Starting phenix.real_space_refine
on Thu Mar 13 20:55:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxr_36710/03_2025/8jxr_36710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxr_36710/03_2025/8jxr_36710.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jxr_36710/03_2025/8jxr_36710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxr_36710/03_2025/8jxr_36710.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxr_36710/03_2025/8jxr_36710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxr_36710/03_2025/8jxr_36710.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 871 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    5550      2.51       5
     N    1421      2.21       5
     O    1604      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 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: 8616
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2146
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 270, 2146
          Classifications: {'peptide': 270}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 260}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 929
          Classifications: {'peptide': 124}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 2649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 341, 2649
          Classifications: {'peptide': 341}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 22, 'TRANS': 318}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "H"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1536
          Classifications: {'peptide': 202}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 13, 'TRANS': 188}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "L"
      Number of atoms: 1309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1309
          Classifications: {'peptide': 171}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 161}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "D"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 23
          Unusual residues: {'GLC': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'7LD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.76, per 1000 atoms: 0.67
  Number of scatterers: 8616
  At special positions: 0
  Unit cell: (135.96, 122.776, 98.056, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      41     16.00
     O    1604      8.00
     N    1421      7.00
     C    5550      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS A 186 " distance=2.08
    Simple disulfide: pdb=" SG  CYS A 298 " - pdb=" SG  CYS A 307 " distance=2.02

  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
  Links applied
    ALPHA1-4
      " GLC D   1 " - " GLC D   2 "
  Time building additional restraints: 2.60
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2078

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 17 sheets defined
      41.8% alpha, 24.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 51
      removed outlier: 3.769A  pdb=" N   PHE A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 56
      removed outlier: 4.029A  pdb=" N   ARG A  55 " --> pdb=" O   PHE A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 76
      removed outlier: 4.069A  pdb=" N   PHE A  61 " --> pdb=" O   LYS A  57 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   PHE A  62 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   VAL A  63 " --> pdb=" O   THR A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 88
    Processing helix  chain 'A' and resid 95 through 127
    Processing helix  chain 'A' and resid 127 through 135
      removed outlier: 3.779A  pdb=" N   ARG A 133 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 161
      removed outlier: 3.953A  pdb=" N   ILE A 157 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
      Proline residue:  A 158  - end of helix
    Processing helix  chain 'A' and resid 191 through 203
    Processing helix  chain 'A' and resid 203 through 236
    Processing helix  chain 'A' and resid 265 through 295
      removed outlier: 4.477A  pdb=" N   VAL A 280 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   PHE A 281 " --> pdb=" O   ILE A 277 " (cutoff:3.500A)
      Proline residue:  A 287  - end of helix
    Processing helix  chain 'A' and resid 309 through 332
      removed outlier: 3.602A  pdb=" N   PHE A 313 " --> pdb=" O   ASP A 309 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   SER A 324 " --> pdb=" O   GLY A 320 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA A 325 " --> pdb=" O   TRP A 321 " (cutoff:3.500A)
      Proline residue:  A 328  - end of helix
    Processing helix  chain 'A' and resid 334 through 345
    Processing helix  chain 'B' and resid 86 through 90
      removed outlier: 3.670A  pdb=" N   THR B  90 " --> pdb=" O   PRO B  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 52
      Proline residue:  C  49  - end of helix
    Processing helix  chain 'C' and resid 65 through 75
      removed outlier: 3.703A  pdb=" N   GLY C  69 " --> pdb=" O   HIS C  65 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   GLY C  70 " --> pdb=" O   ASP C  66 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER C  74 " --> pdb=" O   GLY C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 83 through 89
      removed outlier: 3.626A  pdb=" N   LYS C  89 " --> pdb=" O   ALA C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 98
      removed outlier: 3.571A  pdb=" N   TRP C  95 " --> pdb=" O   TYR C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 131
      No H-bonds generated for 'chain 'C' and resid 129 through 131'
    Processing helix  chain 'C' and resid 132 through 141
    Processing helix  chain 'C' and resid 154 through 165
      removed outlier: 4.153A  pdb=" N   THR C 158 " --> pdb=" O   GLU C 154 " (cutoff:3.500A)
      Proline residue:  C 160  - end of helix
      removed outlier: 4.475A  pdb=" N   ASP C 165 " --> pdb=" O   LEU C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 202
    Processing helix  chain 'C' and resid 210 through 220
    Processing helix  chain 'C' and resid 229 through 233
    Processing helix  chain 'C' and resid 316 through 328
    Processing helix  chain 'C' and resid 336 through 352
    Processing helix  chain 'C' and resid 357 through 370
      removed outlier: 3.507A  pdb=" N   MET C 370 " --> pdb=" O   GLN C 366 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 374 through 388
    Processing helix  chain 'C' and resid 391 through 404
    Processing helix  chain 'C' and resid 504 through 517
      removed outlier: 4.076A  pdb=" N   ALA C 509 " --> pdb=" O   THR C 505 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 4.124A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 102 through 107
    Processing helix  chain 'H' and resid 166 through 168
      No H-bonds generated for 'chain 'H' and resid 166 through 168'
    Processing helix  chain 'L' and resid 85 through 89
      removed outlier: 3.626A  pdb=" N   LEU L  89 " --> pdb=" O   PRO L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 126 through 133
      removed outlier: 3.875A  pdb=" N   SER L 132 " --> pdb=" O   GLU L 128 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12
      removed outlier: 5.829A  pdb=" N   ARG B  38 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   LEU B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12
    Processing sheet with id=AA4, first strand: chain 'C' and resid 63 through 64
      removed outlier: 7.091A  pdb=" N   GLY C 261 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 5.356A  pdb=" N   VAL C 111 " --> pdb=" O   GLY C 261 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   LEU C 263 " --> pdb=" O   ILE C 109 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 63 through 64
    Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 100
    Processing sheet with id=AA7, first strand: chain 'C' and resid 225 through 228
    Processing sheet with id=AA8, first strand: chain 'C' and resid 172 through 173
    Processing sheet with id=AA9, first strand: chain 'C' and resid 532 through 535
      removed outlier: 6.153A  pdb=" N   VAL C 486 " --> pdb=" O   VAL C 534 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   LYS C 493 " --> pdb=" O   ASP H 218 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.893A  pdb=" N   GLY H  33 " --> pdb=" O   ARG H  99 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.674A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 130 through 134
      removed outlier: 3.562A  pdb=" N   ASP H 154 " --> pdb=" O   TYR H 186 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 130 through 134
      removed outlier: 3.562A  pdb=" N   ASP H 154 " --> pdb=" O   TYR H 186 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   TYR H 186 " --> pdb=" O   ASP H 154 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 4 through 6
    Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.800A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   LYS L 112 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   VAL L  13 " --> pdb=" O   LYS L 112 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 14
      removed outlier: 6.800A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 110 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   LYS L 112 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   VAL L  13 " --> pdb=" O   LYS L 112 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   GLN L  96 " --> pdb=" O   THR L 102 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   THR L 102 " --> pdb=" O   GLN L  96 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 119 through 123
      removed outlier: 5.431A  pdb=" N   LEU L 140 " --> pdb=" O   SER L 182 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   SER L 182 " --> pdb=" O   LEU L 140 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   ASN L 142 " --> pdb=" O   LEU L 180 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   LEU L 180 " --> pdb=" O   ASN L 142 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1293 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: 2.83

  Time building geometry restraints manager: 3.03 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: 2696
        1.34 -     1.47: 2283
        1.47 -     1.60: 3783
        1.60 -     1.73: 0
        1.73 -     1.86: 62
  Bond restraints: 8824
  Sorted by residual:
  bond pdb=" C14 7LD A 401 "
       pdb=" C16 7LD A 401 "
    ideal  model  delta    sigma   weight residual
    1.525  1.403  0.122 2.00e-02 2.50e+03 3.69e+01
  bond pdb=" C11 7LD A 401 "
       pdb=" C9  7LD A 401 "
    ideal  model  delta    sigma   weight residual
    1.525  1.406  0.119 2.00e-02 2.50e+03 3.55e+01
  bond pdb=" C10 7LD A 401 "
       pdb=" C14 7LD A 401 "
    ideal  model  delta    sigma   weight residual
    1.501  1.398  0.103 2.00e-02 2.50e+03 2.64e+01
  bond pdb=" C15 7LD A 401 "
       pdb=" C7  7LD A 401 "
    ideal  model  delta    sigma   weight residual
    1.491  1.395  0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" C3  7LD A 401 "
       pdb=" C7  7LD A 401 "
    ideal  model  delta    sigma   weight residual
    1.414  1.322  0.092 2.00e-02 2.50e+03 2.11e+01
  ... (remaining 8819 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 11853
        1.82 -     3.64: 117
        3.64 -     5.46: 25
        5.46 -     7.28: 6
        7.28 -     9.10: 1
  Bond angle restraints: 12002
  Sorted by residual:
  angle pdb=" N   LEU A 190 "
        pdb=" CA  LEU A 190 "
        pdb=" C   LEU A 190 "
      ideal   model   delta    sigma   weight residual
     109.40  115.95   -6.55 1.63e+00 3.76e-01 1.61e+01
  angle pdb=" N   ILE C 109 "
        pdb=" CA  ILE C 109 "
        pdb=" C   ILE C 109 "
      ideal   model   delta    sigma   weight residual
     111.48  108.95    2.53 9.40e-01 1.13e+00 7.23e+00
  angle pdb=" CA  LEU A  39 "
        pdb=" CB  LEU A  39 "
        pdb=" CG  LEU A  39 "
      ideal   model   delta    sigma   weight residual
     116.30  125.40   -9.10 3.50e+00 8.16e-02 6.76e+00
  angle pdb=" CA  CYS A 298 "
        pdb=" CB  CYS A 298 "
        pdb=" SG  CYS A 298 "
      ideal   model   delta    sigma   weight residual
     114.40  120.20   -5.80 2.30e+00 1.89e-01 6.37e+00
  angle pdb=" C   ILE A  24 "
        pdb=" CA  ILE A  24 "
        pdb=" CB  ILE A  24 "
      ideal   model   delta    sigma   weight residual
     111.97  108.84    3.13 1.28e+00 6.10e-01 6.00e+00
  ... (remaining 11997 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.34: 5110
       30.34 -    60.68: 107
       60.68 -    91.02: 14
       91.02 -   121.36: 0
      121.36 -   151.70: 1
  Dihedral angle restraints: 5232
    sinusoidal: 2017
      harmonic: 3215
  Sorted by residual:
  dihedral pdb=" CB  CYS A 298 "
           pdb=" SG  CYS A 298 "
           pdb=" SG  CYS A 307 "
           pdb=" CB  CYS A 307 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  163.95  -70.95     1      1.00e+01 1.00e-02 6.47e+01
  dihedral pdb=" C16 7LD A 401 "
           pdb=" C17 7LD A 401 "
           pdb=" N3  7LD A 401 "
           pdb=" C18 7LD A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      91.75 -116.55 -151.70     1      3.00e+01 1.11e-03 2.01e+01
  dihedral pdb=" CB  CYS A  96 "
           pdb=" SG  CYS A  96 "
           pdb=" SG  CYS A 186 "
           pdb=" CB  CYS A 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -55.29  -30.71     1      1.00e+01 1.00e-02 1.35e+01
  ... (remaining 5229 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.141: 1352
       0.141 -    0.281: 5
       0.281 -    0.422: 3
       0.422 -    0.562: 0
       0.562 -    0.703: 1
  Chirality restraints: 1361
  Sorted by residual:
  chirality pdb=" C1  GLC D   2 "
            pdb=" O4  GLC D   1 "
            pdb=" C2  GLC D   2 "
            pdb=" O5  GLC D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    1.70    0.70 2.00e-02 2.50e+03 1.24e+03
  chirality pdb=" C14 7LD A 401 "
            pdb=" C10 7LD A 401 "
            pdb=" C13 7LD A 401 "
            pdb=" C16 7LD A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.63    2.30    0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" C1  GLC D   1 "
            pdb=" C2  GLC D   1 "
            pdb=" O1  GLC D   1 "
            pdb=" O5  GLC D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.04   -2.34    0.30 2.00e-01 2.50e+01 2.32e+00
  ... (remaining 1358 not shown)

  Planarity restraints: 1505
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 185 "   -0.008 2.00e-02 2.50e+03   1.57e-02 2.47e+00
        pdb=" C   ASN A 185 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ASN A 185 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   CYS A 186 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  7LD A 401 "   -0.001 2.00e-02 2.50e+03   8.05e-03 1.78e+00
        pdb=" C15 7LD A 401 "   -0.014 2.00e-02 2.50e+03
        pdb=" C2  7LD A 401 "   -0.006 2.00e-02 2.50e+03
        pdb=" C3  7LD A 401 "    0.004 2.00e-02 2.50e+03
        pdb=" C4  7LD A 401 "    0.001 2.00e-02 2.50e+03
        pdb=" C5  7LD A 401 "    0.001 2.00e-02 2.50e+03
        pdb=" C6  7LD A 401 "   -0.011 2.00e-02 2.50e+03
        pdb=" C7  7LD A 401 "    0.008 2.00e-02 2.50e+03
        pdb=" C8  7LD A 401 "    0.002 2.00e-02 2.50e+03
        pdb=" C9  7LD A 401 "    0.016 2.00e-02 2.50e+03
        pdb=" N1  7LD A 401 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 205 "   -0.015 5.00e-02 4.00e+02   2.33e-02 8.66e-01
        pdb=" N   PRO A 206 "    0.040 5.00e-02 4.00e+02
        pdb=" CA  PRO A 206 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 206 "   -0.013 5.00e-02 4.00e+02
  ... (remaining 1502 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 64
        2.60 -     3.17: 7429
        3.17 -     3.75: 13161
        3.75 -     4.32: 17937
        4.32 -     4.90: 30837
  Nonbonded interactions: 69428
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C 154 "
            pdb=" O6  GLC D   2 "
     model   vdw
     2.023 3.040
  nonbonded pdb=" O   PHE A  62 "
            pdb=" OG  SER A  65 "
     model   vdw
     2.119 3.040
  nonbonded pdb=" O   ALA A 101 "
            pdb=" OG  SER A 155 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" ND2 ASN H 207 "
            pdb=" OD1 ASN H 209 "
     model   vdw
     2.183 3.120
  nonbonded pdb=" N   GLU C  45 "
            pdb=" OE1 GLU C  45 "
     model   vdw
     2.275 3.120
  ... (remaining 69423 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.030
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7076
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      :  0.004   0.122   8824  Z= 0.259
  Angle     :  0.497   9.103  12002  Z= 0.263
  Chirality :  0.047   0.703   1361
  Planarity :  0.002   0.023   1505
  Dihedral  : 12.642 151.705   3148
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  4.79 %
    Favored  : 95.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.24), residues: 1072
  helix: -0.02 (0.25), residues: 397
  sheet: -1.31 (0.28), residues: 250
  loop : -1.17 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP C 130 
 HIS   0.002   0.000   HIS H  35 
 PHE   0.004   0.000   PHE A 102 
 TYR   0.005   0.000   TYR H  95 
 ARG   0.001   0.000   ARG A 133 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.858 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 SER cc_start: 0.7715 (t) cc_final: 0.7330 (p)
REVERT: A  132 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7386 (mm-30)
REVERT: A  160 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7897 (mm-40)
REVERT: A  339 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7666 (ttpp)
REVERT: L   42 TYR cc_start: 0.8533 (m-80) cc_final: 0.8108 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 176
  average time/residue: 0.2345
  time to fit residues: 55.6224
Evaluate side-chains
  107 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:   10.0000
   chunk 83 optimal weight:    3.9990
   chunk 46 optimal weight:    8.9990
   chunk 28 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 86 optimal weight:   30.0000
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9980
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 327 ASN
B  61 ASN
B  83 ASN
B 115 GLN
B 123 HIS
C 219 ASN
C 333 ASN
H  84 ASN
H 165 ASN
H 207 ASN
L  27 GLN
L  48 GLN
L 163 ASN
L 165 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.170661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.144790 restraints weight = 9963.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.142718 restraints weight = 18438.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.139377 restraints weight = 16750.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.100   8824  Z= 0.481
  Angle     :  0.705   8.836  12002  Z= 0.362
  Chirality :  0.047   0.191   1361
  Planarity :  0.005   0.035   1505
  Dihedral  :  7.073 157.766   1239
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 11.98 %
    Favored  : 84.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.15 (0.25), residues: 1072
  helix:  0.85 (0.25), residues: 398
  sheet: -0.42 (0.31), residues: 257
  loop : -0.68 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 341 
 HIS   0.009   0.002   HIS H  35 
 PHE   0.023   0.003   PHE A 316 
 TYR   0.022   0.003   TYR L  97 
 ARG   0.007   0.001   ARG C 378 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 107
  time to evaluate  : 0.900 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8885 (mp)
REVERT: A  103 ASP cc_start: 0.8852 (t70) cc_final: 0.8586 (t0)
REVERT: A  160 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7919 (mm-40)
REVERT: A  231 LEU cc_start: 0.7531 (mp) cc_final: 0.7325 (mp)
REVERT: A  329 ILE cc_start: 0.9165 (mm) cc_final: 0.8930 (mt)
REVERT: B   64 LYS cc_start: 0.9131 (tptt) cc_final: 0.8919 (tppt)
REVERT: C   43 LYS cc_start: 0.7668 (mmmt) cc_final: 0.7435 (mtpt)
REVERT: C  333 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7614 (t0)
REVERT: H   57 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8623 (p)
REVERT: H   93 MET cc_start: 0.7844 (tpp) cc_final: 0.7363 (tpp)
  outliers start: 32
  outliers final: 18
  residues processed: 131
  average time/residue: 0.1831
  time to fit residues: 34.4584
Evaluate side-chains
  113 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   92 PHE
Chi-restraints excluded: chain A residue  186 CYS
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  283 CYS
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  330 ILE
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  168 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 79 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 104 optimal weight:    0.5980
   chunk 106 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  52 HIS
L   1 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.176381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.147864 restraints weight = 9948.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.145351 restraints weight = 16245.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.146704 restraints weight = 14563.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8824  Z= 0.165
  Angle     :  0.508   6.951  12002  Z= 0.258
  Chirality :  0.041   0.152   1361
  Planarity :  0.003   0.040   1505
  Dihedral  :  6.474 141.612   1239
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.92 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1072
  helix:  1.58 (0.26), residues: 403
  sheet: -0.35 (0.33), residues: 232
  loop : -0.47 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H 164 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.018   0.001   PHE L 121 
 TYR   0.019   0.001   TYR H 155 
 ARG   0.005   0.000   ARG H  19 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 1.144 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8828 (mp)
REVERT: A   52 ARG cc_start: 0.7031 (tpt170) cc_final: 0.6733 (tpt-90)
REVERT: A  103 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8628 (t0)
REVERT: A  160 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7910 (mm-40)
REVERT: A  231 LEU cc_start: 0.7590 (mp) cc_final: 0.7352 (mp)
REVERT: A  278 MET cc_start: 0.7940 (tpt) cc_final: 0.7601 (tpt)
REVERT: A  329 ILE cc_start: 0.9116 (mm) cc_final: 0.8887 (mt)
REVERT: A  344 LEU cc_start: 0.8083 (tt) cc_final: 0.7775 (tp)
  outliers start: 19
  outliers final: 11
  residues processed: 118
  average time/residue: 0.2528
  time to fit residues: 40.7822
Evaluate side-chains
  106 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 1.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  103 ASP
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue  225 MET
Chi-restraints excluded: chain C residue  330 ILE
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue   91 VAL
Chi-restraints excluded: chain L residue  168 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 38 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 109 optimal weight:    0.0170
   chunk 12 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9980
   chunk 48 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.7418

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

Flipped N/Q/H residues before XYZ refinement:
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L   1 ASN
L 129 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.178088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.153401 restraints weight = 9910.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.151657 restraints weight = 16490.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.152080 restraints weight = 14739.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8824  Z= 0.159
  Angle     :  0.496   7.012  12002  Z= 0.249
  Chirality :  0.040   0.150   1361
  Planarity :  0.004   0.044   1505
  Dihedral  :  6.197 132.015   1239
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.90 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.26), residues: 1072
  helix:  1.96 (0.26), residues: 404
  sheet: -0.22 (0.32), residues: 246
  loop : -0.30 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP H 164 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.016   0.001   PHE L 121 
 TYR   0.015   0.001   TYR H 155 
 ARG   0.006   0.001   ARG H  19 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8840 (mp)
REVERT: A   52 ARG cc_start: 0.7024 (tpt170) cc_final: 0.6726 (tpt-90)
REVERT: A  231 LEU cc_start: 0.7612 (mp) cc_final: 0.7359 (mp)
REVERT: A  278 MET cc_start: 0.7725 (tpt) cc_final: 0.7509 (tpt)
REVERT: A  344 LEU cc_start: 0.8116 (tt) cc_final: 0.7820 (tp)
REVERT: C  315 ASP cc_start: 0.6581 (m-30) cc_final: 0.6374 (m-30)
REVERT: C  333 ASN cc_start: 0.7811 (t0) cc_final: 0.7588 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 124
  average time/residue: 0.2227
  time to fit residues: 38.8935
Evaluate side-chains
  113 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  330 ILE
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue   91 VAL
Chi-restraints excluded: chain L residue  168 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 54 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   1 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.176377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.148619 restraints weight = 9912.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.146241 restraints weight = 16333.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.147572 restraints weight = 15922.286|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8824  Z= 0.161
  Angle     :  0.494   6.811  12002  Z= 0.248
  Chirality :  0.040   0.159   1361
  Planarity :  0.003   0.038   1505
  Dihedral  :  5.894 118.068   1239
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 15.25 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1072
  helix:  2.14 (0.26), residues: 403
  sheet: -0.17 (0.31), residues: 257
  loop : -0.23 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 318 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.014   0.001   PHE A 288 
 TYR   0.012   0.001   TYR L  97 
 ARG   0.006   0.000   ARG H  19 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8854 (mp)
REVERT: A   52 ARG cc_start: 0.7002 (tpt170) cc_final: 0.6712 (tpt-90)
REVERT: A  231 LEU cc_start: 0.7538 (mp) cc_final: 0.7294 (mp)
REVERT: A  278 MET cc_start: 0.7917 (tpt) cc_final: 0.7706 (tpt)
REVERT: A  344 LEU cc_start: 0.8187 (tt) cc_final: 0.7927 (tp)
REVERT: C  333 ASN cc_start: 0.7872 (t0) cc_final: 0.7531 (t0)
  outliers start: 30
  outliers final: 20
  residues processed: 131
  average time/residue: 0.2051
  time to fit residues: 37.7387
Evaluate side-chains
  117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  267 GLU
Chi-restraints excluded: chain A residue  283 CYS
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  330 ILE
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue    9 SER
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue   91 VAL
Chi-restraints excluded: chain L residue  168 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   chunk 97 optimal weight:    2.9990
   chunk 79 optimal weight:    0.8980
   chunk 109 optimal weight:    3.9990
   chunk 51 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.162598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.137157 restraints weight = 9943.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.135231 restraints weight = 17991.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.135852 restraints weight = 18027.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   8824  Z= 0.290
  Angle     :  0.570   7.225  12002  Z= 0.290
  Chirality :  0.042   0.153   1361
  Planarity :  0.004   0.036   1505
  Dihedral  :  6.183 113.713   1239
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 15.47 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.26), residues: 1072
  helix:  1.95 (0.26), residues: 405
  sheet: -0.08 (0.31), residues: 265
  loop : -0.28 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.019   0.002   PHE A 288 
 TYR   0.018   0.002   TYR L  97 
 ARG   0.005   0.001   ARG H  19 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 1.224 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8837 (mp)
REVERT: A   52 ARG cc_start: 0.7003 (tpt170) cc_final: 0.6713 (tpt-90)
REVERT: A  278 MET cc_start: 0.7983 (tpt) cc_final: 0.7688 (tpt)
REVERT: A  344 LEU cc_start: 0.8324 (tt) cc_final: 0.8092 (tp)
REVERT: L   67 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7976 (ptt-90)
  outliers start: 32
  outliers final: 25
  residues processed: 123
  average time/residue: 0.2503
  time to fit residues: 43.0535
Evaluate side-chains
  121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  283 CYS
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  330 ILE
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue    9 SER
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   67 ARG
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue   91 VAL
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain L residue  168 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 77 optimal weight:    0.4980
   chunk 62 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 79 optimal weight:    0.0970
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 43 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 78 optimal weight:    0.3980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.168412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.143162 restraints weight = 9976.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.140491 restraints weight = 17577.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.141044 restraints weight = 17873.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8824  Z= 0.154
  Angle     :  0.510   6.575  12002  Z= 0.254
  Chirality :  0.040   0.160   1361
  Planarity :  0.003   0.036   1505
  Dihedral  :  5.372  90.493   1239
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.12 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.12 (0.26), residues: 1072
  helix:  2.28 (0.26), residues: 404
  sheet: -0.06 (0.31), residues: 255
  loop : -0.22 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.014   0.001   PHE L 121 
 TYR   0.030   0.001   TYR H 155 
 ARG   0.006   0.000   ARG H  19 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.926 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8801 (mp)
REVERT: A   52 ARG cc_start: 0.6965 (tpt170) cc_final: 0.6670 (tpt-90)
REVERT: A  344 LEU cc_start: 0.8248 (tt) cc_final: 0.8033 (tp)
  outliers start: 28
  outliers final: 22
  residues processed: 128
  average time/residue: 0.2204
  time to fit residues: 38.9926
Evaluate side-chains
  122 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain A residue  283 CYS
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  330 ILE
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain L residue  168 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 94 optimal weight:    8.9990
   chunk 108 optimal weight:    9.9990
   chunk 15 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 13 optimal weight:    0.0030
   chunk 78 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0870
   chunk 67 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0970
   chunk 79 optimal weight:    3.9990
   overall best weight:    0.3766

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.168511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.140692 restraints weight = 10008.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.137830 restraints weight = 14625.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.138425 restraints weight = 13951.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.3567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8824  Z= 0.136
  Angle     :  0.506   7.249  12002  Z= 0.251
  Chirality :  0.040   0.169   1361
  Planarity :  0.003   0.038   1505
  Dihedral  :  4.613  59.711   1239
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.21 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.26), residues: 1072
  helix:  2.42 (0.26), residues: 404
  sheet:  0.01 (0.31), residues: 255
  loop : -0.12 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.020   0.001   PHE L 121 
 TYR   0.030   0.001   TYR H 155 
 ARG   0.006   0.000   ARG H  19 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.958 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8849 (mp)
REVERT: A  344 LEU cc_start: 0.8216 (tt) cc_final: 0.8010 (tp)
REVERT: H   93 MET cc_start: 0.7533 (tpp) cc_final: 0.7255 (tpp)
  outliers start: 21
  outliers final: 17
  residues processed: 120
  average time/residue: 0.1854
  time to fit residues: 31.9573
Evaluate side-chains
  115 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  330 ILE
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain L residue  168 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 95 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   chunk 4 optimal weight:    0.7980
   chunk 45 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.165250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.138469 restraints weight = 9907.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.136080 restraints weight = 17888.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.136630 restraints weight = 17430.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8824  Z= 0.190
  Angle     :  0.528   7.647  12002  Z= 0.262
  Chirality :  0.040   0.174   1361
  Planarity :  0.003   0.036   1505
  Dihedral  :  4.355  38.516   1239
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 16.99 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.26), residues: 1072
  helix:  2.39 (0.26), residues: 404
  sheet:  0.02 (0.30), residues: 255
  loop : -0.10 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.017   0.001   PHE L 121 
 TYR   0.029   0.001   TYR H 155 
 ARG   0.006   0.000   ARG H  19 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8860 (mp)
REVERT: A   52 ARG cc_start: 0.6996 (tpt170) cc_final: 0.6697 (tpt-90)
REVERT: A  344 LEU cc_start: 0.8272 (tt) cc_final: 0.8063 (tp)
  outliers start: 22
  outliers final: 19
  residues processed: 119
  average time/residue: 0.2032
  time to fit residues: 34.8314
Evaluate side-chains
  118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  330 ILE
Chi-restraints excluded: chain C residue  353 SER
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain L residue  168 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 16 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 104 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0970
   chunk 46 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.165614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.138993 restraints weight = 9911.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.136625 restraints weight = 17905.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.137202 restraints weight = 17994.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8824  Z= 0.196
  Angle     :  0.530   7.508  12002  Z= 0.264
  Chirality :  0.040   0.185   1361
  Planarity :  0.003   0.036   1505
  Dihedral  :  4.309  43.392   1239
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.43 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.26), residues: 1072
  helix:  2.31 (0.26), residues: 406
  sheet:  0.01 (0.30), residues: 255
  loop : -0.11 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.017   0.001   PHE L 121 
 TYR   0.027   0.001   TYR H 155 
 ARG   0.004   0.000   ARG L  60 

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.920 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8828 (mp)
REVERT: A   52 ARG cc_start: 0.7002 (tpt170) cc_final: 0.6707 (tpt-90)
REVERT: A  344 LEU cc_start: 0.8311 (tt) cc_final: 0.8103 (tp)
REVERT: C   91 TYR cc_start: 0.4817 (m-80) cc_final: 0.4584 (m-10)
REVERT: L   87 GLU cc_start: 0.7838 (pt0) cc_final: 0.7631 (pt0)
  outliers start: 20
  outliers final: 19
  residues processed: 115
  average time/residue: 0.1966
  time to fit residues: 32.7892
Evaluate side-chains
  116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 LEU
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  213 THR
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   88 GLU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  228 ASN
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  330 ILE
Chi-restraints excluded: chain C residue  353 SER
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue  138 VAL
Chi-restraints excluded: chain L residue  168 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 40 optimal weight:    0.0470
   chunk 106 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9980
   chunk 41 optimal weight:   10.0000
   chunk 86 optimal weight:    8.9990
   chunk 80 optimal weight:    0.9990
   chunk 107 optimal weight:    0.0870
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.5458

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

Flipped N/Q/H residues before XYZ refinement:
** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.166675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.142120 restraints weight = 9973.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.140182 restraints weight = 15458.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.139401 restraints weight = 14991.831|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8824  Z= 0.149
  Angle     :  0.515   7.178  12002  Z= 0.255
  Chirality :  0.040   0.184   1361
  Planarity :  0.003   0.036   1505
  Dihedral  :  4.231  46.465   1239
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.32 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.26), residues: 1072
  helix:  2.41 (0.26), residues: 407
  sheet:  0.05 (0.30), residues: 255
  loop : -0.02 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.018   0.001   PHE L 121 
 TYR   0.028   0.001   TYR H 155 
 ARG   0.006   0.000   ARG H  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3259.86 seconds
wall clock time: 59 minutes 40.74 seconds (3580.74 seconds total)