Starting phenix.real_space_refine
on Wed Apr 30 05:31:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxr_36710/04_2025/8jxr_36710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxr_36710/04_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_36710/04_2025/8jxr_36710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxr_36710/04_2025/8jxr_36710.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxr_36710/04_2025/8jxr_36710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxr_36710/04_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-5669/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: 5.41, per 1000 atoms: 0.63
  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: 3.08
  Conformation dependent library (CDL) restraints added in 1.2 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: 2.73

  Time building geometry restraints manager: 3.11 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:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.230
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.400
  Find NCS groups from input model:        0.080
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.080
-------------------------------------------------------------------------------
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   8827  Z= 0.208
  Angle     :  0.523  10.237  12009  Z= 0.272
  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 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.02599 (    1)
  link_ALPHA1-4        : angle       6.98020 (    3)
  hydrogen bonds       : bond        0.13175 (  455)
  hydrogen bonds       : angle       6.04129 ( 1293)
  SS BOND              : bond        0.03758 (    2)
  SS BOND              : angle       6.76440 (    4)
  covalent geometry    : bond        0.00395 ( 8824)
  covalent geometry    : angle       0.49661 (12002)

*********************** 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  : 0.967 
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: 0.2317
  time to fit residues: 54.8495
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  : 0.925 
-------------------------------------------------------------------------------
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   8827  Z= 0.312
  Angle     :  0.706   8.836  12009  Z= 0.363
  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 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.02650 (    1)
  link_ALPHA1-4        : angle       2.32589 (    3)
  hydrogen bonds       : bond        0.04280 (  455)
  hydrogen bonds       : angle       4.82738 ( 1293)
  SS BOND              : bond        0.00038 (    2)
  SS BOND              : angle       1.34175 (    4)
  covalent geometry    : bond        0.00753 ( 8824)
  covalent geometry    : angle       0.70479 (12002)

*********************** 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  : 0.957 
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: 0.1995
  time to fit residues: 37.2728
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  : 0.950 
-------------------------------------------------------------------------------
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:    0.8980
   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:    0.7580

-------------------------------------------------------------------------------
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 = 0.3891 r_free = 0.3891 target = 0.174020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.148559 restraints weight = 9948.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.146694 restraints weight = 16643.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.146406 restraints weight = 15479.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8827  Z= 0.113
  Angle     :  0.509   7.013  12009  Z= 0.259
  Chirality :  0.040   0.144   1361
  Planarity :  0.003   0.037   1505
  Dihedral  :  6.490 141.980   1239
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.71 %
    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:  0.46 (0.26), residues: 1072
  helix:  1.58 (0.26), residues: 403
  sheet: -0.34 (0.32), residues: 246
  loop : -0.43 (0.30), residues: 423

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   0.017   0.001   PHE L 121 
 TYR   0.019   0.001   TYR H 155 
 ARG   0.005   0.000   ARG H  19 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00134 (    1)
  link_ALPHA1-4        : angle       1.56847 (    3)
  hydrogen bonds       : bond        0.03162 (  455)
  hydrogen bonds       : angle       4.32435 ( 1293)
  SS BOND              : bond        0.00243 (    2)
  SS BOND              : angle       0.58634 (    4)
  covalent geometry    : bond        0.00257 ( 8824)
  covalent geometry    : angle       0.50866 (12002)

*********************** 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
  125 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 1.164 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8822 (mp)
REVERT: A   52 ARG cc_start: 0.7048 (tpt170) cc_final: 0.6740 (tpt-90)
REVERT: A  103 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8644 (t0)
REVERT: A  160 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7925 (mm-40)
REVERT: A  231 LEU cc_start: 0.7620 (mp) cc_final: 0.7382 (mp)
REVERT: A  278 MET cc_start: 0.7904 (tpt) cc_final: 0.7562 (tpt)
REVERT: A  329 ILE cc_start: 0.9117 (mm) cc_final: 0.8893 (mt)
REVERT: A  344 LEU cc_start: 0.8081 (tt) cc_final: 0.7770 (tp)
  outliers start: 21
  outliers final: 12
  residues processed: 119
  average time/residue: 0.2194
  time to fit residues: 36.5937
Evaluate side-chains
  108 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
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  318 ILE
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:    0.9990
   chunk 50 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 109 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.9386

-------------------------------------------------------------------------------
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 = 0.3918 r_free = 0.3918 target = 0.176553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.152673 restraints weight = 9922.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.151207 restraints weight = 15810.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.147952 restraints weight = 15122.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.3102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8827  Z= 0.118
  Angle     :  0.505   7.131  12009  Z= 0.254
  Chirality :  0.040   0.149   1361
  Planarity :  0.004   0.045   1505
  Dihedral  :  6.263 133.052   1239
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.25 %
    Favored  : 81.92 %
  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:  0.77 (0.26), residues: 1072
  helix:  1.90 (0.26), residues: 404
  sheet: -0.24 (0.32), residues: 246
  loop : -0.31 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP H 164 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.015   0.001   PHE L 121 
 TYR   0.015   0.001   TYR H 155 
 ARG   0.005   0.000   ARG H  19 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00001 (    1)
  link_ALPHA1-4        : angle       1.32166 (    3)
  hydrogen bonds       : bond        0.02970 (  455)
  hydrogen bonds       : angle       4.18692 ( 1293)
  SS BOND              : bond        0.00162 (    2)
  SS BOND              : angle       0.50836 (    4)
  covalent geometry    : bond        0.00279 ( 8824)
  covalent geometry    : angle       0.50484 (12002)

*********************** 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: 26
    poor density    : 102
  time to evaluate  : 1.208 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8830 (mp)
REVERT: A   52 ARG cc_start: 0.6961 (tpt170) cc_final: 0.6679 (tpt-90)
REVERT: A  160 GLN cc_start: 0.8167 (mm-40) cc_final: 0.7949 (mm-40)
REVERT: A  278 MET cc_start: 0.7968 (tpt) cc_final: 0.7690 (tpt)
REVERT: A  344 LEU cc_start: 0.8131 (tt) cc_final: 0.7823 (tp)
  outliers start: 26
  outliers final: 17
  residues processed: 123
  average time/residue: 0.2359
  time to fit residues: 41.5765
Evaluate side-chains
  111 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 1.721 
-------------------------------------------------------------------------------
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  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  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:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 48 optimal weight:    6.9990
   chunk 91 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.175134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.149755 restraints weight = 9917.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.148163 restraints weight = 17385.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.148579 restraints weight = 15798.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8827  Z= 0.119
  Angle     :  0.505   7.053  12009  Z= 0.254
  Chirality :  0.040   0.156   1361
  Planarity :  0.004   0.037   1505
  Dihedral  :  5.980 118.738   1239
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 15.14 %
    Favored  : 81.70 %
  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:  0.90 (0.26), residues: 1072
  helix:  2.07 (0.26), residues: 404
  sheet: -0.21 (0.32), residues: 246
  loop : -0.28 (0.30), residues: 422

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   0.015   0.001   PHE A 288 
 TYR   0.013   0.001   TYR L  97 
 ARG   0.005   0.000   ARG H  19 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00028 (    1)
  link_ALPHA1-4        : angle       1.21650 (    3)
  hydrogen bonds       : bond        0.02965 (  455)
  hydrogen bonds       : angle       4.11526 ( 1293)
  SS BOND              : bond        0.00169 (    2)
  SS BOND              : angle       0.51665 (    4)
  covalent geometry    : bond        0.00279 ( 8824)
  covalent geometry    : angle       0.50480 (12002)

*********************** 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
  133 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 1.528 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8845 (mp)
REVERT: A   52 ARG cc_start: 0.7007 (tpt170) cc_final: 0.6713 (tpt-90)
REVERT: A  278 MET cc_start: 0.7816 (tpt) cc_final: 0.7503 (tpt)
REVERT: A  344 LEU cc_start: 0.8222 (tt) cc_final: 0.7963 (tp)
REVERT: H   93 MET cc_start: 0.7614 (tpp) cc_final: 0.7034 (tpp)
  outliers start: 29
  outliers final: 22
  residues processed: 129
  average time/residue: 0.2503
  time to fit residues: 46.4321
Evaluate side-chains
  117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 1.441 
-------------------------------------------------------------------------------
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   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  138 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:    3.9990
   chunk 45 optimal weight:    0.0970
   chunk 97 optimal weight:    4.9990
   chunk 79 optimal weight:    0.6980
   chunk 109 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 52 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   overall best weight:    1.3382

-------------------------------------------------------------------------------
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 = 0.3796 r_free = 0.3796 target = 0.165591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.139642 restraints weight = 9900.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.137632 restraints weight = 18437.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.138509 restraints weight = 17435.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8827  Z= 0.140
  Angle     :  0.529   7.175  12009  Z= 0.266
  Chirality :  0.041   0.160   1361
  Planarity :  0.004   0.037   1505
  Dihedral  :  6.004 111.746   1239
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 14.92 %
    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:  0.93 (0.26), residues: 1072
  helix:  2.07 (0.26), residues: 405
  sheet: -0.17 (0.31), residues: 255
  loop : -0.25 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 318 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.016   0.002   PHE A 288 
 TYR   0.014   0.001   TYR L  97 
 ARG   0.005   0.000   ARG H  19 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00036 (    1)
  link_ALPHA1-4        : angle       1.19750 (    3)
  hydrogen bonds       : bond        0.03110 (  455)
  hydrogen bonds       : angle       4.16814 ( 1293)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       1.07451 (    4)
  covalent geometry    : bond        0.00335 ( 8824)
  covalent geometry    : angle       0.52815 (12002)

*********************** 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
  136 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 0.970 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8829 (mp)
REVERT: A   52 ARG cc_start: 0.6986 (tpt170) cc_final: 0.6689 (tpt-90)
REVERT: A  278 MET cc_start: 0.7905 (tpt) cc_final: 0.7578 (tpt)
REVERT: A  344 LEU cc_start: 0.8266 (tt) cc_final: 0.8025 (tp)
  outliers start: 32
  outliers final: 25
  residues processed: 128
  average time/residue: 0.1984
  time to fit residues: 35.9875
Evaluate side-chains
  121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
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   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:    0.9990
   chunk 62 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 40 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3821 r_free = 0.3821 target = 0.167741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.141736 restraints weight = 10019.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.139330 restraints weight = 18459.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.140388 restraints weight = 17498.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.3543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8827  Z= 0.115
  Angle     :  0.519   6.949  12009  Z= 0.257
  Chirality :  0.040   0.161   1361
  Planarity :  0.003   0.037   1505
  Dihedral  :  5.408  91.767   1239
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 15.90 %
    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:  1.07 (0.26), residues: 1072
  helix:  2.24 (0.26), residues: 404
  sheet: -0.08 (0.31), residues: 255
  loop : -0.23 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.015   0.001   PHE L 121 
 TYR   0.031   0.001   TYR H 155 
 ARG   0.004   0.000   ARG L  60 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00112 (    1)
  link_ALPHA1-4        : angle       1.18937 (    3)
  hydrogen bonds       : bond        0.02919 (  455)
  hydrogen bonds       : angle       4.07555 ( 1293)
  SS BOND              : bond        0.00167 (    2)
  SS BOND              : angle       0.57908 (    4)
  covalent geometry    : bond        0.00271 ( 8824)
  covalent geometry    : angle       0.51847 (12002)

*********************** 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
  132 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.975 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8850 (mp)
REVERT: A   52 ARG cc_start: 0.6988 (tpt170) cc_final: 0.6697 (tpt-90)
REVERT: A  278 MET cc_start: 0.7864 (tpt) cc_final: 0.7610 (tpt)
REVERT: A  344 LEU cc_start: 0.8243 (tt) cc_final: 0.8024 (tp)
REVERT: H   93 MET cc_start: 0.7622 (tpp) cc_final: 0.7069 (tpp)
  outliers start: 30
  outliers final: 23
  residues processed: 126
  average time/residue: 0.2168
  time to fit residues: 38.5275
Evaluate side-chains
  117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
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  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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 94 optimal weight:    8.9990
   chunk 108 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 101 optimal weight:    0.0770
   chunk 13 optimal weight:    0.2980
   chunk 78 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
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 = 0.3905 r_free = 0.3905 target = 0.175510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 121)---------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.146519 restraints weight = 10083.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.144529 restraints weight = 13350.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.144901 restraints weight = 12363.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8827  Z= 0.101
  Angle     :  0.510   7.316  12009  Z= 0.252
  Chirality :  0.040   0.171   1361
  Planarity :  0.003   0.038   1505
  Dihedral  :  4.679  61.329   1239
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.99 %
    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:  1.22 (0.26), residues: 1072
  helix:  2.37 (0.26), residues: 404
  sheet: -0.02 (0.31), residues: 255
  loop : -0.16 (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   0.014   0.001   PHE L 121 
 TYR   0.027   0.001   TYR H 155 
 ARG   0.004   0.000   ARG H  19 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00164 (    1)
  link_ALPHA1-4        : angle       1.11656 (    3)
  hydrogen bonds       : bond        0.02749 (  455)
  hydrogen bonds       : angle       4.01048 ( 1293)
  SS BOND              : bond        0.00132 (    2)
  SS BOND              : angle       0.38786 (    4)
  covalent geometry    : bond        0.00232 ( 8824)
  covalent geometry    : angle       0.51012 (12002)

*********************** 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
  120 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8844 (mp)
REVERT: A   52 ARG cc_start: 0.6976 (tpt170) cc_final: 0.6673 (tpt-90)
REVERT: A  344 LEU cc_start: 0.8250 (tt) cc_final: 0.8039 (tp)
  outliers start: 21
  outliers final: 19
  residues processed: 117
  average time/residue: 0.2159
  time to fit residues: 36.2345
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  : 1.067 
-------------------------------------------------------------------------------
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  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   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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.9386

-------------------------------------------------------------------------------
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 = 0.3885 r_free = 0.3885 target = 0.173469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.143336 restraints weight = 9961.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.141412 restraints weight = 15392.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.142065 restraints weight = 13875.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.3664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8827  Z= 0.119
  Angle     :  0.527   7.993  12009  Z= 0.260
  Chirality :  0.040   0.175   1361
  Planarity :  0.003   0.037   1505
  Dihedral  :  4.351  37.917   1239
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.32 %
    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:  2.34 (0.26), residues: 404
  sheet:  0.03 (0.31), residues: 255
  loop : -0.15 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  47 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.019   0.001   PHE L 121 
 TYR   0.026   0.001   TYR H 155 
 ARG   0.003   0.000   ARG L  60 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00053 (    1)
  link_ALPHA1-4        : angle       1.13203 (    3)
  hydrogen bonds       : bond        0.02910 (  455)
  hydrogen bonds       : angle       4.05799 ( 1293)
  SS BOND              : bond        0.00157 (    2)
  SS BOND              : angle       0.47007 (    4)
  covalent geometry    : bond        0.00283 ( 8824)
  covalent geometry    : angle       0.52721 (12002)

*********************** 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
  118 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8856 (mp)
REVERT: A   52 ARG cc_start: 0.6995 (tpt170) cc_final: 0.6699 (tpt-90)
REVERT: A  344 LEU cc_start: 0.8268 (tt) cc_final: 0.8058 (tp)
  outliers start: 21
  outliers final: 20
  residues processed: 114
  average time/residue: 0.1977
  time to fit residues: 32.0265
Evaluate side-chains
  116 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
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  330 ILE
Chi-restraints excluded: chain C residue  369 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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 16 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 104 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 74 optimal weight:    7.9990
   chunk 58 optimal weight:    0.5980
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.4784

-------------------------------------------------------------------------------
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**
L  48 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.162364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.135462 restraints weight = 9958.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.133448 restraints weight = 16384.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.133880 restraints weight = 15758.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   8827  Z= 0.155
  Angle     :  0.560   7.931  12009  Z= 0.278
  Chirality :  0.041   0.188   1361
  Planarity :  0.004   0.037   1505
  Dihedral  :  4.486  45.641   1239
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.88 %
    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:  1.14 (0.26), residues: 1072
  helix:  2.23 (0.26), residues: 404
  sheet:  0.03 (0.31), residues: 257
  loop : -0.17 (0.32), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.017   0.002   PHE L 121 
 TYR   0.024   0.001   TYR H 155 
 ARG   0.004   0.000   ARG L  60 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00142 (    1)
  link_ALPHA1-4        : angle       1.25502 (    3)
  hydrogen bonds       : bond        0.03241 (  455)
  hydrogen bonds       : angle       4.20222 ( 1293)
  SS BOND              : bond        0.00208 (    2)
  SS BOND              : angle       0.55002 (    4)
  covalent geometry    : bond        0.00379 ( 8824)
  covalent geometry    : angle       0.55979 (12002)

********************** 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
  117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A   43 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8816 (mp)
REVERT: A   52 ARG cc_start: 0.6988 (tpt170) cc_final: 0.6686 (tpt-90)
REVERT: A  278 MET cc_start: 0.7820 (mmm) cc_final: 0.7583 (tpt)
REVERT: A  344 LEU cc_start: 0.8366 (tt) cc_final: 0.8155 (tp)
REVERT: C   91 TYR cc_start: 0.4904 (m-80) cc_final: 0.4662 (m-10)
  outliers start: 23
  outliers final: 20
  residues processed: 111
  average time/residue: 0.2078
  time to fit residues: 32.8377
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  : 0.965 
-------------------------------------------------------------------------------
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  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   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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 108 optimal weight:    9.9990
   chunk 41 optimal weight:    6.9990
   chunk 86 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 107 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.3729 r_free = 0.3729 target = 0.159868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.130695 restraints weight = 10051.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.128030 restraints weight = 17672.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.128907 restraints weight = 17148.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.4104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.077   8827  Z= 0.198
  Angle     :  0.598   9.763  12009  Z= 0.300
  Chirality :  0.042   0.185   1361
  Planarity :  0.004   0.037   1505
  Dihedral  :  4.820  50.347   1239
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.67 %
    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:  1.01 (0.26), residues: 1072
  helix:  2.02 (0.26), residues: 406
  sheet:  0.09 (0.31), residues: 264
  loop : -0.23 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.018   0.002   PHE A 288 
 TYR   0.023   0.002   TYR H 155 
 ARG   0.007   0.001   ARG H  19 

Details of bonding type rmsd
  link_ALPHA1-4        : bond        0.00389 (    1)
  link_ALPHA1-4        : angle       1.27291 (    3)
  hydrogen bonds       : bond        0.03570 (  455)
  hydrogen bonds       : angle       4.40187 ( 1293)
  SS BOND              : bond        0.00235 (    2)
  SS BOND              : angle       0.72206 (    4)
  covalent geometry    : bond        0.00483 ( 8824)
  covalent geometry    : angle       0.59807 (12002)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3400.81 seconds
wall clock time: 60 minutes 52.94 seconds (3652.94 seconds total)