m-30)
REVERT: A  191 ASN cc_start: 0.8445 (m-40) cc_final: 0.7919 (t0)
REVERT: A  198 ASN cc_start: 0.9147 (m-40) cc_final: 0.8752 (p0)
REVERT: A  212 LYS cc_start: 0.9085 (tptt) cc_final: 0.8859 (tppt)
REVERT: A  224 GLU cc_start: 0.9208 (mp0) cc_final: 0.9003 (mp0)
REVERT: A  268 TYR cc_start: 0.7892 (t80) cc_final: 0.7686 (t80)
REVERT: A  288 PHE cc_start: 0.9066 (m-10) cc_final: 0.8592 (m-10)
REVERT: A  294 LEU cc_start: 0.9393 (tp) cc_final: 0.9187 (tp)
REVERT: A  296 ARG cc_start: 0.6447 (ttm170) cc_final: 0.6001 (ttt180)
REVERT: A  312 MET cc_start: 0.8978 (mmm) cc_final: 0.8478 (mmm)
REVERT: B   53 ASP cc_start: 0.7867 (p0) cc_final: 0.7449 (p0)
REVERT: B   75 MET cc_start: 0.8925 (mmt) cc_final: 0.8618 (mmm)
REVERT: B   98 MET cc_start: 0.9223 (ttm) cc_final: 0.8262 (tpp)
REVERT: B  105 PHE cc_start: 0.8264 (m-10) cc_final: 0.7769 (m-10)
REVERT: B  133 GLU cc_start: 0.9003 (tp30) cc_final: 0.8776 (mm-30)
REVERT: B  163 TYR cc_start: 0.8335 (m-80) cc_final: 0.8006 (m-80)
REVERT: B  190 ARG cc_start: 0.8949 (mtt180) cc_final: 0.8399 (ptt180)
REVERT: B  191 ASN cc_start: 0.8205 (m-40) cc_final: 0.7918 (t0)
REVERT: B  257 LEU cc_start: 0.9520 (pp) cc_final: 0.9197 (pp)
REVERT: B  261 LEU cc_start: 0.9258 (mt) cc_final: 0.8852 (tp)
REVERT: B  295 MET cc_start: 0.8209 (tmm) cc_final: 0.7950 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1419
  time to fit residues: 49.0789
Evaluate side-chains
  204 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
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:    0.0070
   chunk 103 optimal weight:   30.0000
   chunk 59 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 93 optimal weight:   50.0000
   chunk 22 optimal weight:    0.9980
   chunk 58 optimal weight:    0.1980
   chunk 90 optimal weight:   30.0000
   chunk 0 optimal weight:    5.9990
   chunk 87 optimal weight:    0.6980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3950 r_free = 0.3950 target = 0.117956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.091815 restraints weight = 22693.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.093985 restraints weight = 15485.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.095590 restraints weight = 11469.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.6181

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= 0.188
  Angle     :  0.642   7.796  10195  Z= 0.334
  Chirality :  0.045   0.213   1284
  Planarity :  0.004   0.042   1327
  Dihedral  :  4.046  29.715   1184
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.31 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  2.00 %
    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:  0.12 (0.26), residues: 1136
  helix:  1.15 (0.19), residues: 773
  sheet: -2.22 (0.93), residues: 32
  loop : -2.30 (0.36), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  66 
 HIS   0.006   0.002   HIS A 214 
 PHE   0.045   0.002   PHE B 230 
 TYR   0.012   0.001   TYR A  87 
 ARG   0.003   0.000   ARG A 190 

*********************** 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
  253 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 252
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9194 (m-80) cc_final: 0.8523 (m-10)
REVERT: A   63 VAL cc_start: 0.9193 (p) cc_final: 0.8948 (m)
REVERT: A   98 MET cc_start: 0.9019 (tpp) cc_final: 0.8684 (tpp)
REVERT: A  117 ASP cc_start: 0.8034 (m-30) cc_final: 0.7504 (t0)
REVERT: A  131 ASP cc_start: 0.8480 (m-30) cc_final: 0.8130 (m-30)
REVERT: A  191 ASN cc_start: 0.8476 (m-40) cc_final: 0.8017 (t0)
REVERT: A  192 ILE cc_start: 0.8936 (mt) cc_final: 0.8706 (mt)
REVERT: A  198 ASN cc_start: 0.9125 (m-40) cc_final: 0.8704 (p0)
REVERT: A  212 LYS cc_start: 0.9098 (tptt) cc_final: 0.8853 (tppt)
REVERT: A  216 GLU cc_start: 0.9359 (mt-10) cc_final: 0.8854 (pt0)
REVERT: A  288 PHE cc_start: 0.9103 (m-10) cc_final: 0.8696 (m-10)
REVERT: A  295 MET cc_start: 0.8568 (tpp) cc_final: 0.8156 (tmm)
REVERT: A  296 ARG cc_start: 0.6424 (ttm170) cc_final: 0.6061 (ttt180)
REVERT: A  312 MET cc_start: 0.9124 (mmm) cc_final: 0.8620 (mmm)
REVERT: B   53 ASP cc_start: 0.7664 (p0) cc_final: 0.7363 (p0)
REVERT: B   75 MET cc_start: 0.9018 (mmt) cc_final: 0.8808 (mmm)
REVERT: B   98 MET cc_start: 0.9316 (ttm) cc_final: 0.8293 (tpp)
REVERT: B  105 PHE cc_start: 0.8159 (m-10) cc_final: 0.7905 (m-10)
REVERT: B  111 MET cc_start: 0.7143 (ttt) cc_final: 0.6248 (tmm)
REVERT: B  125 LEU cc_start: 0.9451 (tt) cc_final: 0.9204 (mt)
REVERT: B  131 ASP cc_start: 0.8390 (m-30) cc_final: 0.8122 (m-30)
REVERT: B  158 ILE cc_start: 0.8530 (mm) cc_final: 0.8328 (mm)
REVERT: B  190 ARG cc_start: 0.8958 (mtt180) cc_final: 0.8413 (ptt180)
REVERT: B  191 ASN cc_start: 0.8272 (m-40) cc_final: 0.8033 (t0)
REVERT: B  218 LEU cc_start: 0.9437 (mp) cc_final: 0.9057 (mp)
REVERT: B  228 LYS cc_start: 0.9333 (mttt) cc_final: 0.9007 (tttt)
REVERT: B  257 LEU cc_start: 0.9548 (pp) cc_final: 0.9235 (pp)
REVERT: B  261 LEU cc_start: 0.9296 (mt) cc_final: 0.8863 (tp)
REVERT: B  288 PHE cc_start: 0.8917 (m-80) cc_final: 0.8622 (m-80)
REVERT: B  295 MET cc_start: 0.8134 (tmm) cc_final: 0.7869 (tmm)
REVERT: B  296 ARG cc_start: 0.4685 (ttm170) cc_final: 0.4214 (tmt170)
  outliers start: 1
  outliers final: 0
  residues processed: 253
  average time/residue: 0.1474
  time to fit residues: 53.7078
Evaluate side-chains
  210 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 109 optimal weight:   50.0000
   chunk 73 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 95 optimal weight:   20.0000
   chunk 84 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 89 optimal weight:   20.0000
   chunk 40 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 ** 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 = 0.3853 r_free = 0.3853 target = 0.110775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.084735 restraints weight = 24216.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.086878 restraints weight = 15644.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.088407 restraints weight = 11261.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.5844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7474  Z= 0.323
  Angle     :  0.756   8.838  10195  Z= 0.401
  Chirality :  0.047   0.251   1284
  Planarity :  0.004   0.051   1327
  Dihedral  :  4.496  23.468   1184
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.81 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.91 %
    Favored  : 99.09 %
  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: -0.38 (0.26), residues: 1136
  helix:  0.78 (0.19), residues: 776
  sheet: -3.23 (0.83), residues: 25
  loop : -2.46 (0.35), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.003   TRP B  91 
 HIS   0.003   0.002   HIS A 214 
 PHE   0.031   0.003   PHE B 230 
 TYR   0.017   0.002   TYR B  83 
 ARG   0.004   0.001   ARG A 101 

*********************** 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
  235 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 ASP cc_start: 0.8204 (m-30) cc_final: 0.7931 (m-30)
REVERT: A   98 MET cc_start: 0.8827 (tpp) cc_final: 0.8332 (tpp)
REVERT: A  131 ASP cc_start: 0.8642 (m-30) cc_final: 0.8263 (m-30)
REVERT: A  191 ASN cc_start: 0.8413 (m-40) cc_final: 0.7934 (t0)
REVERT: A  198 ASN cc_start: 0.9106 (m-40) cc_final: 0.8694 (p0)
REVERT: A  208 GLU cc_start: 0.8421 (tp30) cc_final: 0.8219 (tp30)
REVERT: A  212 LYS cc_start: 0.9177 (tptt) cc_final: 0.8726 (tppt)
REVERT: A  216 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8792 (pt0)
REVERT: A  288 PHE cc_start: 0.8973 (m-10) cc_final: 0.8546 (m-10)
REVERT: A  312 MET cc_start: 0.9052 (mmm) cc_final: 0.8644 (mmm)
REVERT: B   53 ASP cc_start: 0.7867 (p0) cc_final: 0.7488 (p0)
REVERT: B   75 MET cc_start: 0.8909 (mmt) cc_final: 0.8703 (mmm)
REVERT: B   98 MET cc_start: 0.9184 (ttm) cc_final: 0.8277 (tpp)
REVERT: B  105 PHE cc_start: 0.8289 (m-10) cc_final: 0.7455 (m-10)
REVERT: B  111 MET cc_start: 0.7511 (ttt) cc_final: 0.6497 (tmm)
REVERT: B  190 ARG cc_start: 0.9040 (mtt180) cc_final: 0.8556 (ptt180)
REVERT: B  191 ASN cc_start: 0.8327 (m-40) cc_final: 0.8007 (t0)
REVERT: B  214 HIS cc_start: 0.8041 (t70) cc_final: 0.7819 (t-90)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.1450
  time to fit residues: 49.1627
Evaluate side-chains
  192 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 10 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0870
   chunk 39 optimal weight:    7.9990
   chunk 87 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9980
   chunk 67 optimal weight:    8.9990
   chunk 36 optimal weight:   50.0000
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.7158

-------------------------------------------------------------------------------
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 214 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.115049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.089071 restraints weight = 23090.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.091336 restraints weight = 15043.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.092940 restraints weight = 10770.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.6254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7474  Z= 0.212
  Angle     :  0.707   9.091  10195  Z= 0.364
  Chirality :  0.045   0.224   1284
  Planarity :  0.004   0.039   1327
  Dihedral  :  4.226  20.987   1184
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.75 %
    Favored  : 95.16 %
  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:  0.98 (0.19), residues: 779
  sheet: -2.67 (0.91), residues: 30
  loop : -2.34 (0.37), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  91 
 HIS   0.009   0.003   HIS A 214 
 PHE   0.030   0.003   PHE B 116 
 TYR   0.011   0.001   TYR A 268 
 ARG   0.003   0.001   ARG A 101 

********************** 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
  239 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 PHE cc_start: 0.9106 (m-80) cc_final: 0.8630 (m-80)
REVERT: A   98 MET cc_start: 0.8819 (tpp) cc_final: 0.8286 (tpp)
REVERT: A  131 ASP cc_start: 0.8455 (m-30) cc_final: 0.8140 (m-30)
REVERT: A  191 ASN cc_start: 0.8320 (m-40) cc_final: 0.7913 (t0)
REVERT: A  198 ASN cc_start: 0.9015 (m-40) cc_final: 0.8639 (p0)
REVERT: A  211 LEU cc_start: 0.9544 (mt) cc_final: 0.9316 (mt)
REVERT: A  212 LYS cc_start: 0.9092 (tptt) cc_final: 0.8775 (tppt)
REVERT: A  216 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8854 (pt0)
REVERT: A  288 PHE cc_start: 0.8904 (m-10) cc_final: 0.8448 (m-10)
REVERT: A  312 MET cc_start: 0.9081 (mmm) cc_final: 0.8549 (mmm)
REVERT: B   53 ASP cc_start: 0.7705 (p0) cc_final: 0.7269 (p0)
REVERT: B   98 MET cc_start: 0.9176 (ttm) cc_final: 0.8161 (tpp)
REVERT: B  105 PHE cc_start: 0.8047 (m-10) cc_final: 0.7560 (m-10)
REVERT: B  111 MET cc_start: 0.7115 (ttt) cc_final: 0.6895 (tmm)
REVERT: B  117 ASP cc_start: 0.8535 (m-30) cc_final: 0.8212 (p0)
REVERT: B  130 TYR cc_start: 0.8583 (t80) cc_final: 0.8366 (t80)
REVERT: B  131 ASP cc_start: 0.8273 (m-30) cc_final: 0.8010 (m-30)
REVERT: B  190 ARG cc_start: 0.8980 (mtt180) cc_final: 0.8521 (ptt180)
REVERT: B  191 ASN cc_start: 0.8232 (m-40) cc_final: 0.7974 (t0)
REVERT: B  257 LEU cc_start: 0.9515 (pp) cc_final: 0.9178 (pp)
REVERT: B  261 LEU cc_start: 0.9288 (mt) cc_final: 0.8859 (tp)
REVERT: B  296 ARG cc_start: 0.5344 (ttm170) cc_final: 0.4782 (tmt170)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1486
  time to fit residues: 50.4686
Evaluate side-chains
  201 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 45 optimal weight:   40.0000
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 110 optimal weight:    9.9990
   chunk 63 optimal weight:    0.6980
   chunk 88 optimal weight:    0.4980
   chunk 49 optimal weight:    0.7980
   chunk 113 optimal weight:   30.0000
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 ** 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 = 0.3912 r_free = 0.3912 target = 0.112470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.088445 restraints weight = 22757.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.090779 restraints weight = 14987.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.092471 restraints weight = 10789.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.6437

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= 0.202
  Angle     :  0.689   8.346  10195  Z= 0.357
  Chirality :  0.046   0.213   1284
  Planarity :  0.004   0.042   1327
  Dihedral  :  4.108  20.283   1184
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.84 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  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:  0.03 (0.26), residues: 1136
  helix:  1.08 (0.19), residues: 780
  sheet: -2.61 (0.92), residues: 30
  loop : -2.34 (0.37), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  66 
 HIS   0.012   0.004   HIS B 214 
 PHE   0.028   0.002   PHE B 116 
 TYR   0.013   0.001   TYR A 268 
 ARG   0.008   0.001   ARG A  61 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2366.86 seconds
wall clock time: 42 minutes 55.40 seconds (2575.40 seconds total)