Starting phenix.real_space_refine
on Tue Mar 11 17:16:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e1m_27825/03_2025/8e1m_27825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e1m_27825/03_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_27825/03_2025/8e1m_27825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e1m_27825/03_2025/8e1m_27825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e1m_27825/03_2025/8e1m_27825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e1m_27825/03_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-5624/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: 5.43, per 1000 atoms: 0.95
  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: 1.77
  Conformation dependent library (CDL) restraints added in 984.2 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: 0.73
  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: 2.35

  Time building geometry restraints manager: 2.15 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:             0.680
  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:             0.020
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     21.650
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:17.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.050
-------------------------------------------------------------------------------
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  : 0.636 
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: 1.2044
  time to fit residues: 139.9871
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  : 0.594 
-------------------------------------------------------------------------------
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 = 0.081663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.060367 restraints weight = 12693.684|
|-----------------------------------------------------------------------------|
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  : 10.281  64.740    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  : 0.646 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.8269 (m) cc_final: 0.7971 (p)
REVERT: A   76 ASP cc_start: 0.9052 (t0) cc_final: 0.8826 (t0)
REVERT: B  127 ASN cc_start: 0.7968 (t0) cc_final: 0.7684 (t0)
REVERT: B  162 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8233 (mp)
REVERT: B  204 MET cc_start: 0.9159 (mtm) cc_final: 0.8948 (mtm)
REVERT: L  103 GLU cc_start: 0.8306 (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: 0.8530 (mtmp)
  outliers start: 8
  outliers final: 3
  residues processed: 95
  average time/residue: 1.0996
  time to fit residues: 109.8352
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  : 0.597 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 10 optimal weight:    7.9990
   chunk 73 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    1.7988

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

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

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 = 0.080726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.059572 restraints weight = 12840.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.55
r_work: 0.2741 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5805  Z= 0.308
  Angle     :  0.570   8.172   7840  Z= 0.295
  Chirality :  0.043   0.141    856
  Planarity :  0.004   0.044   1003
  Dihedral  :  9.932  67.736    916
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 12.18 %
    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:  1.39 (0.32), residues: 748
  helix:  2.11 (0.26), residues: 372
  sheet: -0.09 (0.46), residues: 135
  loop : -0.29 (0.43), residues: 241

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   0.014   0.001   TYR H 117 
 ARG   0.005   0.000   ARG C 181 

*********************** 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
  103 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.665 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 VAL cc_start: 0.8257 (m) cc_final: 0.7966 (p)
REVERT: A  131 MET cc_start: 0.7939 (mmt) cc_final: 0.7718 (mmm)
REVERT: B  127 ASN cc_start: 0.7957 (t0) cc_final: 0.7617 (t0)
REVERT: B  162 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8291 (mp)
REVERT: B  195 LEU cc_start: 0.8180 (mm) cc_final: 0.7841 (tm)
REVERT: B  198 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7722 (mmt)
REVERT: B  200 TYR cc_start: 0.8673 (m-80) cc_final: 0.8365 (m-10)
REVERT: B  204 MET cc_start: 0.9193 (mtm) cc_final: 0.8906 (mtm)
REVERT: C  179 GLN cc_start: 0.8917 (mp10) cc_final: 0.8704 (mm-40)
REVERT: C  431 THR cc_start: 0.8503 (m) cc_final: 0.7959 (p)
REVERT: L  103 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8169 (mt-10)
REVERT: L  127 LYS cc_start: 0.9001 (tttp) cc_final: 0.8709 (tttp)
REVERT: L  129 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7965 (mt-10)
REVERT: H   24 LYS cc_start: 0.9033 (tppp) cc_final: 0.8660 (mtmp)
  outliers start: 12
  outliers final: 6
  residues processed: 96
  average time/residue: 1.0162
  time to fit residues: 102.9122
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  : 0.665 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 35 optimal weight:   20.0000
   chunk 25 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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
H  32 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.082185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2971 r_free = 0.2971 target = 0.061037 restraints weight = 12998.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.58
r_work: 0.2785 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2478

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= 0.200
  Angle     :  0.540   9.579   7840  Z= 0.276
  Chirality :  0.042   0.185    856
  Planarity :  0.004   0.046   1003
  Dihedral  :  9.516  65.054    916
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.02 %
    Favored  : 83.76 %
  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:  1.68 (0.32), residues: 748
  helix:  2.35 (0.26), residues: 372
  sheet: -0.01 (0.45), residues: 142
  loop : -0.12 (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
  106 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8054 (mp0)
REVERT: B  127 ASN cc_start: 0.7886 (t0) cc_final: 0.7568 (t0)
REVERT: B  162 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8269 (mp)
REVERT: B  195 LEU cc_start: 0.8123 (mm) cc_final: 0.7793 (tm)
REVERT: B  198 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7668 (mmt)
REVERT: B  200 TYR cc_start: 0.8637 (m-80) cc_final: 0.8310 (m-10)
REVERT: B  204 MET cc_start: 0.9202 (mtm) cc_final: 0.8895 (mtm)
REVERT: C  431 THR cc_start: 0.8495 (m) cc_final: 0.7988 (p)
REVERT: L  103 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8363 (mt-10)
REVERT: L  104 GLU cc_start: 0.7922 (tp30) cc_final: 0.7608 (tm-30)
REVERT: L  127 LYS cc_start: 0.8968 (tttp) cc_final: 0.8632 (tttp)
REVERT: L  129 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7946 (mt-10)
REVERT: H   24 LYS cc_start: 0.9026 (tppp) cc_final: 0.8687 (mtmp)
  outliers start: 12
  outliers final: 6
  residues processed: 99
  average time/residue: 0.9804
  time to fit residues: 102.3963
Evaluate side-chains
  97 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 47 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 20 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 70 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0870
   chunk 23 optimal weight:    0.7980
   overall best weight:    1.1162

-------------------------------------------------------------------------------
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
L  66 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.082042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.060874 restraints weight = 12783.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.57
r_work: 0.2776 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5805  Z= 0.222
  Angle     :  0.547   9.878   7840  Z= 0.278
  Chirality :  0.042   0.159    856
  Planarity :  0.004   0.044   1003
  Dihedral  :  9.327  64.736    916
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 14.39 %
    Favored  : 83.03 %
  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:  1.89 (0.32), residues: 748
  helix:  2.51 (0.27), residues: 372
  sheet:  0.12 (0.46), residues: 142
  loop : -0.02 (0.44), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  32 
 HIS   0.002   0.001   HIS A  33 
 PHE   0.013   0.001   PHE A  96 
 TYR   0.011   0.001   TYR H 117 
 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
  106 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 MET cc_start: 0.8117 (mtt) cc_final: 0.7817 (mtp)
REVERT: A   45 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8074 (mp0)
REVERT: A  131 MET cc_start: 0.7976 (mmt) cc_final: 0.7702 (mmm)
REVERT: B   96 ASP cc_start: 0.8904 (m-30) cc_final: 0.8617 (m-30)
REVERT: B  127 ASN cc_start: 0.7838 (t0) cc_final: 0.7532 (t0)
REVERT: B  162 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8247 (mp)
REVERT: B  195 LEU cc_start: 0.8181 (mm) cc_final: 0.7876 (tm)
REVERT: B  198 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7649 (mmt)
REVERT: B  200 TYR cc_start: 0.8612 (m-80) cc_final: 0.8316 (m-10)
REVERT: B  204 MET cc_start: 0.9228 (mtm) cc_final: 0.8967 (mtm)
REVERT: C  179 GLN cc_start: 0.8872 (mp10) cc_final: 0.8661 (mm-40)
REVERT: C  431 THR cc_start: 0.8416 (m) cc_final: 0.7963 (p)
REVERT: L  103 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8239 (mt-10)
REVERT: L  127 LYS cc_start: 0.8935 (tttp) cc_final: 0.8627 (tttp)
REVERT: H   24 LYS cc_start: 0.8993 (tppp) cc_final: 0.8673 (mtmp)
  outliers start: 14
  outliers final: 6
  residues processed: 99
  average time/residue: 1.0101
  time to fit residues: 105.8123
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  : 0.628 
-------------------------------------------------------------------------------
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  109 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 63 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 28 optimal weight:   20.0000
   chunk 7 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 35 optimal weight:    9.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 122 GLN
C 408 GLN
L  66 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.082486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.061328 restraints weight = 12715.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 2.57
r_work: 0.2788 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5805  Z= 0.191
  Angle     :  0.549  10.005   7840  Z= 0.274
  Chirality :  0.042   0.187    856
  Planarity :  0.004   0.042   1003
  Dihedral  :  9.107  64.688    916
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.87 %
    Favored  : 81.92 %
  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:  1.98 (0.32), residues: 748
  helix:  2.60 (0.27), residues: 372
  sheet:  0.22 (0.47), residues: 135
  loop : -0.04 (0.42), residues: 241

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   0.012   0.001   PHE A  96 
 TYR   0.010   0.001   TYR H 117 
 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
  109 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8079 (mp0)
REVERT: A  131 MET cc_start: 0.7871 (mmt) cc_final: 0.7642 (mmm)
REVERT: B   96 ASP cc_start: 0.8887 (m-30) cc_final: 0.8596 (m-30)
REVERT: B  127 ASN cc_start: 0.7870 (t0) cc_final: 0.7638 (t0)
REVERT: B  131 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8253 (tttt)
REVERT: B  162 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8270 (mp)
REVERT: B  195 LEU cc_start: 0.8196 (mm) cc_final: 0.7886 (tm)
REVERT: B  198 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7600 (mmt)
REVERT: B  200 TYR cc_start: 0.8608 (m-80) cc_final: 0.8280 (m-10)
REVERT: B  204 MET cc_start: 0.9219 (mtm) cc_final: 0.8933 (mtm)
REVERT: C  431 THR cc_start: 0.8426 (m) cc_final: 0.8032 (p)
REVERT: L  103 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8427 (mt-10)
REVERT: L  104 GLU cc_start: 0.7841 (tp30) cc_final: 0.7436 (tm-30)
REVERT: L  127 LYS cc_start: 0.8963 (tttp) cc_final: 0.8711 (tttp)
REVERT: H   24 LYS cc_start: 0.8988 (tppp) cc_final: 0.8666 (mtmt)
  outliers start: 12
  outliers final: 6
  residues processed: 103
  average time/residue: 1.0079
  time to fit residues: 109.5300
Evaluate side-chains
  99 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 73 optimal weight:    0.0570
   chunk 2 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0470
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.5398

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.083540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.062528 restraints weight = 12731.632|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.57
r_work: 0.2825 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5805  Z= 0.171
  Angle     :  0.549  10.681   7840  Z= 0.273
  Chirality :  0.042   0.199    856
  Planarity :  0.004   0.048   1003
  Dihedral  :  8.771  64.163    916
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.16 %
    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:  2.07 (0.32), residues: 748
  helix:  2.63 (0.27), residues: 372
  sheet:  0.36 (0.47), residues: 135
  loop :  0.01 (0.42), residues: 241

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   0.008   0.001   TYR C 325 
 ARG   0.002   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
  111 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.603 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8090 (mp0)
REVERT: A  131 MET cc_start: 0.8014 (mmt) cc_final: 0.7807 (mmm)
REVERT: B   96 ASP cc_start: 0.8855 (m-30) cc_final: 0.8577 (m-30)
REVERT: B  127 ASN cc_start: 0.7842 (t0) cc_final: 0.7628 (t0)
REVERT: B  131 LYS cc_start: 0.8752 (ttmt) cc_final: 0.8278 (tttt)
REVERT: B  162 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8255 (mp)
REVERT: B  195 LEU cc_start: 0.8294 (mm) cc_final: 0.7981 (tm)
REVERT: B  200 TYR cc_start: 0.8577 (m-80) cc_final: 0.8249 (m-10)
REVERT: B  204 MET cc_start: 0.9205 (mtm) cc_final: 0.8931 (mtm)
REVERT: C  431 THR cc_start: 0.8353 (m) cc_final: 0.7982 (p)
REVERT: L  127 LYS cc_start: 0.8935 (tttp) cc_final: 0.8615 (tttp)
REVERT: H   24 LYS cc_start: 0.8957 (tppp) cc_final: 0.8672 (mtmt)
  outliers start: 9
  outliers final: 7
  residues processed: 107
  average time/residue: 1.0509
  time to fit residues: 118.3405
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  : 0.644 
-------------------------------------------------------------------------------
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   30 LEU
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:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0570
   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:    1.6104

-------------------------------------------------------------------------------
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 = 0.3403 r_free = 0.3403 target = 0.081903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.060569 restraints weight = 12612.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 2.56
r_work: 0.2772 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5805  Z= 0.282
  Angle     :  0.581   9.488   7840  Z= 0.291
  Chirality :  0.044   0.249    856
  Planarity :  0.004   0.048   1003
  Dihedral  :  9.083  65.298    916
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 17.34 %
    Favored  : 80.44 %
  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:  2.08 (0.32), residues: 748
  helix:  2.65 (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
 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   0.014   0.001   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
  106 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8112 (mp0)
REVERT: B   96 ASP cc_start: 0.8868 (m-30) cc_final: 0.8585 (m-30)
REVERT: B  131 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8275 (tttt)
REVERT: B  195 LEU cc_start: 0.8340 (mm) cc_final: 0.8038 (tm)
REVERT: B  200 TYR cc_start: 0.8614 (m-80) cc_final: 0.8347 (m-10)
REVERT: B  204 MET cc_start: 0.9231 (mtm) cc_final: 0.8999 (mtm)
REVERT: C  431 THR cc_start: 0.8387 (m) cc_final: 0.7997 (p)
REVERT: L  104 GLU cc_start: 0.7586 (tp30) cc_final: 0.7239 (tm-30)
REVERT: L  127 LYS cc_start: 0.8983 (tttp) cc_final: 0.8692 (tttp)
  outliers start: 12
  outliers final: 6
  residues processed: 99
  average time/residue: 1.0737
  time to fit residues: 111.8944
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  : 0.581 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0670
   chunk 44 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 13 optimal weight:    0.1980
   chunk 70 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0770
   overall best weight:    0.4478

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.083678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.062601 restraints weight = 12634.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.58
r_work: 0.2825 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   5805  Z= 0.165
  Angle     :  0.565  11.602   7840  Z= 0.282
  Chirality :  0.042   0.191    856
  Planarity :  0.004   0.044   1003
  Dihedral  :  8.671  64.241    916
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 17.90 %
    Favored  : 80.63 %
  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:  2.12 (0.32), residues: 748
  helix:  2.68 (0.27), residues: 374
  sheet:  0.41 (0.46), residues: 135
  loop : -0.03 (0.42), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  32 
 HIS   0.002   0.001   HIS A  33 
 PHE   0.012   0.001   PHE A  96 
 TYR   0.008   0.001   TYR C 325 
 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
  104 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8076 (mp0)
REVERT: B   96 ASP cc_start: 0.8878 (m-30) cc_final: 0.8602 (m-30)
REVERT: B  131 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8276 (tttt)
REVERT: B  195 LEU cc_start: 0.8208 (mm) cc_final: 0.7908 (tm)
REVERT: B  200 TYR cc_start: 0.8574 (m-80) cc_final: 0.8281 (m-10)
REVERT: B  204 MET cc_start: 0.9223 (mtm) cc_final: 0.8940 (mtm)
REVERT: C  431 THR cc_start: 0.8353 (m) cc_final: 0.7969 (p)
REVERT: L  104 GLU cc_start: 0.7543 (tp30) cc_final: 0.6930 (tm-30)
REVERT: L  106 ASP cc_start: 0.9017 (p0) cc_final: 0.8800 (p0)
REVERT: L  127 LYS cc_start: 0.8950 (tttp) cc_final: 0.8696 (tttp)
REVERT: H   24 LYS cc_start: 0.9059 (mtpm) cc_final: 0.8487 (mtmp)
  outliers start: 8
  outliers final: 4
  residues processed: 101
  average time/residue: 1.0099
  time to fit residues: 107.5686
Evaluate side-chains
  93 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain B residue  118 MET
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 49 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3426 r_free = 0.3426 target = 0.083066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.062115 restraints weight = 12834.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.57
r_work: 0.2810 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.3173

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= 0.208
  Angle     :  0.579  10.585   7840  Z= 0.292
  Chirality :  0.043   0.267    856
  Planarity :  0.004   0.045   1003
  Dihedral  :  8.636  63.631    916
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 18.63 %
    Favored  : 80.44 %
  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:  2.18 (0.32), residues: 748
  helix:  2.77 (0.27), residues: 372
  sheet:  0.46 (0.46), residues: 135
  loop : -0.08 (0.41), 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   0.012   0.001   PHE A  96 
 TYR   0.010   0.001   TYR H 117 
 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
  97 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8074 (mp0)
REVERT: A  131 MET cc_start: 0.7985 (mmt) cc_final: 0.7630 (mmm)
REVERT: B  131 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8283 (tttt)
REVERT: B  200 TYR cc_start: 0.8593 (m-80) cc_final: 0.8327 (m-10)
REVERT: B  204 MET cc_start: 0.9218 (mtm) cc_final: 0.8959 (mtm)
REVERT: C  431 THR cc_start: 0.8377 (m) cc_final: 0.7991 (p)
REVERT: L  104 GLU cc_start: 0.7582 (tp30) cc_final: 0.6851 (tm-30)
REVERT: L  127 LYS cc_start: 0.8952 (tttp) cc_final: 0.8710 (tttp)
REVERT: H   24 LYS cc_start: 0.9071 (mtpm) cc_final: 0.8502 (mtmt)
  outliers start: 5
  outliers final: 3
  residues processed: 94
  average time/residue: 1.1483
  time to fit residues: 113.1866
Evaluate side-chains
  92 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  211 VAL
Chi-restraints excluded: chain L residue  103 GLU
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:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 55 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 122 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 = 0.3435 r_free = 0.3435 target = 0.083423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.062024 restraints weight = 12837.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.60
r_work: 0.2819 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8266
moved from start:          0.3233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5805  Z= 0.193
  Angle     :  0.576  10.848   7840  Z= 0.291
  Chirality :  0.042   0.189    856
  Planarity :  0.004   0.045   1003
  Dihedral  :  8.489  63.587    916
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 19.56 %
    Favored  : 79.52 %
  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:  2.16 (0.32), residues: 748
  helix:  2.73 (0.26), residues: 374
  sheet:  0.48 (0.46), residues: 135
  loop : -0.09 (0.41), residues: 239

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   0.009   0.001   TYR H 117 
 ARG   0.005   0.000   ARG L  85 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3910.28 seconds
wall clock time: 67 minutes 24.72 seconds (4044.72 seconds total)