Starting phenix.real_space_refine
on Fri Aug 22 17:22:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e1m_27825/08_2025/8e1m_27825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e1m_27825/08_2025/8e1m_27825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e1m_27825/08_2025/8e1m_27825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e1m_27825/08_2025/8e1m_27825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e1m_27825/08_2025/8e1m_27825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e1m_27825/08_2025/8e1m_27825.cif"
  }
  resolution = 2.9
  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=   0.003 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      29      5.16       5
     C    3627      2.51       5
     N     980      2.21       5
     O    1052      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 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: 5691
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 955
          Classifications: {'peptide': 133}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 127}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "B"
      Number of atoms: 958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 958
          Classifications: {'peptide': 135}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 128}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 1921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 1921
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 58}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 256}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 205
          Unresolved non-hydrogen angles: 248
          Unresolved non-hydrogen dihedrals: 166
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLU:plan': 14, 'HIS:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 104
    Chain: "L"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 837
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "H"
      Number of atoms: 901
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 901
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 113}
          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: "A"
      Number of atoms: 69
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 69
          Unusual residues: {'CDL': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 31
    Chain: "B"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 50
          Unusual residues: {'PTY': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.59, per 1000 atoms: 0.28
  Number of scatterers: 5691
  At special positions: 0
  Unit cell: (93.45, 122.85, 79.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      29     16.00
     P       3     15.00
     O    1052      8.00
     N     980      7.00
     C    3627      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  10 " - pdb=" SG  CYS A  77 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  43 " - pdb=" SG  CYS L 112 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 114 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.53
  Conformation dependent library (CDL) restraints added in 338.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1352

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 9 sheets defined
      53.3% alpha, 26.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 41
      removed outlier: 3.970A  pdb=" N   ILE A  14 " --> pdb=" O   CYS A  10 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   LEU A  15 " --> pdb=" O   PRO A  11 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ASN A  16 " --> pdb=" O   ILE A  12 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 46
      removed outlier: 4.199A  pdb=" N   ARG A  46 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 84
      Proline residue:  A  59  - end of helix
      removed outlier: 3.681A  pdb=" N   SER A  73 " --> pdb=" O   GLY A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 102
      removed outlier: 3.694A  pdb=" N   ILE A  92 " --> pdb=" O   PRO A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 138
      removed outlier: 3.608A  pdb=" N   ARG A 112 " --> pdb=" O   TRP A 108 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   TRP A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 92 through 123
      removed outlier: 3.717A  pdb=" N   ASP B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLN B 122 " --> pdb=" O   MET B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 169
      Proline residue:  B 146  - end of helix
    Processing helix  chain 'B' and resid 174 through 190
    Processing helix  chain 'B' and resid 195 through 220
      removed outlier: 3.525A  pdb=" N   GLY B 199 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TYR B 200 " --> pdb=" O   LYS B 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 126
    Processing helix  chain 'C' and resid 126 through 152
      Proline residue:  C 149  - end of helix
    Processing helix  chain 'C' and resid 153 through 164
    Processing helix  chain 'C' and resid 166 through 172
      removed outlier: 3.767A  pdb=" N   SER C 169 " --> pdb=" O   GLY C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 190
      removed outlier: 3.525A  pdb=" N   LYS C 183 " --> pdb=" O   GLN C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 256 through 265
      removed outlier: 3.662A  pdb=" N   PHE C 265 " --> pdb=" O   VAL C 261 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 281
    Processing helix  chain 'C' and resid 285 through 296
    Processing helix  chain 'C' and resid 296 through 308
    Processing helix  chain 'C' and resid 309 through 317
      removed outlier: 3.870A  pdb=" N   LYS C 315 " --> pdb=" O   LYS C 311 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 318 through 335
      removed outlier: 3.502A  pdb=" N   VAL C 324 " --> pdb=" O   ALA C 320 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 105 through 109
      removed outlier: 3.830A  pdb=" N   THR H 109 " --> pdb=" O   ALA H 106 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 118 through 122
    Processing sheet with id=AA1, first strand: chain 'C' and resid 337 through 339
      removed outlier: 6.045A  pdb=" N   ILE C 362 " --> pdb=" O   LYS C 355 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LYS C 355 " --> pdb=" O   ILE C 362 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   VAL C 364 " --> pdb=" O   SER C 353 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   SER C 353 " --> pdb=" O   VAL C 364 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   VAL C 366 " --> pdb=" O   ILE C 351 " (cutoff:3.500A)
      removed outlier: 4.635A  pdb=" N   ILE C 351 " --> pdb=" O   VAL C 366 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   GLY C 368 " --> pdb=" O   VAL C 349 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   VAL C 349 " --> pdb=" O   GLY C 368 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ASP C 345 " --> pdb=" O   GLN C 372 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ILE C 374 " --> pdb=" O   ILE C 343 " (cutoff:3.500A)
      removed outlier: 5.753A  pdb=" N   ILE C 343 " --> pdb=" O   ILE C 374 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 337 through 339
      removed outlier: 5.005A  pdb=" N   ARG C 404 " --> pdb=" O   PRO C 363 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   ASN C 375 " --> pdb=" O   ASN C 392 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ASN C 392 " --> pdb=" O   ASN C 375 " (cutoff:3.500A)
      removed outlier: 9.443A  pdb=" N   TYR C 377 " --> pdb=" O   GLU C 390 " (cutoff:3.500A)
      removed outlier: 8.188A  pdb=" N   GLU C 390 " --> pdb=" O   TYR C 377 " (cutoff:3.500A)
      removed outlier: 10.487A  pdb=" N   LYS C 379 " --> pdb=" O   GLY C 388 " (cutoff:3.500A)
      removed outlier: 12.788A  pdb=" N   GLY C 388 " --> pdb=" O   LYS C 379 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLU C 421 " --> pdb=" O   VAL C 401 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   THR C 403 " --> pdb=" O   ILE C 419 " (cutoff:3.500A)
      removed outlier: 5.002A  pdb=" N   ILE C 419 " --> pdb=" O   THR C 403 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 25 through 27
      removed outlier: 3.531A  pdb=" N   ASP L  94 " --> pdb=" O   SER L  91 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER L  96 " --> pdb=" O   SER L  89 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 30 through 33
      removed outlier: 7.084A  pdb=" N   LEU L  31 " --> pdb=" O   GLU L 129 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   MET L  57 " --> pdb=" O   TYR L  73 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   TYR L  73 " --> pdb=" O   MET L  57 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   TRP L  59 " --> pdb=" O   LEU L  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 30 through 33
      removed outlier: 7.084A  pdb=" N   LEU L  31 " --> pdb=" O   GLU L 129 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   THR L 121 " --> pdb=" O   GLN L 114 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 50 through 51
    Processing sheet with id=AA7, first strand: chain 'H' and resid 22 through 26
    Processing sheet with id=AA8, first strand: chain 'H' and resid 76 through 78
      removed outlier: 6.843A  pdb=" N   TRP H  55 " --> pdb=" O   LEU H  67 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   VAL H  69 " --> pdb=" O   VAL H  53 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL H  53 " --> pdb=" O   VAL H  69 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLY H  52 " --> pdb=" O   TYR H 117 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   TYR H 125 " --> pdb=" O   ARG H 116 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 76 through 78
      removed outlier: 6.843A  pdb=" N   TRP H  55 " --> pdb=" O   LEU H  67 " (cutoff:3.500A)
      removed outlier: 4.770A  pdb=" N   VAL H  69 " --> pdb=" O   VAL H  53 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   VAL H  53 " --> pdb=" O   VAL H  69 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   GLY H  52 " --> pdb=" O   TYR H 117 " (cutoff:3.500A)

    398 hydrogen bonds defined for protein.
    1128 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: 0.95

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1826
        1.34 -     1.46: 1421
        1.46 -     1.59: 2506
        1.59 -     1.71: 6
        1.71 -     1.84: 46
  Bond restraints: 5805
  Sorted by residual:
  bond pdb=" CA7 CDL A 301 "
       pdb=" OA8 CDL A 301 "
    ideal  model  delta    sigma   weight residual
    1.334  1.452 -0.118 1.10e-02 8.26e+03 1.15e+02
  bond pdb=" CB7 CDL A 301 "
       pdb=" OB8 CDL A 301 "
    ideal  model  delta    sigma   weight residual
    1.334  1.446 -0.112 1.10e-02 8.26e+03 1.04e+02
  bond pdb=" CB5 CDL A 301 "
       pdb=" OB6 CDL A 301 "
    ideal  model  delta    sigma   weight residual
    1.342  1.450 -0.108 1.50e-02 4.44e+03 5.23e+01
  bond pdb=" CA5 CDL A 301 "
       pdb=" OA6 CDL A 301 "
    ideal  model  delta    sigma   weight residual
    1.342  1.449 -0.107 1.50e-02 4.44e+03 5.12e+01
  bond pdb=" C8  PTY B 301 "
       pdb=" O7  PTY B 301 "
    ideal  model  delta    sigma   weight residual
    1.331  1.454 -0.123 2.00e-02 2.50e+03 3.77e+01
  ... (remaining 5800 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 7661
        2.19 -     4.38: 139
        4.38 -     6.57: 31
        6.57 -     8.76: 3
        8.76 -    10.94: 6
  Bond angle restraints: 7840
  Sorted by residual:
  angle pdb=" C51 CDL A 301 "
        pdb=" CB5 CDL A 301 "
        pdb=" OB6 CDL A 301 "
      ideal   model   delta    sigma   weight residual
     111.33  121.20   -9.87 1.32e+00 5.72e-01 5.58e+01
  angle pdb=" C11 CDL A 301 "
        pdb=" CA5 CDL A 301 "
        pdb=" OA6 CDL A 301 "
      ideal   model   delta    sigma   weight residual
     111.33  120.23   -8.90 1.32e+00 5.72e-01 4.53e+01
  angle pdb=" C31 CDL A 301 "
        pdb=" CA7 CDL A 301 "
        pdb=" OA8 CDL A 301 "
      ideal   model   delta    sigma   weight residual
     111.64  121.14   -9.50 1.65e+00 3.69e-01 3.33e+01
  angle pdb=" OB6 CDL A 301 "
        pdb=" CB5 CDL A 301 "
        pdb=" OB7 CDL A 301 "
      ideal   model   delta    sigma   weight residual
     123.92  118.41    5.51 1.00e+00 9.92e-01 3.01e+01
  angle pdb=" C71 CDL A 301 "
        pdb=" CB7 CDL A 301 "
        pdb=" OB8 CDL A 301 "
      ideal   model   delta    sigma   weight residual
     111.64  120.27   -8.63 1.65e+00 3.69e-01 2.75e+01
  ... (remaining 7835 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.84: 3219
       23.84 -    47.68: 188
       47.68 -    71.52: 24
       71.52 -    95.36: 5
       95.36 -   119.20: 1
  Dihedral angle restraints: 3437
    sinusoidal: 1309
      harmonic: 2128
  Sorted by residual:
  dihedral pdb=" CB  CYS A  10 "
           pdb=" SG  CYS A  10 "
           pdb=" SG  CYS A  77 "
           pdb=" CB  CYS A  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -124.76   38.76     1      1.00e+01 1.00e-02 2.11e+01
  dihedral pdb=" N1  PTY B 301 "
           pdb=" C2  PTY B 301 "
           pdb=" C3  PTY B 301 "
           pdb=" O11 PTY B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      65.33  -53.87  119.20     1      3.00e+01 1.11e-03 1.59e+01
  dihedral pdb=" CA  ILE B 166 "
           pdb=" C   ILE B 166 "
           pdb=" N   ASP B 167 "
           pdb=" CA  ASP B 167 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.55   19.45     0      5.00e+00 4.00e-02 1.51e+01
  ... (remaining 3434 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 508
       0.031 -    0.063: 235
       0.063 -    0.094: 68
       0.094 -    0.125: 38
       0.125 -    0.156: 7
  Chirality restraints: 856
  Sorted by residual:
  chirality pdb=" CA  ILE L  72 "
            pdb=" N   ILE L  72 "
            pdb=" C   ILE L  72 "
            pdb=" CB  ILE L  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.12e-01
  chirality pdb=" CA  ILE C 362 "
            pdb=" N   ILE C 362 "
            pdb=" C   ILE C 362 "
            pdb=" CB  ILE C 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.36e-01
  chirality pdb=" CA  ILE L 130 "
            pdb=" N   ILE L 130 "
            pdb=" C   ILE L 130 "
            pdb=" CB  ILE L 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.17e-01
  ... (remaining 853 not shown)

  Planarity restraints: 1003
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 145 "   -0.032 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO B 146 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 146 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 146 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A   8 "   -0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO A   9 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A   9 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A   9 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO L  67 "    0.025 5.00e-02 4.00e+02   3.86e-02 2.38e+00
        pdb=" N   PRO L  68 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO L  68 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO L  68 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1000 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 263
        2.72 -     3.27: 5714
        3.27 -     3.81: 9339
        3.81 -     4.36: 12101
        4.36 -     4.90: 20858
  Nonbonded interactions: 48275
  Sorted by model distance:
  nonbonded pdb=" O   LEU B  97 "
            pdb=" OG1 THR B 101 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OD1 ASP L  50 "
            pdb=" OG  SER L  55 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" OG  SER L  48 "
            pdb=" OD2 ASP L  50 "
     model   vdw
     2.185 3.040
  nonbonded pdb=" NZ  LYS L  63 "
            pdb=" O   ASP L 105 "
     model   vdw
     2.231 3.120
  nonbonded pdb=" NZ  LYS C 278 "
            pdb=" O   PRO C 282 "
     model   vdw
     2.249 3.120
  ... (remaining 48270 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.230
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:6.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8309
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   0.123   5808  Z= 0.364
  Angle     :  0.770  10.945   7846  Z= 0.412
  Chirality :  0.043   0.156    856
  Planarity :  0.004   0.049   1003
  Dihedral  : 14.841 119.204   2076
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.83 (0.31), residues: 748
  helix: -0.30 (0.26), residues: 370
  sheet: -0.54 (0.45), residues: 142
  loop : -0.63 (0.42), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG L  38 
 TYR   0.016   0.002   TYR H 117 
 PHE   0.012   0.002   PHE A  96 
 TRP   0.019   0.002   TRP H  66 
 HIS   0.003   0.001   HIS B 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00678 ( 5805)
  covalent geometry    : angle       0.76531 ( 7840)
  SS BOND              : bond        0.00267 (    3)
  SS BOND              : angle       3.10585 (    6)
  hydrogen bonds       : bond        0.22590 (  380)
  hydrogen bonds       : angle       9.56264 ( 1128)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  200 TYR cc_start: 0.7366 (m-80) cc_final: 0.6891 (m-80)
  outliers start: 0
  outliers final: 2
  residues processed: 111
  average time/residue: 0.5775
  time to fit residues: 66.9225
Evaluate side-chains
  85 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain B residue  161 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:   30.0000
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B 122 GLN
L  66 GLN
H  32 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.082556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.061337 restraints weight = 12783.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 2.57
r_work: 0.2779 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5808  Z= 0.152
  Angle     :  0.592   8.460   7846  Z= 0.308
  Chirality :  0.043   0.148    856
  Planarity :  0.005   0.044   1003
  Dihedral  : 10.153  64.617    920
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.89 %
    Favored  : 87.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  0.77 (0.31), residues: 748
  helix:  1.37 (0.26), residues: 372
  sheet: -0.20 (0.45), residues: 142
  loop : -0.26 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 170 
 TYR   0.010   0.001   TYR H 117 
 PHE   0.017   0.001   PHE A  96 
 TRP   0.011   0.001   TRP A 108 
 HIS   0.003   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 5805)
  covalent geometry    : angle       0.59016 ( 7840)
  SS BOND              : bond        0.00176 (    3)
  SS BOND              : angle       1.63121 (    6)
  hydrogen bonds       : bond        0.03900 (  380)
  hydrogen bonds       : angle       5.08416 ( 1128)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.8295 (m) cc_final: 0.7919 (p)
REVERT: A   76 ASP cc_start: 0.9057 (t0) cc_final: 0.8834 (t0)
REVERT: B  127 ASN cc_start: 0.7804 (t0) cc_final: 0.7498 (t0)
REVERT: B  204 MET cc_start: 0.9088 (mtm) cc_final: 0.8847 (mtm)
REVERT: L  103 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7981 (mt-10)
REVERT: L  127 LYS cc_start: 0.9039 (tttp) cc_final: 0.8728 (tttp)
REVERT: L  129 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8025 (mt-10)
REVERT: H   24 LYS cc_start: 0.9002 (tppp) cc_final: 0.8558 (mtmp)
  outliers start: 7
  outliers final: 4
  residues processed: 98
  average time/residue: 0.5378
  time to fit residues: 55.2165
Evaluate side-chains
  91 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain L residue  105 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
B 123 ASN
L  66 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.082318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.061207 restraints weight = 12778.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 2.56
r_work: 0.2780 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5808  Z= 0.147
  Angle     :  0.546   9.195   7846  Z= 0.282
  Chirality :  0.042   0.152    856
  Planarity :  0.004   0.044   1003
  Dihedral  :  9.586  64.688    916
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.92 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.43 (0.32), residues: 748
  helix:  2.14 (0.26), residues: 372
  sheet: -0.14 (0.45), residues: 142
  loop : -0.21 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 181 
 TYR   0.010   0.001   TYR H 117 
 PHE   0.014   0.001   PHE A  96 
 TRP   0.009   0.001   TRP A  32 
 HIS   0.003   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 5805)
  covalent geometry    : angle       0.54539 ( 7840)
  SS BOND              : bond        0.00214 (    3)
  SS BOND              : angle       0.93652 (    6)
  hydrogen bonds       : bond        0.03656 (  380)
  hydrogen bonds       : angle       4.53965 ( 1128)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.8220 (m) cc_final: 0.7945 (p)
REVERT: A  131 MET cc_start: 0.7945 (mmt) cc_final: 0.7698 (mmm)
REVERT: B  127 ASN cc_start: 0.7823 (t0) cc_final: 0.7512 (t0)
REVERT: B  131 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8278 (tttt)
REVERT: B  162 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8225 (mp)
REVERT: B  195 LEU cc_start: 0.8117 (mm) cc_final: 0.7799 (tm)
REVERT: B  198 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7623 (mmt)
REVERT: B  200 TYR cc_start: 0.8651 (m-80) cc_final: 0.8356 (m-10)
REVERT: B  204 MET cc_start: 0.9173 (mtm) cc_final: 0.8898 (mtm)
REVERT: C  431 THR cc_start: 0.8406 (m) cc_final: 0.7862 (p)
REVERT: L  103 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8252 (mt-10)
REVERT: L  127 LYS cc_start: 0.8965 (tttp) cc_final: 0.8632 (tttp)
REVERT: L  129 GLU cc_start: 0.8323 (mt-10) cc_final: 0.7899 (mt-10)
REVERT: H   24 LYS cc_start: 0.9004 (tppp) cc_final: 0.8645 (mtmp)
  outliers start: 12
  outliers final: 4
  residues processed: 98
  average time/residue: 0.5384
  time to fit residues: 55.3708
Evaluate side-chains
  92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain H residue   86 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 60 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0270
   chunk 56 optimal weight:    0.6980
   chunk 54 optimal weight:   10.0000
   chunk 14 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
C 335 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.084902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.062496 restraints weight = 13034.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 2.59
r_work: 0.2825 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5808  Z= 0.118
  Angle     :  0.526   9.840   7846  Z= 0.267
  Chirality :  0.042   0.150    856
  Planarity :  0.004   0.050   1003
  Dihedral  :  9.060  63.974    916
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 13.84 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.75 (0.32), residues: 748
  helix:  2.40 (0.26), residues: 372
  sheet:  0.08 (0.45), residues: 142
  loop : -0.10 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 181 
 TYR   0.008   0.001   TYR H 117 
 PHE   0.013   0.001   PHE A  96 
 TRP   0.009   0.001   TRP A  32 
 HIS   0.003   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5805)
  covalent geometry    : angle       0.52513 ( 7840)
  SS BOND              : bond        0.00244 (    3)
  SS BOND              : angle       1.41155 (    6)
  hydrogen bonds       : bond        0.03312 (  380)
  hydrogen bonds       : angle       4.25332 ( 1128)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8117 (mp0)
REVERT: B  127 ASN cc_start: 0.7723 (t0) cc_final: 0.7400 (t0)
REVERT: B  131 LYS cc_start: 0.8771 (ttmt) cc_final: 0.8281 (tttt)
REVERT: B  162 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8293 (mp)
REVERT: B  195 LEU cc_start: 0.8123 (mm) cc_final: 0.7810 (tm)
REVERT: B  198 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7638 (mmt)
REVERT: B  200 TYR cc_start: 0.8629 (m-80) cc_final: 0.8310 (m-10)
REVERT: B  204 MET cc_start: 0.9202 (mtm) cc_final: 0.8923 (mtm)
REVERT: C  431 THR cc_start: 0.8297 (m) cc_final: 0.7821 (p)
REVERT: L  103 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8338 (mt-10)
REVERT: L  127 LYS cc_start: 0.8973 (tttp) cc_final: 0.8628 (tttp)
REVERT: H   24 LYS cc_start: 0.9005 (tppp) cc_final: 0.8746 (mtmt)
  outliers start: 15
  outliers final: 6
  residues processed: 106
  average time/residue: 0.4858
  time to fit residues: 54.2379
Evaluate side-chains
  98 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain L residue  105 ASP
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  109 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 47 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 72 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 57 optimal weight:    0.0970
   chunk 63 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.1982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.082505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.061208 restraints weight = 12887.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 2.59
r_work: 0.2784 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5808  Z= 0.157
  Angle     :  0.556   9.808   7846  Z= 0.282
  Chirality :  0.043   0.167    856
  Planarity :  0.004   0.047   1003
  Dihedral  :  8.981  64.000    916
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 15.87 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.94 (0.32), residues: 748
  helix:  2.53 (0.27), residues: 372
  sheet:  0.19 (0.46), residues: 142
  loop :  0.01 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 181 
 TYR   0.016   0.001   TYR B 159 
 PHE   0.013   0.001   PHE A  96 
 TRP   0.007   0.001   TRP A  32 
 HIS   0.003   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5805)
  covalent geometry    : angle       0.55539 ( 7840)
  SS BOND              : bond        0.00245 (    3)
  SS BOND              : angle       1.31521 (    6)
  hydrogen bonds       : bond        0.03407 (  380)
  hydrogen bonds       : angle       4.10158 ( 1128)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8036 (mp0)
REVERT: A  131 MET cc_start: 0.7999 (mmt) cc_final: 0.7654 (mmm)
REVERT: B  127 ASN cc_start: 0.7813 (t0) cc_final: 0.7495 (t0)
REVERT: B  131 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8286 (tttt)
REVERT: B  162 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8207 (mp)
REVERT: B  195 LEU cc_start: 0.8115 (mm) cc_final: 0.7795 (tm)
REVERT: B  198 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7660 (mmt)
REVERT: B  200 TYR cc_start: 0.8586 (m-80) cc_final: 0.8246 (m-10)
REVERT: B  204 MET cc_start: 0.9229 (mtm) cc_final: 0.8933 (mtm)
REVERT: C  431 THR cc_start: 0.8324 (m) cc_final: 0.7837 (p)
REVERT: L  127 LYS cc_start: 0.8950 (tttp) cc_final: 0.8634 (tttp)
REVERT: H   24 LYS cc_start: 0.8988 (tppp) cc_final: 0.8656 (mtmt)
  outliers start: 13
  outliers final: 7
  residues processed: 102
  average time/residue: 0.4700
  time to fit residues: 50.4460
Evaluate side-chains
  98 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  198 MET
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  109 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 26 optimal weight:   50.0000
   chunk 32 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 10 optimal weight:    6.9990
   chunk 73 optimal weight:    0.0470
   chunk 69 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   overall best weight:    0.8680

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

Flipped N/Q/H residues before XYZ refinement:
C 408 GLN
L  66 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.083065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.061957 restraints weight = 12757.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.2966 rms_B_bonded: 2.58
r_work: 0.2803 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5808  Z= 0.132
  Angle     :  0.547  10.523   7846  Z= 0.272
  Chirality :  0.042   0.181    856
  Planarity :  0.004   0.043   1003
  Dihedral  :  8.672  64.206    916
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.79 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.02 (0.32), residues: 748
  helix:  2.61 (0.27), residues: 372
  sheet:  0.23 (0.46), residues: 142
  loop :  0.02 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 181 
 TYR   0.019   0.001   TYR B 159 
 PHE   0.010   0.001   PHE A  96 
 TRP   0.008   0.001   TRP A  32 
 HIS   0.002   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 5805)
  covalent geometry    : angle       0.54606 ( 7840)
  SS BOND              : bond        0.00227 (    3)
  SS BOND              : angle       0.97092 (    6)
  hydrogen bonds       : bond        0.03263 (  380)
  hydrogen bonds       : angle       3.95320 ( 1128)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8087 (mp0)
REVERT: A  131 MET cc_start: 0.7772 (mmt) cc_final: 0.7518 (mmm)
REVERT: B  127 ASN cc_start: 0.7795 (t0) cc_final: 0.7506 (t0)
REVERT: B  131 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8311 (tttt)
REVERT: B  162 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8219 (mp)
REVERT: B  195 LEU cc_start: 0.8110 (mm) cc_final: 0.7824 (tm)
REVERT: B  200 TYR cc_start: 0.8573 (m-80) cc_final: 0.8202 (m-10)
REVERT: B  204 MET cc_start: 0.9242 (mtm) cc_final: 0.8934 (mtm)
REVERT: C  431 THR cc_start: 0.8252 (m) cc_final: 0.7779 (p)
REVERT: H   24 LYS cc_start: 0.8976 (tppp) cc_final: 0.8678 (mtmp)
  outliers start: 11
  outliers final: 6
  residues processed: 101
  average time/residue: 0.4762
  time to fit residues: 50.5613
Evaluate side-chains
  96 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 89
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue   91 ASP
Chi-restraints excluded: chain H residue  109 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 35 optimal weight:   20.0000
   chunk 6 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 16 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
B 122 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.081085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.059629 restraints weight = 12961.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 2.57
r_work: 0.2746 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   5808  Z= 0.234
  Angle     :  0.600   9.305   7846  Z= 0.303
  Chirality :  0.045   0.225    856
  Planarity :  0.004   0.045   1003
  Dihedral  :  9.142  64.273    916
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 16.61 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.01 (0.32), residues: 748
  helix:  2.61 (0.27), residues: 372
  sheet:  0.29 (0.47), residues: 135
  loop : -0.03 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  57 
 TYR   0.017   0.002   TYR H 117 
 PHE   0.013   0.001   PHE A  96 
 TRP   0.009   0.001   TRP H  66 
 HIS   0.004   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 5805)
  covalent geometry    : angle       0.60008 ( 7840)
  SS BOND              : bond        0.00275 (    3)
  SS BOND              : angle       0.97677 (    6)
  hydrogen bonds       : bond        0.03618 (  380)
  hydrogen bonds       : angle       4.08257 ( 1128)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8088 (mp0)
REVERT: A  131 MET cc_start: 0.7801 (mmt) cc_final: 0.7554 (mmm)
REVERT: B  127 ASN cc_start: 0.7883 (t0) cc_final: 0.7662 (t0)
REVERT: B  131 LYS cc_start: 0.8835 (ttmt) cc_final: 0.8348 (tttt)
REVERT: B  195 LEU cc_start: 0.8333 (mm) cc_final: 0.8021 (tm)
REVERT: B  200 TYR cc_start: 0.8616 (m-80) cc_final: 0.8321 (m-10)
REVERT: B  204 MET cc_start: 0.9250 (mtm) cc_final: 0.8977 (mtm)
REVERT: C  431 THR cc_start: 0.8343 (m) cc_final: 0.7874 (p)
REVERT: L  104 GLU cc_start: 0.7615 (tp30) cc_final: 0.7268 (tm-30)
  outliers start: 11
  outliers final: 6
  residues processed: 97
  average time/residue: 0.4844
  time to fit residues: 49.3952
Evaluate side-chains
  90 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  109 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0270
   chunk 71 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.5244

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

Flipped N/Q/H residues before XYZ refinement:
C 408 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.081987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.060525 restraints weight = 12658.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 2.57
r_work: 0.2770 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5808  Z= 0.185
  Angle     :  0.603  10.994   7846  Z= 0.301
  Chirality :  0.045   0.243    856
  Planarity :  0.004   0.047   1003
  Dihedral  :  9.078  65.327    916
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 16.97 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.02 (0.32), residues: 748
  helix:  2.57 (0.27), residues: 372
  sheet:  0.36 (0.47), residues: 135
  loop :  0.00 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 181 
 TYR   0.013   0.001   TYR H 117 
 PHE   0.012   0.001   PHE A  96 
 TRP   0.010   0.001   TRP H  66 
 HIS   0.003   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 5805)
  covalent geometry    : angle       0.59527 ( 7840)
  SS BOND              : bond        0.00324 (    3)
  SS BOND              : angle       3.61364 (    6)
  hydrogen bonds       : bond        0.03492 (  380)
  hydrogen bonds       : angle       4.03992 ( 1128)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8121 (mp0)
REVERT: A  131 MET cc_start: 0.7849 (mmt) cc_final: 0.7598 (mmm)
REVERT: B  131 LYS cc_start: 0.8809 (ttmt) cc_final: 0.8321 (tttt)
REVERT: B  195 LEU cc_start: 0.8315 (mm) cc_final: 0.8026 (tm)
REVERT: B  200 TYR cc_start: 0.8611 (m-80) cc_final: 0.8320 (m-10)
REVERT: B  204 MET cc_start: 0.9244 (mtm) cc_final: 0.8961 (mtm)
REVERT: C  431 THR cc_start: 0.8384 (m) cc_final: 0.7916 (p)
REVERT: L  104 GLU cc_start: 0.7607 (tp30) cc_final: 0.7113 (tm-30)
REVERT: H   24 LYS cc_start: 0.9084 (mtpm) cc_final: 0.8512 (mtmp)
  outliers start: 8
  outliers final: 7
  residues processed: 95
  average time/residue: 0.5305
  time to fit residues: 52.8488
Evaluate side-chains
  93 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain L residue  105 ASP
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  109 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9980
   chunk 35 optimal weight:   20.0000
   chunk 12 optimal weight:   10.0000
   chunk 28 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 34 optimal weight:    8.9990
   chunk 27 optimal weight:   20.0000
   overall best weight:    2.5184

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

Flipped N/Q/H residues before XYZ refinement:
C 408 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.080631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.059069 restraints weight = 12878.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 2.58
r_work: 0.2734 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   5808  Z= 0.273
  Angle     :  0.646   9.868   7846  Z= 0.329
  Chirality :  0.046   0.225    856
  Planarity :  0.004   0.048   1003
  Dihedral  :  9.564  65.544    916
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.97 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  1.87 (0.32), residues: 748
  helix:  2.48 (0.26), residues: 373
  sheet:  0.32 (0.48), residues: 135
  loop : -0.15 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  85 
 TYR   0.019   0.002   TYR H 117 
 PHE   0.012   0.001   PHE C 289 
 TRP   0.011   0.001   TRP H  66 
 HIS   0.005   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00624 ( 5805)
  covalent geometry    : angle       0.63989 ( 7840)
  SS BOND              : bond        0.00248 (    3)
  SS BOND              : angle       3.13883 (    6)
  hydrogen bonds       : bond        0.03750 (  380)
  hydrogen bonds       : angle       4.15296 ( 1128)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8131 (mp0)
REVERT: A  131 MET cc_start: 0.7896 (mmt) cc_final: 0.7643 (mmm)
REVERT: B  195 LEU cc_start: 0.8359 (mm) cc_final: 0.8060 (tm)
REVERT: B  200 TYR cc_start: 0.8635 (m-80) cc_final: 0.8379 (m-80)
REVERT: B  204 MET cc_start: 0.9268 (mtm) cc_final: 0.9027 (mtm)
REVERT: C  431 THR cc_start: 0.8402 (m) cc_final: 0.7891 (p)
REVERT: L  104 GLU cc_start: 0.7630 (tp30) cc_final: 0.7050 (tm-30)
REVERT: H   24 LYS cc_start: 0.9076 (mtpm) cc_final: 0.8488 (mtmp)
  outliers start: 10
  outliers final: 7
  residues processed: 92
  average time/residue: 0.5388
  time to fit residues: 51.9784
Evaluate side-chains
  94 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain L residue  103 GLU
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  109 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 56 optimal weight:    0.0870
   chunk 66 optimal weight:    0.9980
   chunk 21 optimal weight:    9.9990
   chunk 6 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 39 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
C 408 GLN
L  66 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.083218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.061498 restraints weight = 12862.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.73
r_work: 0.2779 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5808  Z= 0.131
  Angle     :  0.587  12.228   7846  Z= 0.294
  Chirality :  0.043   0.259    856
  Planarity :  0.004   0.045   1003
  Dihedral  :  8.968  66.615    916
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 17.71 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.03 (0.32), residues: 748
  helix:  2.61 (0.27), residues: 373
  sheet:  0.41 (0.47), residues: 135
  loop : -0.09 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 181 
 TYR   0.012   0.001   TYR B 159 
 PHE   0.011   0.001   PHE A  96 
 TRP   0.011   0.001   TRP H  66 
 HIS   0.002   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5805)
  covalent geometry    : angle       0.58324 ( 7840)
  SS BOND              : bond        0.00255 (    3)
  SS BOND              : angle       2.33735 (    6)
  hydrogen bonds       : bond        0.03209 (  380)
  hydrogen bonds       : angle       3.94104 ( 1128)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8061 (mp0)
REVERT: A  131 MET cc_start: 0.7813 (mmt) cc_final: 0.7568 (mmm)
REVERT: B  195 LEU cc_start: 0.8144 (mm) cc_final: 0.7835 (tm)
REVERT: B  200 TYR cc_start: 0.8593 (m-80) cc_final: 0.8304 (m-10)
REVERT: B  204 MET cc_start: 0.9292 (mtm) cc_final: 0.8976 (mtm)
REVERT: C  431 THR cc_start: 0.8413 (m) cc_final: 0.7916 (p)
REVERT: L  103 GLU cc_start: 0.8508 (mp0) cc_final: 0.8199 (pm20)
REVERT: L  104 GLU cc_start: 0.7556 (tp30) cc_final: 0.6848 (tm-30)
REVERT: H   24 LYS cc_start: 0.9002 (mtpm) cc_final: 0.8351 (mtmp)
  outliers start: 6
  outliers final: 3
  residues processed: 95
  average time/residue: 0.5183
  time to fit residues: 51.7478
Evaluate side-chains
  91 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 88
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain H residue   86 LEU
Chi-restraints excluded: chain H residue  109 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 26 optimal weight:   50.0000
   chunk 3 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 69 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0070
   chunk 41 optimal weight:    0.7980
   chunk 28 optimal weight:   30.0000
   overall best weight:    0.6600

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

Flipped N/Q/H residues before XYZ refinement:
C 408 GLN
L  66 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.083599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.062049 restraints weight = 12753.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 2.72
r_work: 0.2791 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5808  Z= 0.128
  Angle     :  0.587  11.264   7846  Z= 0.296
  Chirality :  0.042   0.193    856
  Planarity :  0.004   0.044   1003
  Dihedral  :  8.612  65.411    916
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 18.27 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.16 (0.32), residues: 748
  helix:  2.73 (0.27), residues: 372
  sheet:  0.35 (0.45), residues: 142
  loop :  0.03 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  85 
 TYR   0.010   0.001   TYR B 159 
 PHE   0.011   0.001   PHE A  96 
 TRP   0.008   0.001   TRP H  66 
 HIS   0.002   0.001   HIS A  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 5805)
  covalent geometry    : angle       0.58045 ( 7840)
  SS BOND              : bond        0.00384 (    3)
  SS BOND              : angle       3.22438 (    6)
  hydrogen bonds       : bond        0.03169 (  380)
  hydrogen bonds       : angle       3.83341 ( 1128)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1947.85 seconds
wall clock time: 33 minutes 54.82 seconds (2034.82 seconds total)