Starting phenix.real_space_refine
on Fri Oct 10 21:38:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jxr_36710/10_2025/8jxr_36710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jxr_36710/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jxr_36710/10_2025/8jxr_36710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jxr_36710/10_2025/8jxr_36710.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jxr_36710/10_2025/8jxr_36710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jxr_36710/10_2025/8jxr_36710.map"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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, 'ASN:plan1': 1, 'GLU:plan': 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: 2.05, per 1000 atoms: 0.24
  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: 0.72
  Conformation dependent library (CDL) restraints added in 339.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.36
  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: 1.56

  Time building geometry restraints manager: 0.96 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:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.870
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.570
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.28 (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
 ARG   0.001   0.000   ARG A 133 
 TYR   0.005   0.000   TYR H  95 
 PHE   0.004   0.000   PHE A 102 
 TRP   0.002   0.000   TRP C 130 
 HIS   0.002   0.000   HIS H  35 

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

*********************** 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  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A  127 SER cc_start: 0.7715 (t) cc_final: 0.7329 (p)
REVERT: A  132 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7385 (mm-30)
REVERT: A  160 GLN cc_start: 0.8277 (mm-40) cc_final: 0.7898 (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: 0.8112 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1064
  time to fit residues: 25.3677
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  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.4980
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:   20.0000
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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
C 219 ASN
C 333 ASN
H  84 ASN
H 207 ASN
L  48 GLN
L 129 GLN
L 163 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.184497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.161702 restraints weight = 9973.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.153821 restraints weight = 13983.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.151681 restraints weight = 15897.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.152508 restraints weight = 13880.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.152761 restraints weight = 11331.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8827  Z= 0.164
  Angle     :  0.560   6.973  12009  Z= 0.285
  Chirality :  0.042   0.148   1361
  Planarity :  0.004   0.034   1505
  Dihedral  :  6.631 146.474   1239
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 11.33 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.25), residues: 1072
  helix:  1.32 (0.26), residues: 402
  sheet: -0.45 (0.31), residues: 252
  loop : -0.64 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  71 
 TYR   0.021   0.002   TYR H 155 
 PHE   0.024   0.002   PHE A 288 
 TRP   0.012   0.001   TRP H 164 
 HIS   0.007   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8824)
  covalent geometry    : angle       0.55920 (12002)
  SS BOND              : bond        0.00863 (    2)
  SS BOND              : angle       0.92470 (    4)
  hydrogen bonds       : bond        0.03132 (  455)
  hydrogen bonds       : angle       4.33362 ( 1293)
  link_ALPHA1-4        : bond        0.00821 (    1)
  link_ALPHA1-4        : angle       2.20034 (    3)

*********************** 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
  145 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.214 
Fit side-chains
REVERT: A  103 ASP cc_start: 0.8595 (t70) cc_final: 0.8247 (t0)
REVERT: A  160 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7804 (mm-40)
REVERT: C   45 GLU cc_start: 0.8474 (pm20) cc_final: 0.7852 (pm20)
REVERT: C  333 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7331 (t0)
  outliers start: 25
  outliers final: 13
  residues processed: 136
  average time/residue: 0.0858
  time to fit residues: 16.6607
Evaluate side-chains
  117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
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  283 CYS
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain C residue  333 ASN
Chi-restraints excluded: chain C residue  348 VAL
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  115 GLN
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 53 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0770
   chunk 40 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 39 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 92 optimal weight:   10.0000
   chunk 16 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.8942

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

Flipped N/Q/H residues before XYZ refinement:
B  52 HIS
C 333 ASN
L  48 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.182825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.157714 restraints weight = 9923.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.155800 restraints weight = 16142.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.156747 restraints weight = 14508.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.156655 restraints weight = 10837.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.156924 restraints weight = 9923.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2305

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= 0.115
  Angle     :  0.502   7.180  12009  Z= 0.251
  Chirality :  0.040   0.133   1361
  Planarity :  0.003   0.049   1505
  Dihedral  :  6.257 137.860   1239
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.96 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.26), residues: 1072
  helix:  1.85 (0.26), residues: 401
  sheet: -0.28 (0.32), residues: 251
  loop : -0.43 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  60 
 TYR   0.017   0.001   TYR H 155 
 PHE   0.015   0.001   PHE A 288 
 TRP   0.013   0.001   TRP H 164 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 8824)
  covalent geometry    : angle       0.50123 (12002)
  SS BOND              : bond        0.00146 (    2)
  SS BOND              : angle       0.59570 (    4)
  hydrogen bonds       : bond        0.02819 (  455)
  hydrogen bonds       : angle       4.14225 ( 1293)
  link_ALPHA1-4        : bond        0.00337 (    1)
  link_ALPHA1-4        : angle       1.54697 (    3)

*********************** 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
  129 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  103 ASP cc_start: 0.8647 (t70) cc_final: 0.8344 (t0)
REVERT: A  160 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7753 (mm-40)
REVERT: A  278 MET cc_start: 0.7715 (tpt) cc_final: 0.7395 (tpt)
REVERT: A  329 ILE cc_start: 0.9012 (mm) cc_final: 0.8699 (mt)
REVERT: A  344 LEU cc_start: 0.7734 (tt) cc_final: 0.7440 (tp)
REVERT: C   45 GLU cc_start: 0.8351 (pm20) cc_final: 0.7478 (pm20)
REVERT: C  333 ASN cc_start: 0.7894 (OUTLIER) cc_final: 0.7643 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 124
  average time/residue: 0.0808
  time to fit residues: 14.5434
Evaluate side-chains
  114 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 100
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   33 ILE
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  333 ASN
Chi-restraints excluded: chain C residue  346 THR
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  208 VAL
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 96 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 69 optimal weight:   10.0000
   chunk 67 optimal weight:    4.9990
   chunk 102 optimal weight:    0.7980
   chunk 3 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
B 123 HIS
C 333 ASN
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L   1 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.178530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.151708 restraints weight = 10071.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.148544 restraints weight = 14584.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.149444 restraints weight = 14710.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.149797 restraints weight = 10802.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.150044 restraints weight = 9776.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8827  Z= 0.136
  Angle     :  0.515   7.277  12009  Z= 0.259
  Chirality :  0.040   0.139   1361
  Planarity :  0.004   0.060   1505
  Dihedral  :  6.083 129.837   1239
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.38 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.26), residues: 1072
  helix:  2.00 (0.26), residues: 402
  sheet: -0.19 (0.31), residues: 260
  loop : -0.29 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  19 
 TYR   0.013   0.001   TYR H 155 
 PHE   0.016   0.001   PHE A 288 
 TRP   0.017   0.001   TRP H 164 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8824)
  covalent geometry    : angle       0.51496 (12002)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.50676 (    4)
  hydrogen bonds       : bond        0.02944 (  455)
  hydrogen bonds       : angle       4.14353 ( 1293)
  link_ALPHA1-4        : bond        0.00151 (    1)
  link_ALPHA1-4        : angle       1.38418 (    3)

*********************** 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
  138 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.7028 (tpt170) cc_final: 0.6722 (tpt-90)
REVERT: A  160 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7764 (mm-40)
REVERT: A  278 MET cc_start: 0.7872 (tpt) cc_final: 0.7404 (tpt)
REVERT: A  344 LEU cc_start: 0.7911 (tt) cc_final: 0.7642 (tp)
REVERT: C  333 ASN cc_start: 0.7897 (t0) cc_final: 0.7650 (t0)
  outliers start: 24
  outliers final: 17
  residues processed: 132
  average time/residue: 0.0924
  time to fit residues: 16.7611
Evaluate side-chains
  119 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  283 CYS
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain B residue   33 ILE
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  346 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  110 MET
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   91 VAL
Chi-restraints excluded: chain L residue  138 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 95 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 45 optimal weight:   10.0000
   chunk 58 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9980
   chunk 14 optimal weight:   10.0000
   chunk 93 optimal weight:    0.0070
   chunk 75 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.8004

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

Flipped N/Q/H residues before XYZ refinement:
C 333 ASN
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L   1 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.173332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.146876 restraints weight = 10026.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.145536 restraints weight = 16543.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.145542 restraints weight = 16553.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.144938 restraints weight = 14108.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.145360 restraints weight = 11509.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8827  Z= 0.176
  Angle     :  0.565   7.510  12009  Z= 0.287
  Chirality :  0.042   0.141   1361
  Planarity :  0.004   0.047   1505
  Dihedral  :  6.199 121.083   1239
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 14.60 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.26), residues: 1072
  helix:  1.94 (0.26), residues: 404
  sheet: -0.14 (0.31), residues: 255
  loop : -0.31 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 133 
 TYR   0.016   0.002   TYR L  97 
 PHE   0.017   0.002   PHE A 288 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 8824)
  covalent geometry    : angle       0.56460 (12002)
  SS BOND              : bond        0.00289 (    2)
  SS BOND              : angle       0.75392 (    4)
  hydrogen bonds       : bond        0.03418 (  455)
  hydrogen bonds       : angle       4.32496 ( 1293)
  link_ALPHA1-4        : bond        0.00278 (    1)
  link_ALPHA1-4        : angle       1.28140 (    3)

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

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.7047 (tpt170) cc_final: 0.6747 (tpt-90)
REVERT: A  160 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7916 (mm-40)
REVERT: A  278 MET cc_start: 0.7847 (tpt) cc_final: 0.7419 (tpt)
REVERT: A  344 LEU cc_start: 0.8217 (tt) cc_final: 0.7991 (tp)
REVERT: B   43 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7584 (mtpp)
  outliers start: 30
  outliers final: 23
  residues processed: 128
  average time/residue: 0.0928
  time to fit residues: 16.7174
Evaluate side-chains
  121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 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   90 THR
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  346 THR
Chi-restraints excluded: chain C residue  369 ILE
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue    7 SER
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   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 82 optimal weight:    5.9990
   chunk 76 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 91 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 14 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9980
   chunk 88 optimal weight:    7.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3901 r_free = 0.3901 target = 0.174793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.149462 restraints weight = 9948.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.147985 restraints weight = 18411.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.148455 restraints weight = 15885.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.147791 restraints weight = 12762.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.148120 restraints weight = 10860.111|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8827  Z= 0.131
  Angle     :  0.529   8.556  12009  Z= 0.265
  Chirality :  0.041   0.153   1361
  Planarity :  0.004   0.048   1505
  Dihedral  :  5.824 103.772   1239
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 15.36 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.26), residues: 1072
  helix:  2.12 (0.26), residues: 404
  sheet: -0.14 (0.31), residues: 255
  loop : -0.30 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  19 
 TYR   0.013   0.001   TYR L  97 
 PHE   0.018   0.001   PHE L 144 
 TRP   0.011   0.001   TRP A 318 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 8824)
  covalent geometry    : angle       0.52891 (12002)
  SS BOND              : bond        0.00180 (    2)
  SS BOND              : angle       0.51039 (    4)
  hydrogen bonds       : bond        0.03107 (  455)
  hydrogen bonds       : angle       4.20646 ( 1293)
  link_ALPHA1-4        : bond        0.00136 (    1)
  link_ALPHA1-4        : angle       1.22701 (    3)

*********************** 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
  137 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 106
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.6994 (tpt170) cc_final: 0.6697 (tpt-90)
REVERT: A  160 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7897 (mm-40)
REVERT: A  278 MET cc_start: 0.7788 (tpt) cc_final: 0.7350 (tpt)
REVERT: A  344 LEU cc_start: 0.8241 (tt) cc_final: 0.8023 (tp)
REVERT: B   43 LYS cc_start: 0.7815 (mtpt) cc_final: 0.7578 (mtpp)
  outliers start: 31
  outliers final: 21
  residues processed: 130
  average time/residue: 0.1017
  time to fit residues: 18.3883
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  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   88 GLU
Chi-restraints excluded: chain B residue   90 THR
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  318 ILE
Chi-restraints excluded: chain C residue  346 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  110 MET
Chi-restraints excluded: chain H residue  120 THR
Chi-restraints excluded: chain H residue  208 VAL
Chi-restraints excluded: chain L residue   37 THR
Chi-restraints excluded: chain L residue   73 SER
Chi-restraints excluded: chain L residue   84 VAL
Chi-restraints excluded: chain L residue   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 90 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 109 optimal weight:    5.9990
   chunk 78 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0870
   chunk 5 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 105 optimal weight:    6.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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 = 0.3898 r_free = 0.3898 target = 0.174502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.149757 restraints weight = 10061.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.148318 restraints weight = 16217.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.148498 restraints weight = 15067.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.147029 restraints weight = 13474.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.147612 restraints weight = 11586.592|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.3503

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= 0.109
  Angle     :  0.519   8.448  12009  Z= 0.256
  Chirality :  0.040   0.166   1361
  Planarity :  0.003   0.043   1505
  Dihedral  :  5.130  79.526   1239
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.34 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.26), residues: 1072
  helix:  2.32 (0.25), residues: 402
  sheet: -0.12 (0.31), residues: 255
  loop : -0.28 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  19 
 TYR   0.011   0.001   TYR L  97 
 PHE   0.015   0.001   PHE L 144 
 TRP   0.010   0.001   TRP A 318 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 8824)
  covalent geometry    : angle       0.51910 (12002)
  SS BOND              : bond        0.00146 (    2)
  SS BOND              : angle       0.46333 (    4)
  hydrogen bonds       : bond        0.02888 (  455)
  hydrogen bonds       : angle       4.10480 ( 1293)
  link_ALPHA1-4        : bond        0.00086 (    1)
  link_ALPHA1-4        : angle       1.16286 (    3)

*********************** 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
  134 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.7013 (tpt170) cc_final: 0.6716 (tpt-90)
REVERT: A  278 MET cc_start: 0.7839 (tpt) cc_final: 0.7417 (tpt)
REVERT: A  344 LEU cc_start: 0.8220 (tt) cc_final: 0.8009 (tp)
REVERT: B   43 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7468 (mtpp)
  outliers start: 25
  outliers final: 20
  residues processed: 128
  average time/residue: 0.0986
  time to fit residues: 17.7433
Evaluate side-chains
  121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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   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  110 MET
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   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 83 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   chunk 41 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 43 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 106 optimal weight:   20.0000
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.6786

-------------------------------------------------------------------------------
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 = 0.3848 r_free = 0.3848 target = 0.169798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.144374 restraints weight = 9974.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.142093 restraints weight = 16972.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.141977 restraints weight = 15744.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.140798 restraints weight = 14182.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.141402 restraints weight = 11902.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8827  Z= 0.167
  Angle     :  0.566   8.235  12009  Z= 0.282
  Chirality :  0.042   0.168   1361
  Planarity :  0.004   0.043   1505
  Dihedral  :  4.971  57.742   1239
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 16.67 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.26), residues: 1072
  helix:  2.19 (0.25), residues: 405
  sheet: -0.13 (0.31), residues: 256
  loop : -0.28 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  19 
 TYR   0.015   0.002   TYR L  97 
 PHE   0.017   0.002   PHE A 288 
 TRP   0.014   0.001   TRP A 318 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 8824)
  covalent geometry    : angle       0.56543 (12002)
  SS BOND              : bond        0.00256 (    2)
  SS BOND              : angle       0.66479 (    4)
  hydrogen bonds       : bond        0.03270 (  455)
  hydrogen bonds       : angle       4.24885 ( 1293)
  link_ALPHA1-4        : bond        0.00274 (    1)
  link_ALPHA1-4        : angle       1.22887 (    3)

*********************** 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
  124 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.7031 (tpt170) cc_final: 0.6725 (tpt-90)
REVERT: A  278 MET cc_start: 0.7838 (tpt) cc_final: 0.7396 (tpt)
REVERT: B   43 LYS cc_start: 0.7765 (mtpt) cc_final: 0.7520 (mtpp)
  outliers start: 27
  outliers final: 24
  residues processed: 117
  average time/residue: 0.0931
  time to fit residues: 15.4765
Evaluate side-chains
  115 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 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    4 LEU
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  346 THR
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  110 MET
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   91 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 52 optimal weight:    6.9990
   chunk 41 optimal weight:   10.0000
   chunk 19 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0070
   chunk 93 optimal weight:    0.9990
   chunk 109 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   chunk 106 optimal weight:   20.0000
   chunk 48 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    1.5404

-------------------------------------------------------------------------------
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 = 0.3834 r_free = 0.3834 target = 0.168423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.142692 restraints weight = 9939.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.139443 restraints weight = 17601.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.138933 restraints weight = 17831.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.137956 restraints weight = 17312.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.138364 restraints weight = 14618.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8827  Z= 0.158
  Angle     :  0.564   7.702  12009  Z= 0.281
  Chirality :  0.042   0.178   1361
  Planarity :  0.004   0.036   1505
  Dihedral  :  4.641  40.787   1239
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.21 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.26), residues: 1072
  helix:  2.21 (0.25), residues: 404
  sheet: -0.12 (0.32), residues: 246
  loop : -0.34 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  19 
 TYR   0.015   0.001   TYR L  97 
 PHE   0.016   0.002   PHE L 144 
 TRP   0.011   0.001   TRP H  47 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 8824)
  covalent geometry    : angle       0.56355 (12002)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       1.02107 (    4)
  hydrogen bonds       : bond        0.03286 (  455)
  hydrogen bonds       : angle       4.28392 ( 1293)
  link_ALPHA1-4        : bond        0.00072 (    1)
  link_ALPHA1-4        : angle       1.25520 (    3)

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

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

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

  2144 Ramachandran restraints generated.
    1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.7051 (tpt170) cc_final: 0.6738 (tpt-90)
REVERT: A  278 MET cc_start: 0.7948 (tpt) cc_final: 0.7538 (tpt)
REVERT: B   43 LYS cc_start: 0.7684 (mtpt) cc_final: 0.7457 (mtpp)
REVERT: B   82 MET cc_start: 0.9228 (mtp) cc_final: 0.8830 (mtp)
REVERT: C  178 ASP cc_start: 0.7792 (t0) cc_final: 0.7230 (t0)
  outliers start: 23
  outliers final: 20
  residues processed: 118
  average time/residue: 0.0956
  time to fit residues: 15.9644
Evaluate side-chains
  117 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 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 B residue    4 LEU
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  346 THR
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  110 MET
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   91 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 70 optimal weight:    8.9990
   chunk 72 optimal weight:   30.0000
   chunk 84 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 100 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0030
   chunk 35 optimal weight:    0.0770
   chunk 58 optimal weight:    8.9990
   overall best weight:    0.8152

-------------------------------------------------------------------------------
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 = 0.3889 r_free = 0.3889 target = 0.173534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.144071 restraints weight = 9943.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.142296 restraints weight = 14624.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.143241 restraints weight = 13610.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.143509 restraints weight = 10234.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.143340 restraints weight = 8738.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3884

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= 0.116
  Angle     :  0.532   7.311  12009  Z= 0.265
  Chirality :  0.041   0.184   1361
  Planarity :  0.003   0.035   1505
  Dihedral  :  4.509  46.547   1239
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 17.97 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.26), residues: 1072
  helix:  2.40 (0.25), residues: 403
  sheet: -0.13 (0.31), residues: 250
  loop : -0.22 (0.31), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  19 
 TYR   0.010   0.001   TYR L  97 
 PHE   0.016   0.001   PHE L 144 
 TRP   0.009   0.001   TRP H  47 
 HIS   0.005   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8824)
  covalent geometry    : angle       0.53198 (12002)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       0.49250 (    4)
  hydrogen bonds       : bond        0.02977 (  455)
  hydrogen bonds       : angle       4.15414 ( 1293)
  link_ALPHA1-4        : bond        0.00086 (    1)
  link_ALPHA1-4        : angle       1.14136 (    3)

********************** 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
  127 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A   52 ARG cc_start: 0.6933 (tpt170) cc_final: 0.6628 (tpt-90)
REVERT: A  278 MET cc_start: 0.7858 (tpt) cc_final: 0.7422 (tpt)
REVERT: B   43 LYS cc_start: 0.7645 (mtpt) cc_final: 0.7406 (mtpp)
REVERT: B   82 MET cc_start: 0.9170 (mtp) cc_final: 0.8782 (mtp)
REVERT: C   91 TYR cc_start: 0.4882 (m-80) cc_final: 0.4540 (m-10)
  outliers start: 20
  outliers final: 19
  residues processed: 124
  average time/residue: 0.0962
  time to fit residues: 16.6453
Evaluate side-chains
  121 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 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 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  346 THR
Chi-restraints excluded: chain C residue  533 THR
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  110 MET
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   91 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 61 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 105 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 52 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3835 r_free = 0.3835 target = 0.168435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.143473 restraints weight = 9921.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.137360 restraints weight = 18036.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.135391 restraints weight = 12149.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.134751 restraints weight = 13141.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.135520 restraints weight = 10515.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.3967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8827  Z= 0.143
  Angle     :  0.558  10.589  12009  Z= 0.277
  Chirality :  0.041   0.186   1361
  Planarity :  0.003   0.031   1505
  Dihedral  :  4.628  47.342   1239
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.19 %
    Favored  : 79.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.26), residues: 1072
  helix:  2.33 (0.25), residues: 404
  sheet: -0.18 (0.31), residues: 260
  loop : -0.16 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  19 
 TYR   0.013   0.001   TYR L  97 
 PHE   0.016   0.001   PHE A 288 
 TRP   0.010   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 8824)
  covalent geometry    : angle       0.55816 (12002)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       0.64312 (    4)
  hydrogen bonds       : bond        0.03160 (  455)
  hydrogen bonds       : angle       4.20389 ( 1293)
  link_ALPHA1-4        : bond        0.00072 (    1)
  link_ALPHA1-4        : angle       1.19284 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1585.89 seconds
wall clock time: 28 minutes 10.06 seconds (1690.06 seconds total)