Starting phenix.real_space_refine
on Sat Aug 23 03:41:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hco_34660/08_2025/8hco_34660_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hco_34660/08_2025/8hco_34660.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hco_34660/08_2025/8hco_34660_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hco_34660/08_2025/8hco_34660_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hco_34660/08_2025/8hco_34660.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hco_34660/08_2025/8hco_34660.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 69 atoms to isotropic.
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      29      5.16       5
     C    5966      2.51       5
     N    1568      2.21       5
     O    1767      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9330
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 2507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 326, 2507
          Classifications: {'peptide': 326}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 11, 'TRANS': 314}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 387
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
    Chain: "C"
      Number of atoms: 303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 303
          Classifications: {'peptide': 37}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 267
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 3, 'TRANS': 31}
    Chain: "E"
      Number of atoms: 295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 295
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 4, 'TRANS': 31}
    Chain: "G"
      Number of atoms: 458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 458
          Classifications: {'peptide': 61}
          Link IDs: {'PTRANS': 4, 'TRANS': 56}
    Chain: "G"
      Number of atoms: 1333
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 163, 1332
          Unusual residues: {'GYS': 1}
          Classifications: {'peptide': 162, 'undetermined': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 155, None: 1}
            Not linked:
              pdbres="GYS G 344 "
              pdbres="VAL G 346 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'GYS:plan-3': 1}
          Unresolved non-hydrogen planarities: 1
      Conformer: "B"
        Number of residues, atoms: 163, 1332
          Unusual residues: {'GYS': 1}
          Classifications: {'peptide': 162, 'undetermined': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 155, None: 1}
            Not linked:
              pdbres="GYS G 344 "
              pdbres="VAL G 346 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'GYS:plan-3': 1}
          Unresolved non-hydrogen planarities: 1
          bond proxies already assigned to first conformer: 1361
    Chain: "I"
      Number of atoms: 2528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 329, 2528
          Classifications: {'peptide': 329}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 316}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "J"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 387
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
    Chain: "K"
      Number of atoms: 303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 303
          Classifications: {'peptide': 37}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "L"
      Number of atoms: 267
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 267
          Classifications: {'peptide': 35}
          Link IDs: {'PTRANS': 3, 'TRANS': 31}
    Chain: "M"
      Number of atoms: 295
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 36, 295
          Classifications: {'peptide': 36}
          Link IDs: {'PTRANS': 4, 'TRANS': 31}
  Time building chain proxies: 2.51, per 1000 atoms: 0.27
  Number of scatterers: 9330
  At special positions: 0
  Unit cell: (98.44, 133.75, 120.91, 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      29     16.00
     O    1767      8.00
     N    1568      7.00
     C    5966      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 additional links: simple=2, symmetry=0
    Simple link:   pdb=" C   GYS G 344 " - pdb=" N   VAL G 346 "
    Simple link:   pdb=" C   PHE G 342 " - pdb=" N   GYS G 344 "
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 346.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2212

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 4 sheets defined
      26.0% alpha, 35.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 56
      removed outlier: 4.378A  pdb=" N   GLN A  53 " --> pdb=" O   HIS A  49 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   SER A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   GLU A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 72
    Processing helix  chain 'A' and resid 133 through 135
      No H-bonds generated for 'chain 'A' and resid 133 through 135'
    Processing helix  chain 'A' and resid 364 through 372
      removed outlier: 3.672A  pdb=" N   GLN A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 135
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'C' and resid 14 through 48
      Proline residue:  C  39  - end of helix
    Processing helix  chain 'D' and resid 30 through 50
    Processing helix  chain 'D' and resid 51 through 58
      removed outlier: 3.588A  pdb=" N   ASP D  55 " --> pdb=" O   SER D  51 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27 through 42
      removed outlier: 3.848A  pdb=" N   TRP E  32 " --> pdb=" O   ALA E  28 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   ILE E  33 " --> pdb=" O   HIS E  29 " (cutoff:3.500A)
      Proline residue:  E  34  - end of helix
    Processing helix  chain 'E' and resid 49 through 55
    Processing helix  chain 'G' and resid 334 through 340
      removed outlier: 4.840A  pdb=" N   THR G 340 " --> pdb=" O   PRO G 336 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 364 through 372
      removed outlier: 3.651A  pdb=" N   GLN I 372 " --> pdb=" O   LEU I 368 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 87 through 135
      Proline residue:  J 112  - end of helix
    Processing helix  chain 'K' and resid 14 through 48
      Proline residue:  K  39  - end of helix
    Processing helix  chain 'L' and resid 30 through 50
    Processing helix  chain 'L' and resid 51 through 58
      removed outlier: 3.786A  pdb=" N   ASP L  55 " --> pdb=" O   SER L  51 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 31 through 43
      removed outlier: 3.552A  pdb=" N   PHE M  35 " --> pdb=" O   GLY M  31 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   HIS M  43 " --> pdb=" O   LEU M  39 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 49 through 55
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 93
      removed outlier: 6.067A  pdb=" N   PHE A  98 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   CYS A 165 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   THR A 194 " --> pdb=" O   PRO A 185 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LEU A 255 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LEU A 275 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ASP A 319 " --> pdb=" O   LYS A 323 " (cutoff:3.500A)
      removed outlier: 4.648A  pdb=" N   LYS A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'G' and resid 290 through 300
      removed outlier: 3.604A  pdb=" N   VAL G 290 " --> pdb=" O   GLY G 313 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY G 313 " --> pdb=" O   VAL G 290 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL G 294 " --> pdb=" O   GLY G 309 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLY G 309 " --> pdb=" O   VAL G 294 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU G 296 " --> pdb=" O   VAL G 307 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   VAL G 307 " --> pdb=" O   LEU G 296 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLY G 298 " --> pdb=" O   PHE G 305 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   PHE G 305 " --> pdb=" O   GLY G 298 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG G 308 " --> pdb=" O   ILE G 325 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LYS G 323 " --> pdb=" O   GLU G 310 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   VAL G 497 " --> pdb=" O   SER G 486 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER G 486 " --> pdb=" O   VAL G 497 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR G 478 " --> pdb=" O   ALA G 505 " (cutoff:3.500A)
      removed outlier: 5.566A  pdb=" N   ASN G 427 " --> pdb=" O   LYS G 444 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   LYS G 444 " --> pdb=" O   ASN G 427 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   TYR G 429 " --> pdb=" O   ASN G 442 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ILE G 439 " --> pdb=" O   ASN G 463 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   PHE G 443 " --> pdb=" O   HIS G 459 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ALA G 457 " --> pdb=" O   ILE G 445 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   HIS G 447 " --> pdb=" O   GLN G 455 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASP G 458 " --> pdb=" O   SER G 377 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE G 406 " --> pdb=" O   THR G 383 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LYS G 391 " --> pdb=" O   VAL G 398 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   ASN G 399 " --> pdb=" O   PRO G 291 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   LEU G 293 " --> pdb=" O   ASN G 399 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   ILE G 401 " --> pdb=" O   LEU G 293 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   GLU G 295 " --> pdb=" O   ILE G 401 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   LEU G 403 " --> pdb=" O   GLU G 295 " (cutoff:3.500A)
      removed outlier: 6.711A  pdb=" N   ASP G 297 " --> pdb=" O   LEU G 403 " (cutoff:3.500A)
      removed outlier: 8.269A  pdb=" N   GLY G 405 " --> pdb=" O   ASP G 297 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ASP G 299 " --> pdb=" O   GLY G 405 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'I' and resid 85 through 91
      removed outlier: 3.773A  pdb=" N   ALA I 257 " --> pdb=" O   THR I 273 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'I' and resid 279 through 281

    549 hydrogen bonds defined for protein.
    1584 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.66

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1874
        1.33 -     1.45: 2305
        1.45 -     1.57: 5309
        1.57 -     1.69: 1
        1.69 -     1.81: 48
  Bond restraints: 9537
  Sorted by residual:
  bond pdb=" CB1 GYS G 344 "
       pdb=" OG1BGYS G 344 "
    ideal  model  delta    sigma   weight residual
    1.408  1.611 -0.203 2.00e-02 2.50e+03 1.04e+02
  bond pdb=" N   VAL G 339 "
       pdb=" CA  VAL G 339 "
    ideal  model  delta    sigma   weight residual
    1.461  1.503 -0.042 1.17e-02 7.31e+03 1.26e+01
  bond pdb=" N   THR G 340 "
       pdb=" CA  THR G 340 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.05e+01
  bond pdb=" N   MET G 366 "
       pdb=" CA  MET G 366 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.033 1.04e-02 9.25e+03 1.03e+01
  bond pdb=" N   ASN I  95 "
       pdb=" CA  ASN I  95 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 9.20e-03 1.18e+04 9.94e+00
  ... (remaining 9532 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 12595
        2.55 -     5.10: 295
        5.10 -     7.65: 36
        7.65 -    10.20: 10
       10.20 -    12.75: 2
  Bond angle restraints: 12938
  Sorted by residual:
  angle pdb=" N   VAL G 339 "
        pdb=" CA  VAL G 339 "
        pdb=" C   VAL G 339 "
      ideal   model   delta    sigma   weight residual
     110.42  116.05   -5.63 9.60e-01 1.09e+00 3.44e+01
  angle pdb=" C   LYS G 436 "
        pdb=" N   ASN G 437 "
        pdb=" CA  ASN G 437 "
      ideal   model   delta    sigma   weight residual
     121.54  131.47   -9.93 1.91e+00 2.74e-01 2.70e+01
  angle pdb=" N   PRO I  96 "
        pdb=" CA  PRO I  96 "
        pdb=" C   PRO I  96 "
      ideal   model   delta    sigma   weight residual
     112.47  102.27   10.20 2.06e+00 2.36e-01 2.45e+01
  angle pdb=" C   ASN A 133 "
        pdb=" N   ASP A 134 "
        pdb=" CA  ASP A 134 "
      ideal   model   delta    sigma   weight residual
     121.54  130.26   -8.72 1.91e+00 2.74e-01 2.08e+01
  angle pdb=" CA  VAL G 339 "
        pdb=" C   VAL G 339 "
        pdb=" O   VAL G 339 "
      ideal   model   delta    sigma   weight residual
     121.17  116.63    4.54 1.06e+00 8.90e-01 1.84e+01
  ... (remaining 12933 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 5007
       17.86 -    35.73: 448
       35.73 -    53.59: 124
       53.59 -    71.45: 35
       71.45 -    89.31: 5
  Dihedral angle restraints: 5619
    sinusoidal: 2192
      harmonic: 3427
  Sorted by residual:
  dihedral pdb=" CA  THR G 316 "
           pdb=" C   THR G 316 "
           pdb=" N   ASN G 317 "
           pdb=" CA  ASN G 317 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.87   24.13     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  ASN A  95 "
           pdb=" C   ASN A  95 "
           pdb=" N   PRO A  96 "
           pdb=" CA  PRO A  96 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.97   23.03     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  ASN A 133 "
           pdb=" C   ASN A 133 "
           pdb=" N   ASP A 134 "
           pdb=" CA  ASP A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.42  -20.58     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 5616 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1081
       0.058 -    0.117: 274
       0.117 -    0.175: 76
       0.175 -    0.233: 14
       0.233 -    0.292: 5
  Chirality restraints: 1450
  Sorted by residual:
  chirality pdb=" CB  ILE I 106 "
            pdb=" CA  ILE I 106 "
            pdb=" CG1 ILE I 106 "
            pdb=" CG2 ILE I 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CB  ILE I 150 "
            pdb=" CA  ILE I 150 "
            pdb=" CG1 ILE I 150 "
            pdb=" CG2 ILE I 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  PHE I  98 "
            pdb=" N   PHE I  98 "
            pdb=" C   PHE I  98 "
            pdb=" CB  PHE I  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.97e+00
  ... (remaining 1447 not shown)

  Planarity restraints: 1668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB2 GYS G 344 "   -0.013 2.00e-02 2.50e+03   8.89e-02 1.97e+02
        pdb=" CG2 GYS G 344 "   -0.141 2.00e-02 2.50e+03
        pdb=" C1  GYS G 344 "    0.043 2.00e-02 2.50e+03
        pdb=" C2  GYS G 344 "    0.065 2.00e-02 2.50e+03
        pdb=" CA1 GYS G 344 "   -0.024 2.00e-02 2.50e+03
        pdb=" CA2 GYS G 344 "    0.088 2.00e-02 2.50e+03
        pdb=" CA3 GYS G 344 "   -0.186 2.00e-02 2.50e+03
        pdb=" N2  GYS G 344 "    0.072 2.00e-02 2.50e+03
        pdb=" N3  GYS G 344 "    0.055 2.00e-02 2.50e+03
        pdb=" O2  GYS G 344 "    0.041 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR G 337 "    0.024 2.00e-02 2.50e+03   4.88e-02 2.38e+01
        pdb=" C   THR G 337 "   -0.084 2.00e-02 2.50e+03
        pdb=" O   THR G 337 "    0.031 2.00e-02 2.50e+03
        pdb=" N   LEU G 338 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB2 GYS G 344 "    0.028 2.00e-02 2.50e+03   2.40e-02 1.15e+01
        pdb=" CG2 GYS G 344 "    0.007 2.00e-02 2.50e+03
        pdb=" CD1 GYS G 344 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 GYS G 344 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 GYS G 344 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 GYS G 344 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ  GYS G 344 "   -0.023 2.00e-02 2.50e+03
        pdb=" OH  GYS G 344 "    0.046 2.00e-02 2.50e+03
  ... (remaining 1665 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2538
        2.81 -     3.33: 7157
        3.33 -     3.86: 15881
        3.86 -     4.38: 16820
        4.38 -     4.90: 30151
  Nonbonded interactions: 72547
  Sorted by model distance:
  nonbonded pdb=" OG1 THR G 383 "
            pdb=" NZ  LYS G 385 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   ALA B  99 "
            pdb=" OG1 THR B 103 "
     model   vdw
     2.363 3.040
  nonbonded pdb=" O   ALA J  99 "
            pdb=" OG1 THR J 103 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" OG  SER A 238 "
            pdb=" O   TRP A 243 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" O   GLN C  20 "
            pdb=" OG1 THR C  24 "
     model   vdw
     2.380 3.040
  ... (remaining 72542 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 'I' and (resid 49 through 282 or resid 291 through 382))
}
ncs_group {
  reference = chain 'B'
  selection = chain 'J'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'K'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'M'
}

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=0.00 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:             1.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     10.400
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6545
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.203   9539  Z= 0.375
  Angle     :  0.966  12.753  12942  Z= 0.561
  Chirality :  0.060   0.292   1450
  Planarity :  0.008   0.089   1667
  Dihedral  : 15.439  89.313   3405
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers : 10.99 %
    Allowed  : 13.76 %
    Favored  : 75.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.38 (0.21), residues: 1166
  helix: -2.53 (0.18), residues: 308
  sheet: -0.53 (0.22), residues: 479
  loop : -1.83 (0.27), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 315 
 TYR   0.014   0.002   TYR M  30 
 PHE   0.028   0.003   PHE G 342 
 TRP   0.013   0.001   TRP K  42 
 HIS   0.004   0.001   HIS M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00663 ( 9537)
  covalent geometry    : angle       0.96549 (12938)
  hydrogen bonds       : bond        0.13476 (  549)
  hydrogen bonds       : angle       7.71174 ( 1584)
  link_TRANS           : bond        0.00729 (    2)
  link_TRANS           : angle       1.28751 (    4)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  494 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 111
    poor density    : 383
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.8022 (ttm-80) cc_final: 0.7140 (ttm-80)
REVERT: A   69 GLU cc_start: 0.8313 (mp0) cc_final: 0.7726 (mp0)
REVERT: A  120 PHE cc_start: 0.8599 (t80) cc_final: 0.8357 (t80)
REVERT: A  132 ASP cc_start: 0.8517 (m-30) cc_final: 0.8209 (m-30)
REVERT: A  169 GLN cc_start: 0.7818 (mt0) cc_final: 0.7417 (mt0)
REVERT: A  183 LEU cc_start: 0.8856 (tp) cc_final: 0.8502 (tp)
REVERT: A  184 ASN cc_start: 0.8548 (m-40) cc_final: 0.8150 (m110)
REVERT: A  201 PHE cc_start: 0.8760 (t80) cc_final: 0.8559 (t80)
REVERT: A  203 GLN cc_start: 0.7945 (tt0) cc_final: 0.7103 (tt0)
REVERT: A  235 ARG cc_start: 0.8632 (ttt180) cc_final: 0.8132 (ttt180)
REVERT: A  240 LYS cc_start: 0.8096 (ptpt) cc_final: 0.7798 (ttpt)
REVERT: A  249 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8691 (mp)
REVERT: A  250 GLN cc_start: 0.7998 (mm110) cc_final: 0.7688 (tp40)
REVERT: A  314 TYR cc_start: 0.8950 (t80) cc_final: 0.8207 (t80)
REVERT: A  336 LEU cc_start: 0.8848 (tp) cc_final: 0.8579 (tt)
REVERT: A  349 ASN cc_start: 0.8280 (m110) cc_final: 0.7974 (t0)
REVERT: A  369 MET cc_start: 0.7713 (mmm) cc_final: 0.7375 (mmm)
REVERT: B  122 GLN cc_start: 0.8078 (tt0) cc_final: 0.7862 (tp40)
REVERT: C   20 GLN cc_start: 0.8507 (tp40) cc_final: 0.8137 (tp40)
REVERT: D   54 MET cc_start: 0.8329 (tpt) cc_final: 0.7842 (tpp)
REVERT: D   56 MET cc_start: 0.6597 (mtt) cc_final: 0.6147 (mtt)
REVERT: E   49 ASN cc_start: 0.8443 (p0) cc_final: 0.7806 (p0)
REVERT: E   52 ASN cc_start: 0.8864 (t0) cc_final: 0.8426 (t0)
REVERT: G  300 VAL cc_start: 0.5146 (OUTLIER) cc_final: 0.4756 (m)
REVERT: G  338 LEU cc_start: -0.1170 (OUTLIER) cc_final: -0.1792 (mp)
REVERT: G  397 LEU cc_start: -0.0330 (OUTLIER) cc_final: -0.0614 (tm)
REVERT: G  398 VAL cc_start: 0.2215 (t) cc_final: 0.1991 (t)
REVERT: G  447 HIS cc_start: 0.3455 (OUTLIER) cc_final: 0.1647 (m-70)
REVERT: I   74 VAL cc_start: 0.9295 (t) cc_final: 0.8932 (m)
REVERT: I   75 PHE cc_start: 0.8939 (m-80) cc_final: 0.8569 (m-80)
REVERT: I   79 TYR cc_start: 0.8508 (m-80) cc_final: 0.8009 (m-10)
REVERT: I   94 MET cc_start: 0.6299 (tpt) cc_final: 0.5880 (tmm)
REVERT: I  120 PHE cc_start: 0.8463 (t80) cc_final: 0.8003 (t80)
REVERT: I  140 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8054 (ttp-110)
REVERT: I  143 TYR cc_start: 0.8661 (t80) cc_final: 0.7903 (t80)
REVERT: I  179 ASN cc_start: 0.7816 (t0) cc_final: 0.7508 (t0)
REVERT: I  181 LYS cc_start: 0.9231 (ptpp) cc_final: 0.8870 (ptmt)
REVERT: I  183 LEU cc_start: 0.8940 (tp) cc_final: 0.8583 (tp)
REVERT: I  184 ASN cc_start: 0.9088 (m-40) cc_final: 0.8707 (m-40)
REVERT: I  187 PHE cc_start: 0.7021 (m-80) cc_final: 0.5502 (p90)
REVERT: I  198 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.8810 (t)
REVERT: I  211 LEU cc_start: 0.9050 (tp) cc_final: 0.8838 (mm)
REVERT: I  227 ASP cc_start: 0.8182 (m-30) cc_final: 0.7500 (t0)
REVERT: I  297 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8855 (p)
REVERT: I  310 ARG cc_start: 0.8120 (ptp90) cc_final: 0.7356 (ptm-80)
REVERT: I  324 VAL cc_start: 0.9259 (t) cc_final: 0.9017 (p)
REVERT: I  359 PHE cc_start: 0.8440 (t80) cc_final: 0.8058 (t80)
REVERT: I  375 ASP cc_start: 0.7520 (t0) cc_final: 0.6715 (t0)
REVERT: J   89 ARG cc_start: 0.5330 (tpt90) cc_final: 0.3900 (mtt90)
REVERT: K   22 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7575 (tp30)
REVERT: K   30 TYR cc_start: 0.6043 (m-10) cc_final: 0.5831 (t80)
REVERT: L   55 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7471 (m-30)
REVERT: L   56 MET cc_start: 0.6355 (mtt) cc_final: 0.5759 (mtp)
REVERT: M   32 TRP cc_start: 0.8257 (t-100) cc_final: 0.7850 (t-100)
REVERT: M   35 PHE cc_start: 0.8328 (t80) cc_final: 0.7811 (t80)
REVERT: M   49 ASN cc_start: 0.8231 (p0) cc_final: 0.7546 (p0)
  outliers start: 111
  outliers final: 29
  residues processed: 443
  average time/residue: 0.0880
  time to fit residues: 55.3980
Evaluate side-chains
  315 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 277
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.0970
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.4582

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 ASN
G 317 ASN
I  67 ASN
I  89 ASN
I 276 GLN
L  38 ASN
M  52 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.165013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.122430 restraints weight = 16648.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.121970 restraints weight = 9952.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.123779 restraints weight = 7816.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.124295 restraints weight = 5514.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.124142 restraints weight = 5046.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3515
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3515 r_free = 0.3515    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3515 r_free = 0.3515    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3515
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   9539  Z= 0.212
  Angle     :  0.682   7.021  12942  Z= 0.356
  Chirality :  0.046   0.169   1450
  Planarity :  0.005   0.051   1667
  Dihedral  :  5.056  44.212   1252
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  4.26 %
    Favored  : 95.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.08 (0.23), residues: 1166
  helix:  0.07 (0.26), residues: 299
  sheet: -0.65 (0.22), residues: 513
  loop : -1.19 (0.31), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 219 
 TYR   0.015   0.002   TYR G 478 
 PHE   0.013   0.001   PHE I  80 
 TRP   0.021   0.002   TRP A 243 
 HIS   0.006   0.001   HIS G 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 9537)
  covalent geometry    : angle       0.68202 (12938)
  hydrogen bonds       : bond        0.03847 (  549)
  hydrogen bonds       : angle       6.00229 ( 1584)
  link_TRANS           : bond        0.00432 (    2)
  link_TRANS           : angle       0.79012 (    4)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 319
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 GLU cc_start: 0.8183 (mp0) cc_final: 0.7953 (mp0)
REVERT: A  111 LEU cc_start: 0.9673 (mm) cc_final: 0.9383 (mm)
REVERT: A  169 GLN cc_start: 0.7863 (mt0) cc_final: 0.7426 (mt0)
REVERT: A  219 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7425 (tpp80)
REVERT: A  240 LYS cc_start: 0.7882 (ptpt) cc_final: 0.7642 (ttpt)
REVERT: A  259 LEU cc_start: 0.9360 (tp) cc_final: 0.9071 (tp)
REVERT: A  298 GLU cc_start: 0.8706 (tp30) cc_final: 0.8458 (tp30)
REVERT: A  339 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9102 (pp)
REVERT: A  349 ASN cc_start: 0.8520 (m110) cc_final: 0.8110 (t0)
REVERT: A  369 MET cc_start: 0.7998 (mmm) cc_final: 0.7684 (mmm)
REVERT: C   20 GLN cc_start: 0.8645 (tp40) cc_final: 0.8367 (tp40)
REVERT: C   23 LYS cc_start: 0.9039 (mttt) cc_final: 0.8560 (tptt)
REVERT: C   24 THR cc_start: 0.9276 (m) cc_final: 0.9015 (m)
REVERT: E   49 ASN cc_start: 0.8388 (p0) cc_final: 0.7840 (p0)
REVERT: G  366 MET cc_start: 0.1181 (mmm) cc_final: -0.0261 (mtp)
REVERT: I   75 PHE cc_start: 0.8833 (m-80) cc_final: 0.8553 (m-80)
REVERT: I   79 TYR cc_start: 0.8152 (m-80) cc_final: 0.7722 (m-80)
REVERT: I  130 ASN cc_start: 0.8322 (t0) cc_final: 0.8064 (t0)
REVERT: I  132 ASP cc_start: 0.7996 (m-30) cc_final: 0.7788 (m-30)
REVERT: I  150 ILE cc_start: 0.9326 (tp) cc_final: 0.9067 (mt)
REVERT: I  179 ASN cc_start: 0.8209 (t0) cc_final: 0.7957 (t0)
REVERT: I  181 LYS cc_start: 0.9168 (ptpp) cc_final: 0.8843 (ptmt)
REVERT: I  227 ASP cc_start: 0.8499 (m-30) cc_final: 0.7931 (t0)
REVERT: I  310 ARG cc_start: 0.8081 (ptp90) cc_final: 0.7487 (ptm-80)
REVERT: I  359 PHE cc_start: 0.8569 (t80) cc_final: 0.8154 (t80)
REVERT: J   89 ARG cc_start: 0.5745 (tpt90) cc_final: 0.4038 (mtt90)
REVERT: J  121 GLN cc_start: 0.7632 (mm110) cc_final: 0.7143 (mt0)
REVERT: K   22 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7852 (tp30)
  outliers start: 2
  outliers final: 1
  residues processed: 320
  average time/residue: 0.0794
  time to fit residues: 36.9768
Evaluate side-chains
  276 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 274
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0040
   chunk 90 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0670
   chunk 52 optimal weight:    0.0980
   chunk 25 optimal weight:    0.7980
   chunk 91 optimal weight:    9.9990
   overall best weight:    0.3530

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

Flipped N/Q/H residues before XYZ refinement:
D  38 ASN
** I 276 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 = 0.4138 r_free = 0.4138 target = 0.170132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.123122 restraints weight = 16394.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.126072 restraints weight = 9113.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.127960 restraints weight = 6233.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.128950 restraints weight = 4912.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.129782 restraints weight = 4275.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9539  Z= 0.117
  Angle     :  0.597   7.549  12942  Z= 0.307
  Chirality :  0.043   0.185   1450
  Planarity :  0.004   0.040   1667
  Dihedral  :  4.628  32.694   1252
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.24), residues: 1166
  helix:  1.10 (0.28), residues: 299
  sheet: -0.63 (0.22), residues: 497
  loop : -0.87 (0.31), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG I 140 
 TYR   0.013   0.001   TYR K  30 
 PHE   0.042   0.002   PHE I 201 
 TRP   0.023   0.001   TRP A 243 
 HIS   0.003   0.001   HIS G 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9537)
  covalent geometry    : angle       0.59687 (12938)
  hydrogen bonds       : bond        0.03093 (  549)
  hydrogen bonds       : angle       5.55098 ( 1584)
  link_TRANS           : bond        0.00140 (    2)
  link_TRANS           : angle       0.28551 (    4)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  333 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 333
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8822 (m-80) cc_final: 0.8520 (m-80)
REVERT: A  111 LEU cc_start: 0.9526 (mm) cc_final: 0.9245 (mm)
REVERT: A  156 GLN cc_start: 0.8211 (tp40) cc_final: 0.7983 (tp40)
REVERT: A  169 GLN cc_start: 0.7694 (mt0) cc_final: 0.7227 (mt0)
REVERT: A  217 TYR cc_start: 0.7480 (t80) cc_final: 0.6845 (t80)
REVERT: A  219 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7383 (tpp80)
REVERT: A  259 LEU cc_start: 0.9307 (tp) cc_final: 0.9013 (tp)
REVERT: A  314 TYR cc_start: 0.8716 (t80) cc_final: 0.7970 (t80)
REVERT: A  349 ASN cc_start: 0.8272 (m110) cc_final: 0.8055 (t0)
REVERT: A  357 LEU cc_start: 0.9365 (pt) cc_final: 0.9129 (pt)
REVERT: C   23 LYS cc_start: 0.8924 (mttt) cc_final: 0.8529 (tptt)
REVERT: D   50 GLN cc_start: 0.8148 (mm110) cc_final: 0.7874 (mm110)
REVERT: E   49 ASN cc_start: 0.8251 (p0) cc_final: 0.7831 (p0)
REVERT: I   74 VAL cc_start: 0.9393 (t) cc_final: 0.9170 (m)
REVERT: I  120 PHE cc_start: 0.8588 (t80) cc_final: 0.8307 (t80)
REVERT: I  132 ASP cc_start: 0.7904 (m-30) cc_final: 0.7654 (m-30)
REVERT: I  170 ASP cc_start: 0.7667 (t0) cc_final: 0.7427 (t0)
REVERT: I  179 ASN cc_start: 0.8170 (t0) cc_final: 0.7587 (t0)
REVERT: I  181 LYS cc_start: 0.9040 (ptpp) cc_final: 0.8828 (ptmt)
REVERT: I  227 ASP cc_start: 0.8312 (m-30) cc_final: 0.7968 (t0)
REVERT: I  310 ARG cc_start: 0.7702 (ptp90) cc_final: 0.7462 (ptm-80)
REVERT: I  359 PHE cc_start: 0.8442 (t80) cc_final: 0.7918 (t80)
REVERT: J   89 ARG cc_start: 0.5881 (tpt90) cc_final: 0.4214 (mtt90)
REVERT: J  121 GLN cc_start: 0.7804 (mm110) cc_final: 0.7304 (mt0)
REVERT: K   22 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7557 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 333
  average time/residue: 0.0787
  time to fit residues: 37.7462
Evaluate side-chains
  283 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 101 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 109 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** D  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  29 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.167270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.123602 restraints weight = 16773.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.123477 restraints weight = 10509.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.125467 restraints weight = 7477.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.125994 restraints weight = 5659.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.125934 restraints weight = 5238.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3553
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3553 r_free = 0.3553    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3553
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.3854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9539  Z= 0.150
  Angle     :  0.605   6.497  12942  Z= 0.312
  Chirality :  0.043   0.189   1450
  Planarity :  0.004   0.040   1667
  Dihedral  :  4.522  33.029   1252
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.25), residues: 1166
  helix:  1.48 (0.29), residues: 301
  sheet: -0.53 (0.23), residues: 497
  loop : -0.50 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  85 
 TYR   0.022   0.001   TYR A 307 
 PHE   0.014   0.001   PHE I  80 
 TRP   0.023   0.001   TRP A 243 
 HIS   0.003   0.001   HIS M  25 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 9537)
  covalent geometry    : angle       0.60494 (12938)
  hydrogen bonds       : bond        0.03132 (  549)
  hydrogen bonds       : angle       5.38591 ( 1584)
  link_TRANS           : bond        0.00185 (    2)
  link_TRANS           : angle       0.51669 (    4)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  311 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 311
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8876 (m-80) cc_final: 0.8515 (m-80)
REVERT: A  152 LYS cc_start: 0.9382 (mttt) cc_final: 0.8934 (mttp)
REVERT: A  169 GLN cc_start: 0.7893 (mt0) cc_final: 0.7378 (mt0)
REVERT: A  217 TYR cc_start: 0.7935 (t80) cc_final: 0.7620 (t80)
REVERT: A  219 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7661 (tpp80)
REVERT: A  244 ILE cc_start: 0.9356 (pt) cc_final: 0.8880 (pt)
REVERT: A  259 LEU cc_start: 0.9378 (tp) cc_final: 0.9093 (tp)
REVERT: A  349 ASN cc_start: 0.8452 (m110) cc_final: 0.8116 (t0)
REVERT: A  357 LEU cc_start: 0.9381 (pt) cc_final: 0.9168 (pt)
REVERT: C   40 MET cc_start: 0.8577 (mpp) cc_final: 0.8274 (mpp)
REVERT: E   49 ASN cc_start: 0.8404 (p0) cc_final: 0.7924 (p0)
REVERT: G  366 MET cc_start: 0.1583 (mmm) cc_final: -0.0132 (mtp)
REVERT: G  496 MET cc_start: -0.0435 (mpp) cc_final: -0.1205 (mtp)
REVERT: I  120 PHE cc_start: 0.8687 (t80) cc_final: 0.8314 (t80)
REVERT: I  132 ASP cc_start: 0.7994 (m-30) cc_final: 0.7613 (m-30)
REVERT: I  159 ASP cc_start: 0.6524 (t70) cc_final: 0.6303 (t70)
REVERT: I  179 ASN cc_start: 0.8131 (t0) cc_final: 0.7891 (t0)
REVERT: I  225 PRO cc_start: 0.5639 (Cg_exo) cc_final: 0.5332 (Cg_endo)
REVERT: I  227 ASP cc_start: 0.8617 (m-30) cc_final: 0.8048 (t0)
REVERT: I  310 ARG cc_start: 0.7947 (ptp90) cc_final: 0.7535 (ptm-80)
REVERT: I  341 CYS cc_start: 0.8303 (p) cc_final: 0.8006 (p)
REVERT: J   89 ARG cc_start: 0.5795 (tpt90) cc_final: 0.4109 (mtt90)
REVERT: J  121 GLN cc_start: 0.7720 (mm110) cc_final: 0.7207 (mt0)
REVERT: K   22 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7732 (tp30)
REVERT: M   52 ASN cc_start: 0.8559 (m-40) cc_final: 0.8135 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 311
  average time/residue: 0.0758
  time to fit residues: 34.4566
Evaluate side-chains
  272 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 106 optimal weight:    0.8980
   chunk 112 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 52 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 95 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 86 optimal weight:    5.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
D  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.167044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.122967 restraints weight = 16721.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.123157 restraints weight = 10111.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.124576 restraints weight = 7467.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.125002 restraints weight = 5653.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.124983 restraints weight = 5451.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3528
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3528 r_free = 0.3528    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3528
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9539  Z= 0.145
  Angle     :  0.609   6.542  12942  Z= 0.312
  Chirality :  0.043   0.185   1450
  Planarity :  0.004   0.041   1667
  Dihedral  :  4.445  27.137   1252
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.25), residues: 1166
  helix:  1.66 (0.29), residues: 298
  sheet: -0.32 (0.23), residues: 497
  loop : -0.53 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  85 
 TYR   0.020   0.001   TYR A 307 
 PHE   0.021   0.001   PHE A 120 
 TRP   0.025   0.001   TRP A 243 
 HIS   0.003   0.001   HIS K  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 9537)
  covalent geometry    : angle       0.60866 (12938)
  hydrogen bonds       : bond        0.03069 (  549)
  hydrogen bonds       : angle       5.32071 ( 1584)
  link_TRANS           : bond        0.00156 (    2)
  link_TRANS           : angle       0.40489 (    4)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 320
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 GLN cc_start: 0.7864 (tp40) cc_final: 0.7561 (tp40)
REVERT: A  169 GLN cc_start: 0.7887 (mt0) cc_final: 0.7441 (mt0)
REVERT: A  217 TYR cc_start: 0.7922 (t80) cc_final: 0.7561 (t80)
REVERT: A  219 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7609 (tpp80)
REVERT: A  259 LEU cc_start: 0.9373 (tp) cc_final: 0.9085 (tp)
REVERT: A  261 ARG cc_start: 0.8436 (tpt-90) cc_final: 0.7611 (tpt-90)
REVERT: A  349 ASN cc_start: 0.8437 (m110) cc_final: 0.8109 (t0)
REVERT: C   40 MET cc_start: 0.8540 (mpp) cc_final: 0.8234 (mpp)
REVERT: D   50 GLN cc_start: 0.8297 (mm110) cc_final: 0.8088 (mm110)
REVERT: E   49 ASN cc_start: 0.8296 (p0) cc_final: 0.7798 (p0)
REVERT: G  366 MET cc_start: 0.1683 (mmm) cc_final: -0.0062 (mtp)
REVERT: G  496 MET cc_start: -0.0436 (mpp) cc_final: -0.1440 (mtp)
REVERT: I  120 PHE cc_start: 0.8707 (t80) cc_final: 0.8338 (t80)
REVERT: I  132 ASP cc_start: 0.8073 (m-30) cc_final: 0.7671 (m-30)
REVERT: I  159 ASP cc_start: 0.6683 (t70) cc_final: 0.6446 (t70)
REVERT: I  225 PRO cc_start: 0.5642 (Cg_exo) cc_final: 0.5326 (Cg_endo)
REVERT: I  227 ASP cc_start: 0.8397 (m-30) cc_final: 0.8018 (t0)
REVERT: I  310 ARG cc_start: 0.8024 (ptp90) cc_final: 0.7560 (ptm-80)
REVERT: I  341 CYS cc_start: 0.8290 (p) cc_final: 0.7993 (p)
REVERT: I  359 PHE cc_start: 0.8313 (t80) cc_final: 0.7979 (t80)
REVERT: J  121 GLN cc_start: 0.7751 (mm110) cc_final: 0.7194 (mt0)
REVERT: K   22 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7743 (tp30)
REVERT: M   52 ASN cc_start: 0.8592 (m-40) cc_final: 0.8129 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 320
  average time/residue: 0.0747
  time to fit residues: 35.1664
Evaluate side-chains
  274 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 274
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0770
   chunk 94 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    6.9990
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 ASN ** 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 = 0.4128 r_free = 0.4128 target = 0.168929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.128091 restraints weight = 16595.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.125207 restraints weight = 11099.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.127182 restraints weight = 9470.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.127453 restraints weight = 7076.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.127749 restraints weight = 6219.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3573
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3580
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
r_final: 0.3580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.4249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9539  Z= 0.130
  Angle     :  0.613   8.343  12942  Z= 0.314
  Chirality :  0.044   0.189   1450
  Planarity :  0.004   0.041   1667
  Dihedral  :  4.386  23.103   1252
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.49 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.26), residues: 1166
  helix:  1.63 (0.29), residues: 305
  sheet: -0.26 (0.24), residues: 498
  loop : -0.49 (0.35), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  85 
 TYR   0.027   0.001   TYR K  30 
 PHE   0.029   0.001   PHE E  35 
 TRP   0.030   0.001   TRP A 243 
 HIS   0.003   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9537)
  covalent geometry    : angle       0.61337 (12938)
  hydrogen bonds       : bond        0.03021 (  549)
  hydrogen bonds       : angle       5.27339 ( 1584)
  link_TRANS           : bond        0.00123 (    2)
  link_TRANS           : angle       0.35255 (    4)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 319
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 LYS cc_start: 0.9219 (mttt) cc_final: 0.8644 (mmtp)
REVERT: A  156 GLN cc_start: 0.7841 (tp40) cc_final: 0.7510 (tp40)
REVERT: A  169 GLN cc_start: 0.7735 (mt0) cc_final: 0.7380 (mt0)
REVERT: A  219 ARG cc_start: 0.8246 (tpp80) cc_final: 0.7618 (tpp80)
REVERT: A  259 LEU cc_start: 0.9300 (tp) cc_final: 0.8969 (tp)
REVERT: A  314 TYR cc_start: 0.8721 (t80) cc_final: 0.8043 (t80)
REVERT: A  349 ASN cc_start: 0.8406 (m110) cc_final: 0.8140 (t0)
REVERT: C   27 GLN cc_start: 0.7539 (mm-40) cc_final: 0.7332 (tp40)
REVERT: D   50 GLN cc_start: 0.8234 (mm110) cc_final: 0.8001 (mm110)
REVERT: E   49 ASN cc_start: 0.8158 (p0) cc_final: 0.7713 (p0)
REVERT: G  366 MET cc_start: 0.1421 (mmm) cc_final: -0.0232 (mtp)
REVERT: G  422 ASN cc_start: 0.3595 (p0) cc_final: 0.3375 (p0)
REVERT: G  496 MET cc_start: -0.0225 (mpp) cc_final: -0.1447 (mtp)
REVERT: I  120 PHE cc_start: 0.8659 (t80) cc_final: 0.8446 (t80)
REVERT: I  132 ASP cc_start: 0.8076 (m-30) cc_final: 0.7801 (m-30)
REVERT: I  178 VAL cc_start: 0.9157 (t) cc_final: 0.8885 (m)
REVERT: I  179 ASN cc_start: 0.8021 (t0) cc_final: 0.7780 (t0)
REVERT: I  183 LEU cc_start: 0.9250 (mp) cc_final: 0.9042 (mt)
REVERT: I  208 GLN cc_start: 0.7448 (mm110) cc_final: 0.7226 (mm-40)
REVERT: I  225 PRO cc_start: 0.5485 (Cg_exo) cc_final: 0.5252 (Cg_endo)
REVERT: I  227 ASP cc_start: 0.8248 (m-30) cc_final: 0.8004 (t0)
REVERT: I  310 ARG cc_start: 0.7951 (ptp90) cc_final: 0.7567 (ptm-80)
REVERT: I  341 CYS cc_start: 0.8150 (p) cc_final: 0.7912 (p)
REVERT: I  359 PHE cc_start: 0.8217 (t80) cc_final: 0.7876 (t80)
REVERT: J  121 GLN cc_start: 0.7811 (mm110) cc_final: 0.7271 (mt0)
REVERT: K   22 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7680 (tp30)
REVERT: M   52 ASN cc_start: 0.8573 (m-40) cc_final: 0.8068 (p0)
  outliers start: 1
  outliers final: 1
  residues processed: 319
  average time/residue: 0.0752
  time to fit residues: 35.0398
Evaluate side-chains
  275 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 274
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 29 optimal weight:    0.1980
   chunk 65 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 GLN
D  38 ASN
I 166 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.166636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.124648 restraints weight = 16747.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.123695 restraints weight = 10729.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.124992 restraints weight = 8252.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.125427 restraints weight = 6957.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.125313 restraints weight = 6082.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3534
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3534 r_free = 0.3534    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       43 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3534 r_free = 0.3534    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3534
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.4422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9539  Z= 0.163
  Angle     :  0.637   8.260  12942  Z= 0.324
  Chirality :  0.044   0.185   1450
  Planarity :  0.004   0.041   1667
  Dihedral  :  4.440  23.047   1252
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.26), residues: 1166
  helix:  1.61 (0.29), residues: 304
  sheet: -0.30 (0.24), residues: 497
  loop : -0.40 (0.35), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  85 
 TYR   0.030   0.002   TYR A 307 
 PHE   0.023   0.002   PHE A 359 
 TRP   0.031   0.001   TRP A 243 
 HIS   0.003   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 9537)
  covalent geometry    : angle       0.63675 (12938)
  hydrogen bonds       : bond        0.03150 (  549)
  hydrogen bonds       : angle       5.35441 ( 1584)
  link_TRANS           : bond        0.00147 (    2)
  link_TRANS           : angle       0.35503 (    4)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 317
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLN cc_start: 0.7615 (mt0) cc_final: 0.7256 (mt0)
REVERT: A  217 TYR cc_start: 0.7700 (t80) cc_final: 0.7286 (t80)
REVERT: A  219 ARG cc_start: 0.8337 (tpp80) cc_final: 0.7663 (tpp80)
REVERT: A  259 LEU cc_start: 0.9272 (tp) cc_final: 0.9031 (tp)
REVERT: A  261 ARG cc_start: 0.8403 (tpt-90) cc_final: 0.7720 (tpt-90)
REVERT: A  314 TYR cc_start: 0.8683 (t80) cc_final: 0.8397 (t80)
REVERT: A  349 ASN cc_start: 0.8395 (m110) cc_final: 0.8121 (t0)
REVERT: B  120 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7988 (mm-30)
REVERT: D   49 ILE cc_start: 0.8653 (tt) cc_final: 0.8407 (tt)
REVERT: D   50 GLN cc_start: 0.8420 (mm110) cc_final: 0.8040 (mm110)
REVERT: D   54 MET cc_start: 0.8171 (tpt) cc_final: 0.7902 (tpp)
REVERT: E   46 ASN cc_start: 0.8538 (p0) cc_final: 0.8297 (p0)
REVERT: E   49 ASN cc_start: 0.8137 (p0) cc_final: 0.7706 (p0)
REVERT: G  422 ASN cc_start: 0.3759 (p0) cc_final: 0.3536 (p0)
REVERT: G  496 MET cc_start: -0.0219 (mpp) cc_final: -0.1342 (mtp)
REVERT: I   69 GLU cc_start: 0.8503 (mp0) cc_final: 0.8091 (mp0)
REVERT: I  120 PHE cc_start: 0.8682 (t80) cc_final: 0.8466 (t80)
REVERT: I  225 PRO cc_start: 0.5674 (Cg_exo) cc_final: 0.5079 (Cg_endo)
REVERT: I  227 ASP cc_start: 0.8293 (m-30) cc_final: 0.8083 (t0)
REVERT: I  310 ARG cc_start: 0.7995 (ptp90) cc_final: 0.7602 (ptm-80)
REVERT: I  341 CYS cc_start: 0.8134 (p) cc_final: 0.7918 (p)
REVERT: I  359 PHE cc_start: 0.8161 (t80) cc_final: 0.7882 (t80)
REVERT: J  121 GLN cc_start: 0.7837 (mm110) cc_final: 0.7303 (mt0)
REVERT: K   18 GLN cc_start: 0.7764 (pm20) cc_final: 0.7529 (pm20)
REVERT: K   22 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7779 (tp30)
REVERT: M   52 ASN cc_start: 0.8605 (m-40) cc_final: 0.8074 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 317
  average time/residue: 0.0799
  time to fit residues: 36.9508
Evaluate side-chains
  273 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0770
   chunk 83 optimal weight:    0.6980
   chunk 36 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0970
   chunk 53 optimal weight:    3.9990
   chunk 66 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   overall best weight:    1.3740

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 166 GLN
K  17 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.164880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.123227 restraints weight = 16616.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.120728 restraints weight = 11347.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.122378 restraints weight = 9829.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.123382 restraints weight = 7242.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.123379 restraints weight = 6340.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3517 r_free = 0.3517    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.4565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9539  Z= 0.193
  Angle     :  0.659   7.979  12942  Z= 0.340
  Chirality :  0.045   0.227   1450
  Planarity :  0.004   0.039   1667
  Dihedral  :  4.592  24.389   1252
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.25), residues: 1166
  helix:  1.53 (0.29), residues: 303
  sheet: -0.46 (0.23), residues: 500
  loop : -0.35 (0.35), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 261 
 TYR   0.029   0.002   TYR A 307 
 PHE   0.024   0.002   PHE E  35 
 TRP   0.039   0.002   TRP I 243 
 HIS   0.004   0.001   HIS C  43 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 9537)
  covalent geometry    : angle       0.65880 (12938)
  hydrogen bonds       : bond        0.03311 (  549)
  hydrogen bonds       : angle       5.48542 ( 1584)
  link_TRANS           : bond        0.00181 (    2)
  link_TRANS           : angle       0.37206 (    4)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 305
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ASN cc_start: 0.8125 (t0) cc_final: 0.7778 (t0)
REVERT: A  152 LYS cc_start: 0.9195 (mttt) cc_final: 0.8611 (mttp)
REVERT: A  156 GLN cc_start: 0.7912 (tp40) cc_final: 0.7615 (tp40)
REVERT: A  169 GLN cc_start: 0.7581 (mt0) cc_final: 0.7233 (mt0)
REVERT: A  219 ARG cc_start: 0.8310 (tpp80) cc_final: 0.7076 (tpp80)
REVERT: A  259 LEU cc_start: 0.9359 (tp) cc_final: 0.9045 (tp)
REVERT: A  314 TYR cc_start: 0.8870 (t80) cc_final: 0.7982 (t80)
REVERT: A  323 LYS cc_start: 0.8686 (ttpt) cc_final: 0.8383 (ttpt)
REVERT: A  349 ASN cc_start: 0.8394 (m110) cc_final: 0.8188 (t0)
REVERT: C   27 GLN cc_start: 0.7646 (tp40) cc_final: 0.7297 (tp-100)
REVERT: D   50 GLN cc_start: 0.8408 (mm110) cc_final: 0.8037 (mm110)
REVERT: D   54 MET cc_start: 0.8058 (tpt) cc_final: 0.7764 (tpp)
REVERT: D   56 MET cc_start: 0.7190 (ttm) cc_final: 0.6843 (ttm)
REVERT: E   46 ASN cc_start: 0.8566 (p0) cc_final: 0.8289 (p0)
REVERT: E   49 ASN cc_start: 0.8170 (p0) cc_final: 0.7769 (p0)
REVERT: G  366 MET cc_start: 0.2746 (tpt) cc_final: -0.1378 (mtp)
REVERT: G  422 ASN cc_start: 0.4115 (p0) cc_final: 0.3793 (p0)
REVERT: G  496 MET cc_start: -0.0328 (mpp) cc_final: -0.1484 (mtp)
REVERT: I   69 GLU cc_start: 0.8498 (mp0) cc_final: 0.8065 (mp0)
REVERT: I  120 PHE cc_start: 0.8685 (t80) cc_final: 0.8459 (t80)
REVERT: I  130 ASN cc_start: 0.8591 (t0) cc_final: 0.8322 (t0)
REVERT: I  181 LYS cc_start: 0.8882 (ptpp) cc_final: 0.8624 (ptmt)
REVERT: I  310 ARG cc_start: 0.8123 (ptp90) cc_final: 0.7748 (ptm-80)
REVERT: I  341 CYS cc_start: 0.8211 (p) cc_final: 0.7990 (p)
REVERT: I  359 PHE cc_start: 0.8211 (t80) cc_final: 0.7923 (t80)
REVERT: J   89 ARG cc_start: 0.5828 (tpt90) cc_final: 0.4383 (mtt90)
REVERT: J  121 GLN cc_start: 0.7823 (mm110) cc_final: 0.7388 (mt0)
REVERT: K   22 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7850 (tp30)
REVERT: M   52 ASN cc_start: 0.8618 (m-40) cc_final: 0.8099 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 305
  average time/residue: 0.0808
  time to fit residues: 36.0229
Evaluate side-chains
  255 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 4 optimal weight:    0.6980
   chunk 85 optimal weight:    0.1980
   chunk 63 optimal weight:    7.9990
   chunk 110 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  38 ASN
M  29 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.167654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.124879 restraints weight = 16578.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.124488 restraints weight = 10404.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.126026 restraints weight = 8062.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.126511 restraints weight = 6467.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.126186 restraints weight = 5619.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3550
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3550 r_free = 0.3550    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3550
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7543
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   0.042   9539  Z= 0.129
  Angle     :  0.639   7.577  12942  Z= 0.325
  Chirality :  0.045   0.186   1450
  Planarity :  0.004   0.041   1667
  Dihedral  :  4.367  23.385   1252
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.26), residues: 1166
  helix:  1.68 (0.29), residues: 304
  sheet: -0.28 (0.24), residues: 490
  loop : -0.28 (0.36), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  85 
 TYR   0.019   0.001   TYR A 307 
 PHE   0.021   0.001   PHE A 359 
 TRP   0.030   0.001   TRP A 243 
 HIS   0.006   0.001   HIS M  29 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9537)
  covalent geometry    : angle       0.63938 (12938)
  hydrogen bonds       : bond        0.03015 (  549)
  hydrogen bonds       : angle       5.32834 ( 1584)
  link_TRANS           : bond        0.00095 (    2)
  link_TRANS           : angle       0.26601 (    4)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 0.404 
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   79 TYR cc_start: 0.7911 (m-80) cc_final: 0.7629 (m-10)
REVERT: A  156 GLN cc_start: 0.7832 (tp40) cc_final: 0.7459 (tp40)
REVERT: A  169 GLN cc_start: 0.7617 (mt0) cc_final: 0.7285 (mt0)
REVERT: A  219 ARG cc_start: 0.8255 (tpp80) cc_final: 0.7541 (tpp80)
REVERT: A  244 ILE cc_start: 0.9259 (pt) cc_final: 0.8904 (pt)
REVERT: A  259 LEU cc_start: 0.9262 (tp) cc_final: 0.8966 (tp)
REVERT: A  261 ARG cc_start: 0.8241 (tpt-90) cc_final: 0.7552 (tpt-90)
REVERT: A  323 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8386 (ttpt)
REVERT: C   40 MET cc_start: 0.8440 (mpp) cc_final: 0.8224 (mpp)
REVERT: D   49 ILE cc_start: 0.8420 (tt) cc_final: 0.8175 (mt)
REVERT: D   50 GLN cc_start: 0.8316 (mm110) cc_final: 0.7807 (mm110)
REVERT: D   54 MET cc_start: 0.8162 (tpt) cc_final: 0.7780 (tpp)
REVERT: D   56 MET cc_start: 0.7117 (ttm) cc_final: 0.6801 (ttm)
REVERT: E   46 ASN cc_start: 0.8475 (p0) cc_final: 0.8195 (p0)
REVERT: E   49 ASN cc_start: 0.8095 (p0) cc_final: 0.7669 (p0)
REVERT: G  496 MET cc_start: -0.0384 (mpp) cc_final: -0.1519 (mtp)
REVERT: I   69 GLU cc_start: 0.8492 (mp0) cc_final: 0.8216 (mp0)
REVERT: I  130 ASN cc_start: 0.8382 (t0) cc_final: 0.8150 (t0)
REVERT: I  150 ILE cc_start: 0.9341 (tp) cc_final: 0.9121 (mt)
REVERT: I  181 LYS cc_start: 0.8721 (ptpp) cc_final: 0.8460 (ptmt)
REVERT: I  310 ARG cc_start: 0.7932 (ptp90) cc_final: 0.7582 (ptm-80)
REVERT: I  341 CYS cc_start: 0.8097 (p) cc_final: 0.7860 (p)
REVERT: I  359 PHE cc_start: 0.8097 (t80) cc_final: 0.7780 (t80)
REVERT: J  121 GLN cc_start: 0.7808 (mm110) cc_final: 0.7246 (mt0)
REVERT: K   22 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7831 (tp30)
REVERT: M   52 ASN cc_start: 0.8598 (m-40) cc_final: 0.8071 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 309
  average time/residue: 0.0884
  time to fit residues: 39.5898
Evaluate side-chains
  270 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 59 optimal weight:    6.9990
   chunk 84 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 60 optimal weight:   20.0000
   chunk 62 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 63 optimal weight:    7.9990
   chunk 92 optimal weight:    7.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    3.7788

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 GLN
B  90 ASN
M  29 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.157062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.116389 restraints weight = 17160.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.114056 restraints weight = 12201.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.115141 restraints weight = 9356.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.115793 restraints weight = 7595.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.115927 restraints weight = 6742.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3401
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3401
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.4997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.080   9539  Z= 0.452
  Angle     :  0.914  11.350  12942  Z= 0.477
  Chirality :  0.055   0.327   1450
  Planarity :  0.005   0.045   1667
  Dihedral  :  5.657  37.505   1252
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 18.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.79 (0.25), residues: 1166
  helix:  0.50 (0.28), residues: 304
  sheet: -0.79 (0.23), residues: 508
  loop : -0.68 (0.36), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG I  72 
 TYR   0.021   0.003   TYR A 114 
 PHE   0.032   0.003   PHE A 347 
 TRP   0.045   0.003   TRP I 243 
 HIS   0.010   0.002   HIS C  17 

Details of bonding type rmsd
  covalent geometry    : bond        0.00988 ( 9537)
  covalent geometry    : angle       0.91369 (12938)
  hydrogen bonds       : bond        0.04483 (  549)
  hydrogen bonds       : angle       6.39974 ( 1584)
  link_TRANS           : bond        0.00412 (    2)
  link_TRANS           : angle       0.53558 (    4)

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

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

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2332 Ramachandran restraints generated.
    1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.9095 (m-80) cc_final: 0.8870 (m-80)
REVERT: A  108 SER cc_start: 0.9126 (t) cc_final: 0.8898 (t)
REVERT: A  120 PHE cc_start: 0.8635 (t80) cc_final: 0.8404 (t80)
REVERT: A  130 ASN cc_start: 0.8782 (t0) cc_final: 0.8389 (t0)
REVERT: A  152 LYS cc_start: 0.9320 (mttt) cc_final: 0.8801 (mttp)
REVERT: A  169 GLN cc_start: 0.7635 (mt0) cc_final: 0.7281 (mt0)
REVERT: A  259 LEU cc_start: 0.9447 (tp) cc_final: 0.9133 (tp)
REVERT: A  314 TYR cc_start: 0.9046 (t80) cc_final: 0.8182 (t80)
REVERT: B  120 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7947 (mm-30)
REVERT: C   20 GLN cc_start: 0.8005 (pm20) cc_final: 0.7579 (pm20)
REVERT: C   27 GLN cc_start: 0.7724 (tp40) cc_final: 0.7413 (tp-100)
REVERT: C   37 VAL cc_start: 0.8975 (t) cc_final: 0.8618 (t)
REVERT: D   50 GLN cc_start: 0.8374 (mm110) cc_final: 0.8013 (mm110)
REVERT: D   56 MET cc_start: 0.7709 (ttm) cc_final: 0.7410 (ttm)
REVERT: E   37 LEU cc_start: 0.9104 (mt) cc_final: 0.8901 (mm)
REVERT: E   46 ASN cc_start: 0.8650 (p0) cc_final: 0.8409 (p0)
REVERT: E   49 ASN cc_start: 0.8250 (p0) cc_final: 0.7901 (p0)
REVERT: G  366 MET cc_start: 0.2780 (tpt) cc_final: 0.2349 (tpp)
REVERT: G  433 ASP cc_start: 0.4753 (p0) cc_final: 0.3285 (m-30)
REVERT: I  117 SER cc_start: 0.8797 (t) cc_final: 0.8552 (t)
REVERT: I  171 TYR cc_start: 0.8362 (t80) cc_final: 0.8098 (t80)
REVERT: I  203 GLN cc_start: 0.8526 (tp40) cc_final: 0.8075 (tp40)
REVERT: I  272 GLU cc_start: 0.8960 (pt0) cc_final: 0.8741 (pt0)
REVERT: I  310 ARG cc_start: 0.8294 (ptp90) cc_final: 0.7712 (ptm-80)
REVERT: I  341 CYS cc_start: 0.8667 (p) cc_final: 0.8382 (p)
REVERT: I  343 GLU cc_start: 0.7679 (tt0) cc_final: 0.7251 (tt0)
REVERT: J   89 ARG cc_start: 0.6326 (tpt90) cc_final: 0.4601 (mtt90)
REVERT: J  120 GLU cc_start: 0.7573 (tp30) cc_final: 0.7330 (tp30)
REVERT: J  121 GLN cc_start: 0.7918 (mm110) cc_final: 0.7493 (mt0)
REVERT: K   22 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7919 (tp30)
REVERT: M   52 ASN cc_start: 0.8745 (m-40) cc_final: 0.8168 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.0852
  time to fit residues: 35.9315
Evaluate side-chains
  248 residues out of total 1018 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 96 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  78 GLN
** D  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 294 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.163707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.122260 restraints weight = 16539.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.121206 restraints weight = 10522.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.122102 restraints weight = 8618.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.122804 restraints weight = 7467.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.122731 restraints weight = 6331.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3504
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3504 r_free = 0.3504    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       44 |
|-----------------------------------------------------------------------------|
r_final: 0.3504
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9539  Z= 0.156
  Angle     :  0.711   9.232  12942  Z= 0.363
  Chirality :  0.046   0.234   1450
  Planarity :  0.004   0.039   1667
  Dihedral  :  4.905  31.640   1252
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.40 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.30 (0.26), residues: 1166
  helix:  1.07 (0.29), residues: 305
  sheet: -0.55 (0.23), residues: 495
  loop : -0.51 (0.36), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG I 235 
 TYR   0.016   0.001   TYR I 236 
 PHE   0.026   0.002   PHE I 120 
 TRP   0.042   0.002   TRP A 243 
 HIS   0.008   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9537)
  covalent geometry    : angle       0.71145 (12938)
  hydrogen bonds       : bond        0.03432 (  549)
  hydrogen bonds       : angle       5.83958 ( 1584)
  link_TRANS           : bond        0.00147 (    2)
  link_TRANS           : angle       0.32177 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1942.50 seconds
wall clock time: 34 minutes 10.42 seconds (2050.42 seconds total)