Starting phenix.real_space_refine
on Tue Feb 11 17:48:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e1m_27825/02_2025/8e1m_27825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e1m_27825/02_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_27825/02_2025/8e1m_27825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e1m_27825/02_2025/8e1m_27825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e1m_27825/02_2025/8e1m_27825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e1m_27825/02_2025/8e1m_27825.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP: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: {'ARG:plan': 1, 'ASP: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: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 3}
          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: 4.00, per 1000 atoms: 0.70
  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: 1.51
  Conformation dependent library (CDL) restraints added in 828.3 milliseconds
  

  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: 0.67
  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: 1.72

  Time building geometry restraints manager: 1.73 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:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.390
  Find NCS groups from input model:        0.070
  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:12.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.440
-------------------------------------------------------------------------------
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   5805  Z= 0.456
  Angle     :  0.765  10.945   7840  Z= 0.411
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (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
 TRP   0.019   0.002   TRP H  66 
 HIS   0.003   0.001   HIS B 173 
 PHE   0.012   0.002   PHE A  96 
 TYR   0.016   0.002   TYR H 117 
 ARG   0.004   0.001   ARG L  38 

*********************** 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  : 0.573 
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: 1.1772
  time to fit residues: 136.5865
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  : 0.584 
-------------------------------------------------------------------------------
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 62 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 35 optimal weight:   20.0000
   chunk 43 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.3392 r_free = 0.3392 target = 0.081661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.060361 restraints weight = 12693.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 2.55
r_work: 0.2756 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5805  Z= 0.272
  Angle     :  0.604   8.133   7840  Z= 0.314
  Chirality :  0.043   0.150    856
  Planarity :  0.005   0.044   1003
  Dihedral  : 10.280  64.738    920
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.89 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.32), residues: 748
  helix:  1.42 (0.26), residues: 372
  sheet: -0.21 (0.45), residues: 142
  loop : -0.30 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 108 
 HIS   0.004   0.001   HIS A  33 
 PHE   0.017   0.001   PHE C 322 
 TYR   0.013   0.001   TYR H 117 
 ARG   0.009   0.001   ARG C 170 

*********************** 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
  102 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.8268 (m) cc_final: 0.7970 (p)
REVERT: A   76 ASP cc_start: 0.9052 (t0) cc_final: 0.8826 (t0)
REVERT: B  127 ASN cc_start: 0.7967 (t0) cc_final: 0.7682 (t0)
REVERT: B  162 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8234 (mp)
REVERT: B  204 MET cc_start: 0.9158 (mtm) cc_final: 0.8947 (mtm)
REVERT: L  103 GLU cc_start: 0.8307 (mt-10) cc_final: 0.7967 (mt-10)
REVERT: L  127 LYS cc_start: 0.9048 (tttp) cc_final: 0.8777 (tttp)
REVERT: L  129 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8092 (mt-10)
REVERT: H   24 LYS cc_start: 0.8975 (tppp) cc_final: 0.8529 (mtmp)
  outliers start: 8
  outliers final: 3
  residues processed: 95
  average time/residue: 1.1517
  time to fit residues: 114.9018
Evaluate side-chains
  89 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain B residue  162 ILE
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain C residue  175 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 10 optimal weight:    7.9990
   chunk 73 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 = 0.3383 r_free = 0.3383 target = 0.081002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.059777 restraints weight = 12820.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.55
r_work: 0.2746 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5805  Z= 0.284
  Angle     :  0.563   8.606   7840  Z= 0.291
  Chirality :  0.043   0.140    856
  Planarity :  0.004   0.045   1003
  Dihedral  :  9.859  66.879    916
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.36 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.32), residues: 748
  helix:  2.12 (0.26), residues: 372
  sheet: -0.14 (0.45), residues: 142
  loop : -0.24 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  32 
 HIS   0.004   0.001   HIS A  33 
 PHE   0.015   0.001   PHE A  96 
 TYR   0.013   0.001   TYR H 117 
 ARG   0.005   0.000   ARG C 170 

*********************** 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
  101 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.8234 (m) cc_final: 0.7937 (p)
REVERT: A  131 MET cc_start: 0.7952 (mmt) cc_final: 0.7736 (mmm)
REVERT: B  127 ASN cc_start: 0.7903 (t0) cc_final: 0.7574 (t0)
REVERT: B  162 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8270 (mp)
REVERT: B  195 LEU cc_start: 0.8160 (mm) cc_final: 0.7832 (tm)
REVERT: B  198 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7705 (mmt)
REVERT: B  200 TYR cc_start: 0.8666 (m-80) cc_final: 0.8368 (m-10)
REVERT: B  204 MET cc_start: 0.9191 (mtm) cc_final: 0.8907 (mtm)
REVERT: C  179 GLN cc_start: 0.8900 (mp10) cc_final: 0.8685 (mm-40)
REVERT: C  431 THR cc_start: 0.8489 (m) cc_final: 0.7949 (p)
REVERT: L  103 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8132 (mt-10)
REVERT: L  127 LYS cc_start: 0.8991 (tttp) cc_final: 0.8692 (tttp)
REVERT: L  129 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7923 (mt-10)
REVERT: H   24 LYS cc_start: 0.9021 (tppp) cc_final: 0.8644 (mtmp)
  outliers start: 11
  outliers final: 6
  residues processed: 94
  average time/residue: 1.0495
  time to fit residues: 103.9846
Evaluate side-chains
  94 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  118 MET
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9990
   chunk 35 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  33 HIS
L  66 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.082617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.061488 restraints weight = 12969.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 2.59
r_work: 0.2788 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.2514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5805  Z= 0.185
  Angle     :  0.531   9.756   7840  Z= 0.271
  Chirality :  0.042   0.160    856
  Planarity :  0.004   0.046   1003
  Dihedral  :  9.391  64.792    916
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.02 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.71 (0.32), residues: 748
  helix:  2.38 (0.26), residues: 372
  sheet: -0.00 (0.45), residues: 142
  loop : -0.10 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  32 
 HIS   0.003   0.001   HIS A  33 
 PHE   0.013   0.001   PHE A  96 
 TYR   0.010   0.001   TYR H 117 
 ARG   0.004   0.000   ARG C 181 

*********************** 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
  109 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8077 (mp0)
REVERT: B  127 ASN cc_start: 0.7837 (t0) cc_final: 0.7496 (t0)
REVERT: B  162 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8237 (mp)
REVERT: B  195 LEU cc_start: 0.8116 (mm) cc_final: 0.7782 (tm)
REVERT: B  198 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7619 (mmt)
REVERT: B  200 TYR cc_start: 0.8638 (m-80) cc_final: 0.8312 (m-10)
REVERT: B  204 MET cc_start: 0.9214 (mtm) cc_final: 0.8910 (mtm)
REVERT: C  431 THR cc_start: 0.8499 (m) cc_final: 0.7988 (p)
REVERT: L  103 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8228 (mt-10)
REVERT: L  104 GLU cc_start: 0.7840 (tp30) cc_final: 0.7560 (tm-30)
REVERT: L  127 LYS cc_start: 0.8954 (tttp) cc_final: 0.8628 (tttp)
REVERT: L  129 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7956 (mt-10)
REVERT: H   24 LYS cc_start: 0.8985 (tppp) cc_final: 0.8649 (mtmp)
  outliers start: 13
  outliers final: 5
  residues processed: 102
  average time/residue: 1.0073
  time to fit residues: 108.5232
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  : 0.643 
-------------------------------------------------------------------------------
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  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  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 14 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 50 optimal weight:    0.7980
   chunk 29 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 16 optimal weight:    8.9990
   chunk 70 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0670
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.3724

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

Flipped N/Q/H residues before XYZ refinement:
C 335 GLN
C 408 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.081812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.060448 restraints weight = 12819.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 2.57
r_work: 0.2767 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5805  Z= 0.254
  Angle     :  0.554   9.671   7840  Z= 0.283
  Chirality :  0.043   0.165    856
  Planarity :  0.004   0.045   1003
  Dihedral  :  9.333  64.665    916
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.76 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.32), residues: 748
  helix:  2.49 (0.27), residues: 372
  sheet:  0.21 (0.47), residues: 135
  loop : -0.07 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  66 
 HIS   0.003   0.001   HIS A  33 
 PHE   0.013   0.001   PHE A  96 
 TYR   0.017   0.001   TYR B 159 
 ARG   0.003   0.000   ARG C 181 

*********************** 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
  105 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.611 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8095 (mp0)
REVERT: A  131 MET cc_start: 0.7957 (mmt) cc_final: 0.7674 (mmm)
REVERT: B  127 ASN cc_start: 0.7820 (t0) cc_final: 0.7524 (t0)
REVERT: B  162 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8231 (mp)
REVERT: B  195 LEU cc_start: 0.8170 (mm) cc_final: 0.7857 (tm)
REVERT: B  198 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7681 (mmt)
REVERT: B  200 TYR cc_start: 0.8633 (m-80) cc_final: 0.8332 (m-10)
REVERT: B  204 MET cc_start: 0.9234 (mtm) cc_final: 0.8972 (mtm)
REVERT: C  179 GLN cc_start: 0.8878 (mp10) cc_final: 0.8661 (mm-40)
REVERT: C  431 THR cc_start: 0.8474 (m) cc_final: 0.7985 (p)
REVERT: L  103 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8388 (mt-10)
REVERT: L  127 LYS cc_start: 0.8944 (tttp) cc_final: 0.8639 (tttp)
  outliers start: 13
  outliers final: 7
  residues processed: 98
  average time/residue: 1.0781
  time to fit residues: 111.3172
Evaluate side-chains
  99 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.675 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 31 optimal weight:   10.0000
   chunk 63 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 28 optimal weight:   30.0000
   chunk 7 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 35 optimal weight:   20.0000
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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

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 = 0.082309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.061179 restraints weight = 12703.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.57
r_work: 0.2781 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5805  Z= 0.205
  Angle     :  0.542  10.464   7840  Z= 0.274
  Chirality :  0.042   0.210    856
  Planarity :  0.004   0.043   1003
  Dihedral  :  9.132  64.891    916
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.76 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.32), residues: 748
  helix:  2.60 (0.27), residues: 372
  sheet:  0.18 (0.46), residues: 142
  loop :  0.03 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  66 
 HIS   0.003   0.001   HIS A  33 
 PHE   0.012   0.001   PHE A  96 
 TYR   0.020   0.001   TYR B 159 
 ARG   0.003   0.000   ARG C 181 

*********************** 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
  114 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8097 (mp0)
REVERT: A  131 MET cc_start: 0.7888 (mmt) cc_final: 0.7645 (mmm)
REVERT: B  127 ASN cc_start: 0.7863 (t0) cc_final: 0.7625 (t0)
REVERT: B  162 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8240 (mp)
REVERT: B  195 LEU cc_start: 0.8201 (mm) cc_final: 0.7894 (tm)
REVERT: B  198 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7626 (mmt)
REVERT: B  200 TYR cc_start: 0.8605 (m-80) cc_final: 0.8319 (m-10)
REVERT: B  204 MET cc_start: 0.9222 (mtm) cc_final: 0.8977 (mtm)
REVERT: C  431 THR cc_start: 0.8431 (m) cc_final: 0.7991 (p)
REVERT: L  103 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8242 (mt-10)
REVERT: L  104 GLU cc_start: 0.7627 (tp30) cc_final: 0.7290 (tm-30)
REVERT: L  127 LYS cc_start: 0.8962 (tttp) cc_final: 0.8698 (tttp)
REVERT: H   24 LYS cc_start: 0.9054 (mtpm) cc_final: 0.8476 (mtmp)
  outliers start: 15
  outliers final: 6
  residues processed: 106
  average time/residue: 1.1349
  time to fit residues: 126.7047
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  : 0.702 
-------------------------------------------------------------------------------
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 73 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0870
   chunk 11 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 30 optimal weight:   20.0000
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.083466 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.062373 restraints weight = 12733.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 2.59
r_work: 0.2812 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.2938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5805  Z= 0.171
  Angle     :  0.557  10.742   7840  Z= 0.277
  Chirality :  0.043   0.206    856
  Planarity :  0.004   0.046   1003
  Dihedral  :  8.796  64.680    916
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 17.53 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.32), residues: 748
  helix:  2.61 (0.27), residues: 372
  sheet:  0.26 (0.46), residues: 142
  loop :  0.08 (0.43), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  32 
 HIS   0.003   0.001   HIS A  33 
 PHE   0.010   0.001   PHE A  96 
 TYR   0.015   0.001   TYR B 159 
 ARG   0.003   0.000   ARG C 181 

*********************** 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
  108 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.870 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8143 (mp0)
REVERT: A  126 GLU cc_start: 0.8710 (tp30) cc_final: 0.8466 (tt0)
REVERT: A  131 MET cc_start: 0.7925 (mmt) cc_final: 0.7721 (mmm)
REVERT: B  127 ASN cc_start: 0.7844 (t0) cc_final: 0.7623 (t0)
REVERT: B  131 LYS cc_start: 0.8742 (ttmt) cc_final: 0.8257 (tttt)
REVERT: B  162 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8209 (mp)
REVERT: B  195 LEU cc_start: 0.8290 (mm) cc_final: 0.7980 (tm)
REVERT: B  200 TYR cc_start: 0.8571 (m-80) cc_final: 0.8259 (m-10)
REVERT: B  204 MET cc_start: 0.9230 (mtm) cc_final: 0.8973 (mtm)
REVERT: C  431 THR cc_start: 0.8356 (m) cc_final: 0.7986 (p)
REVERT: L  103 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8299 (mt-10)
REVERT: H   24 LYS cc_start: 0.9076 (mtpm) cc_final: 0.8498 (mtmt)
  outliers start: 8
  outliers final: 6
  residues processed: 105
  average time/residue: 1.1232
  time to fit residues: 124.0613
Evaluate side-chains
  98 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
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  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  109 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 26 optimal weight:   50.0000
   chunk 28 optimal weight:   30.0000
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.3371 r_free = 0.3371 target = 0.080190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2918 r_free = 0.2918 target = 0.058585 restraints weight = 12716.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 2.55
r_work: 0.2724 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.056   5805  Z= 0.493
  Angle     :  0.654   9.222   7840  Z= 0.331
  Chirality :  0.048   0.260    856
  Planarity :  0.004   0.047   1003
  Dihedral  :  9.641  66.113    916
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.32), residues: 748
  helix:  2.52 (0.27), residues: 372
  sheet:  0.24 (0.47), residues: 135
  loop :  0.01 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  66 
 HIS   0.004   0.001   HIS B 140 
 PHE   0.014   0.002   PHE C 289 
 TYR   0.020   0.002   TYR H 117 
 ARG   0.002   0.000   ARG C 181 

*********************** 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
  97 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.589 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8112 (mp0)
REVERT: B  195 LEU cc_start: 0.8264 (mm) cc_final: 0.7968 (tm)
REVERT: B  200 TYR cc_start: 0.8637 (m-80) cc_final: 0.8387 (m-10)
REVERT: B  204 MET cc_start: 0.9273 (mtm) cc_final: 0.9033 (mtm)
REVERT: C  431 THR cc_start: 0.8487 (m) cc_final: 0.7993 (p)
REVERT: L  103 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8243 (mt-10)
REVERT: L  127 LYS cc_start: 0.8932 (tttm) cc_final: 0.8647 (tttm)
REVERT: L  129 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8157 (mt-10)
REVERT: H   24 LYS cc_start: 0.9079 (mtpm) cc_final: 0.8479 (mtmp)
  outliers start: 11
  outliers final: 7
  residues processed: 92
  average time/residue: 1.0694
  time to fit residues: 103.5146
Evaluate side-chains
  91 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 ASP
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  211 VAL
Chi-restraints excluded: chain C residue  175 ILE
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 16 optimal weight:    5.9990
   chunk 20 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 70 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3369 r_free = 0.3369 target = 0.081118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.059389 restraints weight = 12736.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 2.68
r_work: 0.2728 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5805  Z= 0.329
  Angle     :  0.618  11.073   7840  Z= 0.311
  Chirality :  0.045   0.189    856
  Planarity :  0.004   0.046   1003
  Dihedral  :  9.507  65.711    916
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 17.53 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.32), residues: 748
  helix:  2.48 (0.27), residues: 373
  sheet:  0.25 (0.47), residues: 135
  loop : -0.12 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP H  66 
 HIS   0.003   0.001   HIS A  33 
 PHE   0.013   0.001   PHE C 322 
 TYR   0.015   0.001   TYR H 117 
 ARG   0.002   0.000   ARG C 181 

*********************** 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
  94 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8074 (mp0)
REVERT: B  195 LEU cc_start: 0.8313 (mm) cc_final: 0.8002 (tm)
REVERT: B  200 TYR cc_start: 0.8612 (m-80) cc_final: 0.8346 (m-80)
REVERT: B  204 MET cc_start: 0.9302 (mtm) cc_final: 0.9024 (mtm)
REVERT: C  431 THR cc_start: 0.8437 (m) cc_final: 0.7982 (p)
REVERT: L  103 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8184 (mt-10)
REVERT: L  127 LYS cc_start: 0.8808 (tttm) cc_final: 0.8569 (tttp)
REVERT: L  129 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8062 (mt-10)
REVERT: H   24 LYS cc_start: 0.8995 (mtpm) cc_final: 0.8344 (mtmp)
  outliers start: 7
  outliers final: 7
  residues processed: 91
  average time/residue: 1.0889
  time to fit residues: 104.1266
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  : 0.725 
-------------------------------------------------------------------------------
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  211 VAL
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain L residue  105 ASP
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 49 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 68 optimal weight:    0.3980
   chunk 47 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3401 r_free = 0.3401 target = 0.082784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.061089 restraints weight = 12808.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 2.71
r_work: 0.2771 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5805  Z= 0.190
  Angle     :  0.586  11.448   7840  Z= 0.296
  Chirality :  0.043   0.262    856
  Planarity :  0.004   0.045   1003
  Dihedral  :  9.111  66.443    916
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 17.90 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.01 (0.32), residues: 748
  helix:  2.61 (0.27), residues: 372
  sheet:  0.34 (0.47), residues: 135
  loop : -0.07 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  66 
 HIS   0.002   0.001   HIS A  33 
 PHE   0.012   0.001   PHE A  96 
 TYR   0.013   0.001   TYR B 159 
 ARG   0.002   0.000   ARG C 181 

********************** 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
  95 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8036 (mp0)
REVERT: B  195 LEU cc_start: 0.8295 (mm) cc_final: 0.7968 (tm)
REVERT: B  200 TYR cc_start: 0.8597 (m-80) cc_final: 0.8330 (m-10)
REVERT: B  204 MET cc_start: 0.9285 (mtm) cc_final: 0.9006 (mtm)
REVERT: C  431 THR cc_start: 0.8409 (m) cc_final: 0.7967 (p)
REVERT: L  103 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8229 (mt-10)
REVERT: L  104 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6880 (mm-30)
REVERT: L  129 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8234 (mt-10)
REVERT: H   24 LYS cc_start: 0.8988 (mtpm) cc_final: 0.8338 (mtmp)
  outliers start: 6
  outliers final: 4
  residues processed: 93
  average time/residue: 1.0581
  time to fit residues: 103.5132
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  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 LEU
Chi-restraints excluded: chain B residue  157 LEU
Chi-restraints excluded: chain B residue  211 VAL
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 18 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 31 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3406 r_free = 0.3406 target = 0.083002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.061314 restraints weight = 12915.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 2.72
r_work: 0.2773 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5805  Z= 0.210
  Angle     :  0.588  11.022   7840  Z= 0.297
  Chirality :  0.043   0.201    856
  Planarity :  0.004   0.043   1003
  Dihedral  :  8.858  65.899    916
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 18.45 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.32), residues: 748
  helix:  2.68 (0.27), residues: 372
  sheet:  0.43 (0.46), residues: 135
  loop : -0.05 (0.42), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  66 
 HIS   0.003   0.001   HIS A  33 
 PHE   0.012   0.001   PHE A  96 
 TYR   0.011   0.001   TYR B 159 
 ARG   0.002   0.000   ARG C 181 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3908.95 seconds
wall clock time: 69 minutes 55.55 seconds (4195.55 seconds total)