Starting phenix.real_space_refine
on Wed Sep 17 07:48:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vz6_43682/09_2025/8vz6_43682.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vz6_43682/09_2025/8vz6_43682.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vz6_43682/09_2025/8vz6_43682.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vz6_43682/09_2025/8vz6_43682.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vz6_43682/09_2025/8vz6_43682.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vz6_43682/09_2025/8vz6_43682.cif"
  }
  resolution = 3.56
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      98      5.49       5
     S      28      5.16       5
     C    4098      2.51       5
     N    1194      2.21       5
     O    1536      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6954
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2442
          Classifications: {'peptide': 297}
          Link IDs: {'PTRANS': 18, 'TRANS': 278}
    Chain: "R"
      Number of atoms: 1035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 1035
          Classifications: {'RNA': 49}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 15, 'rna3p_pyr': 20}
          Link IDs: {'rna2p': 14, 'rna3p': 34}
    Chain: "B"
      Number of atoms: 2442
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2442
          Classifications: {'peptide': 297}
          Link IDs: {'PTRANS': 18, 'TRANS': 278}
    Chain: "S"
      Number of atoms: 1035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 1035
          Classifications: {'RNA': 49}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 15, 'rna3p_pyr': 20}
          Link IDs: {'rna2p': 14, 'rna3p': 34}
  Time building chain proxies: 2.08, per 1000 atoms: 0.30
  Number of scatterers: 6954
  At special positions: 0
  Unit cell: (92.4885, 138.235, 64.6425, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     P      98     15.00
     O    1536      8.00
     N    1194      7.00
     C    4098      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 297.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1144

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 0 sheets defined
      71.0% alpha, 0.0% beta
      26 base pairs and 48 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 24
      removed outlier: 3.713A  pdb=" N   VAL A  18 " --> pdb=" O   ALA A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 41
      removed outlier: 3.538A  pdb=" N   THR A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 51
      removed outlier: 4.027A  pdb=" N   ALA A  48 " --> pdb=" O   TYR A  44 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   TYR A  49 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 54
      No H-bonds generated for 'chain 'A' and resid 52 through 54'
    Processing helix  chain 'A' and resid 57 through 61
    Processing helix  chain 'A' and resid 68 through 110
      removed outlier: 4.003A  pdb=" N   VAL A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A  84 " --> pdb=" O   LYS A  80 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLU A  89 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ILE A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   ARG A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 121
      removed outlier: 3.739A  pdb=" N   ASP A 117 " --> pdb=" O   TRP A 114 " (cutoff:3.500A)
      removed outlier: 6.168A  pdb=" N   GLY A 118 " --> pdb=" O   MET A 115 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   SER A 119 " --> pdb=" O   THR A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 139
      removed outlier: 4.299A  pdb=" N   HIS A 129 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU A 133 " --> pdb=" O   HIS A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 153
    Processing helix  chain 'A' and resid 159 through 164
    Processing helix  chain 'A' and resid 168 through 177
      removed outlier: 3.535A  pdb=" N   ASN A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   SER A 177 " --> pdb=" O   THR A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 192
      removed outlier: 3.690A  pdb=" N   LYS A 185 " --> pdb=" O   THR A 181 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 215
      removed outlier: 3.570A  pdb=" N   HIS A 215 " --> pdb=" O   ASN A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 263
      removed outlier: 3.527A  pdb=" N   LEU A 252 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ILE A 261 " --> pdb=" O   TYR A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 279
    Processing helix  chain 'A' and resid 283 through 287
    Processing helix  chain 'A' and resid 292 through 300
      removed outlier: 3.817A  pdb=" N   GLU A 296 " --> pdb=" O   TRP A 293 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 3.680A  pdb=" N   GLN A 300 " --> pdb=" O   PRO A 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 24
      removed outlier: 3.758A  pdb=" N   SER B  19 " --> pdb=" O   HIS B  15 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
      removed outlier: 3.580A  pdb=" N   THR B  34 " --> pdb=" O   ASP B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 51
      removed outlier: 4.063A  pdb=" N   ALA B  48 " --> pdb=" O   TYR B  44 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   TYR B  49 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 52 through 54
      No H-bonds generated for 'chain 'B' and resid 52 through 54'
    Processing helix  chain 'B' and resid 57 through 61
    Processing helix  chain 'B' and resid 68 through 110
      removed outlier: 3.985A  pdb=" N   VAL B  72 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU B  84 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   LYS B  92 " --> pdb=" O   ASN B  88 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ILE B  93 " --> pdb=" O   GLU B  89 " (cutoff:3.500A)
      removed outlier: 4.220A  pdb=" N   ARG B  98 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 121
      removed outlier: 3.737A  pdb=" N   ASP B 117 " --> pdb=" O   TRP B 114 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   GLY B 118 " --> pdb=" O   MET B 115 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   SER B 119 " --> pdb=" O   THR B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 139
      removed outlier: 4.301A  pdb=" N   HIS B 129 " --> pdb=" O   ARG B 125 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASP B 132 " --> pdb=" O   ARG B 128 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   LEU B 133 " --> pdb=" O   HIS B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 153
    Processing helix  chain 'B' and resid 159 through 164
    Processing helix  chain 'B' and resid 168 through 177
      removed outlier: 3.536A  pdb=" N   ASN B 174 " --> pdb=" O   GLY B 170 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   SER B 177 " --> pdb=" O   THR B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 192
      removed outlier: 3.691A  pdb=" N   LYS B 185 " --> pdb=" O   THR B 181 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   PHE B 192 " --> pdb=" O   ILE B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 215
      removed outlier: 3.573A  pdb=" N   HIS B 215 " --> pdb=" O   ASN B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 263
      removed outlier: 3.528A  pdb=" N   LEU B 252 " --> pdb=" O   ILE B 248 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE B 261 " --> pdb=" O   TYR B 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 279
      removed outlier: 3.628A  pdb=" N   ALA B 274 " --> pdb=" O   ALA B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 287
    Processing helix  chain 'B' and resid 292 through 300
      removed outlier: 3.809A  pdb=" N   GLU B 296 " --> pdb=" O   TRP B 293 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 3.715A  pdb=" N   GLN B 300 " --> pdb=" O   PRO B 297 " (cutoff:3.500A)

    239 hydrogen bonds defined for protein.
    669 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      72 hydrogen bonds
      136 hydrogen bond angles
      0 basepair planarities
      26 basepair parallelities
      48 stacking parallelities
  Total time for adding SS restraints: 1.00

  Time building geometry restraints manager: 0.72 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 1331
        1.33 -     1.45: 2242
        1.45 -     1.57: 3506
        1.57 -     1.69: 197
        1.69 -     1.81: 50
  Bond restraints: 7326
  Sorted by residual:
  bond pdb=" CB  GLN B 300 "
       pdb=" CG  GLN B 300 "
    ideal  model  delta    sigma   weight residual
    1.520  1.582 -0.062 3.00e-02 1.11e+03 4.27e+00
  bond pdb=" C   LYS B  64 "
       pdb=" N   PRO B  65 "
    ideal  model  delta    sigma   weight residual
    1.332  1.357 -0.025 1.26e-02 6.30e+03 3.94e+00
  bond pdb=" C   LYS A  64 "
       pdb=" N   PRO A  65 "
    ideal  model  delta    sigma   weight residual
    1.332  1.356 -0.024 1.26e-02 6.30e+03 3.59e+00
  bond pdb=" CB  ARG B 237 "
       pdb=" CG  ARG B 237 "
    ideal  model  delta    sigma   weight residual
    1.520  1.576 -0.056 3.00e-02 1.11e+03 3.54e+00
  bond pdb=" CB  ARG A 237 "
       pdb=" CG  ARG A 237 "
    ideal  model  delta    sigma   weight residual
    1.520  1.576 -0.056 3.00e-02 1.11e+03 3.43e+00
  ... (remaining 7321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.85: 10037
        2.85 -     5.71: 307
        5.71 -     8.56: 40
        8.56 -    11.42: 2
       11.42 -    14.27: 4
  Bond angle restraints: 10390
  Sorted by residual:
  angle pdb=" CB  GLN B 300 "
        pdb=" CG  GLN B 300 "
        pdb=" CD  GLN B 300 "
      ideal   model   delta    sigma   weight residual
     112.60  121.20   -8.60 1.70e+00 3.46e-01 2.56e+01
  angle pdb=" C3'   C S  40 "
        pdb=" O3'   C S  40 "
        pdb=" P     G S  41 "
      ideal   model   delta    sigma   weight residual
     120.20  126.69   -6.49 1.50e+00 4.44e-01 1.87e+01
  angle pdb=" C3'   C R  40 "
        pdb=" O3'   C R  40 "
        pdb=" P     G R  41 "
      ideal   model   delta    sigma   weight residual
     120.20  126.69   -6.49 1.50e+00 4.44e-01 1.87e+01
  angle pdb=" C   TRP B 238 "
        pdb=" N   ILE B 239 "
        pdb=" CA  ILE B 239 "
      ideal   model   delta    sigma   weight residual
     120.35  126.32   -5.97 1.39e+00 5.18e-01 1.84e+01
  angle pdb=" C   TRP A 238 "
        pdb=" N   ILE A 239 "
        pdb=" CA  ILE A 239 "
      ideal   model   delta    sigma   weight residual
     120.35  126.30   -5.95 1.39e+00 5.18e-01 1.83e+01
  ... (remaining 10385 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.63: 4155
       31.63 -    63.26: 302
       63.26 -    94.89: 81
       94.89 -   126.51: 0
      126.51 -   158.14: 4
  Dihedral angle restraints: 4542
    sinusoidal: 2780
      harmonic: 1762
  Sorted by residual:
  dihedral pdb=" CA  PRO A 159 "
           pdb=" C   PRO A 159 "
           pdb=" N   ALA A 160 "
           pdb=" CA  ALA A 160 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.21  -25.79     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  PRO B 159 "
           pdb=" C   PRO B 159 "
           pdb=" N   ALA B 160 "
           pdb=" CA  ALA B 160 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.25  -25.75     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" O4'   C R  25 "
           pdb=" C1'   C R  25 "
           pdb=" N1    C R  25 "
           pdb=" C2    C R  25 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -50.37  -77.63     1      1.70e+01 3.46e-03 2.61e+01
  ... (remaining 4539 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1063
       0.082 -    0.164: 143
       0.164 -    0.246: 19
       0.246 -    0.328: 2
       0.328 -    0.410: 3
  Chirality restraints: 1230
  Sorted by residual:
  chirality pdb=" CG  LEU B  17 "
            pdb=" CB  LEU B  17 "
            pdb=" CD1 LEU B  17 "
            pdb=" CD2 LEU B  17 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.18   -0.41 2.00e-01 2.50e+01 4.21e+00
  chirality pdb=" C3'   C R  40 "
            pdb=" C4'   C R  40 "
            pdb=" O3'   C R  40 "
            pdb=" C2'   C R  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.10   -0.37 2.00e-01 2.50e+01 3.50e+00
  chirality pdb=" C3'   C S  40 "
            pdb=" C4'   C S  40 "
            pdb=" O3'   C S  40 "
            pdb=" C2'   C S  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.10   -0.37 2.00e-01 2.50e+01 3.50e+00
  ... (remaining 1227 not shown)

  Planarity restraints: 954
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  44 "   -0.012 2.00e-02 2.50e+03   2.34e-02 1.09e+01
        pdb=" CG  TYR B  44 "    0.054 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  44 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  44 "   -0.029 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  44 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  44 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  44 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  44 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  44 "   -0.013 2.00e-02 2.50e+03   2.27e-02 1.03e+01
        pdb=" CG  TYR A  44 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  44 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  44 "   -0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  44 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  44 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  44 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A  44 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 289 "    0.007 2.00e-02 2.50e+03   1.99e-02 6.91e+00
        pdb=" CG  PHE B 289 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 289 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 289 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 289 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 289 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 289 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 951 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1376
        2.78 -     3.31: 5950
        3.31 -     3.84: 12336
        3.84 -     4.37: 14365
        4.37 -     4.90: 22246
  Nonbonded interactions: 56273
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 273 "
            pdb=" OG  SER A 277 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   ARG B 227 "
            pdb=" O2'   A S   7 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" O   ARG A 227 "
            pdb=" O2'   A R   7 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   ASP B 273 "
            pdb=" OG  SER B 277 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OG1 THR B 204 "
            pdb=" N4    C S   2 "
     model   vdw
     2.424 3.120
  ... (remaining 56268 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'R'
  selection = chain 'S'
}

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:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.520
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
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      :  0.006   0.067   7326  Z= 0.301
  Angle     :  1.160  14.274  10390  Z= 0.614
  Chirality :  0.060   0.410   1230
  Planarity :  0.008   0.046    954
  Dihedral  : 21.093 158.143   3398
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 1.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  9.18 %
    Favored  : 90.45 %
  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: -1.51 (0.30), residues: 590
  helix: -1.38 (0.22), residues: 340
  sheet:  None (None), residues: 0
  loop : -0.14 (0.38), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  36 
 TYR   0.054   0.004   TYR B  44 
 PHE   0.042   0.004   PHE B 289 
 TRP   0.039   0.004   TRP A 220 
 HIS   0.006   0.002   HIS B  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 7326)
  covalent geometry    : angle       1.15951 (10390)
  hydrogen bonds       : bond        0.15620 (  311)
  hydrogen bonds       : angle       5.55665 (  805)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 97
  time to evaluate  : 0.232 
Fit side-chains
REVERT: A  120 ASN cc_start: 0.7184 (OUTLIER) cc_final: 0.6641 (t0)
REVERT: B  120 ASN cc_start: 0.7188 (OUTLIER) cc_final: 0.6673 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 99
  average time/residue: 0.0977
  time to fit residues: 12.7330
Evaluate side-chains
  67 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain B residue  120 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 151 GLN
B 151 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.164182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.137022 restraints weight = 10590.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.139557 restraints weight = 6583.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.141286 restraints weight = 4942.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.142320 restraints weight = 4115.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.143081 restraints weight = 3679.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7326  Z= 0.182
  Angle     :  0.639   7.572  10390  Z= 0.333
  Chirality :  0.040   0.185   1230
  Planarity :  0.006   0.046    954
  Dihedral  : 23.048 172.899   2182
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 11.61 %
    Favored  : 85.58 %
  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:  0.11 (0.34), residues: 590
  helix:  0.01 (0.27), residues: 350
  sheet:  None (None), residues: 0
  loop :  0.45 (0.41), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 125 
 TYR   0.012   0.002   TYR B  37 
 PHE   0.017   0.002   PHE B 289 
 TRP   0.010   0.001   TRP A 299 
 HIS   0.003   0.001   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7326)
  covalent geometry    : angle       0.63908 (10390)
  hydrogen bonds       : bond        0.06418 (  311)
  hydrogen bonds       : angle       3.74577 (  805)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 12
  residues processed: 95
  average time/residue: 0.0758
  time to fit residues: 10.1215
Evaluate side-chains
  83 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 71
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  284 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 2 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 29 optimal weight:    9.9990
   chunk 41 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   chunk 32 optimal weight:   10.0000
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
A 151 GLN
A 266 ASN
B 120 ASN
B 151 GLN
B 266 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.165973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.139240 restraints weight = 10667.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.141876 restraints weight = 6594.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.143503 restraints weight = 4898.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.144654 restraints weight = 4103.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.145302 restraints weight = 3654.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7326  Z= 0.129
  Angle     :  0.548   7.665  10390  Z= 0.281
  Chirality :  0.036   0.192   1230
  Planarity :  0.006   0.056    954
  Dihedral  : 22.961 175.038   2178
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.23 %
    Favored  : 83.90 %
  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:  0.56 (0.35), residues: 590
  helix:  0.48 (0.28), residues: 346
  sheet:  None (None), residues: 0
  loop :  0.46 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 125 
 TYR   0.008   0.001   TYR B 249 
 PHE   0.012   0.001   PHE B 289 
 TRP   0.007   0.001   TRP B 299 
 HIS   0.002   0.000   HIS A  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 7326)
  covalent geometry    : angle       0.54833 (10390)
  hydrogen bonds       : bond        0.05116 (  311)
  hydrogen bonds       : angle       3.46481 (  805)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 78
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 5
  residues processed: 88
  average time/residue: 0.0774
  time to fit residues: 9.5704
Evaluate side-chains
  77 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue  284 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 33 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
A 285 ASN
B 120 ASN
B 285 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.161202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.133801 restraints weight = 10710.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.136405 restraints weight = 6541.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.138038 restraints weight = 4844.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.139213 restraints weight = 4039.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.139913 restraints weight = 3594.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7326  Z= 0.218
  Angle     :  0.640   8.311  10390  Z= 0.328
  Chirality :  0.040   0.202   1230
  Planarity :  0.006   0.055    954
  Dihedral  : 22.935 175.593   2178
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 14.98 %
    Favored  : 81.09 %
  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:  0.27 (0.34), residues: 590
  helix:  0.32 (0.27), residues: 344
  sheet:  None (None), residues: 0
  loop :  0.19 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 125 
 TYR   0.010   0.002   TYR B  11 
 PHE   0.020   0.002   PHE A 289 
 TRP   0.012   0.002   TRP A 220 
 HIS   0.003   0.001   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00505 ( 7326)
  covalent geometry    : angle       0.64040 (10390)
  hydrogen bonds       : bond        0.06484 (  311)
  hydrogen bonds       : angle       3.68343 (  805)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7588 (t0)
REVERT: B  120 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7619 (t0)
  outliers start: 21
  outliers final: 15
  residues processed: 84
  average time/residue: 0.0649
  time to fit residues: 8.1639
Evaluate side-chains
  84 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue  120 ASN
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   90 ILE
Chi-restraints excluded: chain B residue  120 ASN
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  284 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 45 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0570
   chunk 6 optimal weight:    4.9990
   chunk 3 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    1.8102

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
B 120 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.163798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.136553 restraints weight = 10731.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.139240 restraints weight = 6555.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.141034 restraints weight = 4838.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.142207 restraints weight = 3995.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.142852 restraints weight = 3538.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7326  Z= 0.139
  Angle     :  0.555   7.553  10390  Z= 0.281
  Chirality :  0.036   0.190   1230
  Planarity :  0.006   0.054    954
  Dihedral  : 22.829 176.796   2178
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 15.54 %
    Favored  : 80.34 %
  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:  0.53 (0.34), residues: 590
  helix:  0.62 (0.27), residues: 344
  sheet:  None (None), residues: 0
  loop :  0.17 (0.41), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  98 
 TYR   0.007   0.001   TYR B 249 
 PHE   0.012   0.001   PHE A 289 
 TRP   0.006   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 7326)
  covalent geometry    : angle       0.55505 (10390)
  hydrogen bonds       : bond        0.05237 (  311)
  hydrogen bonds       : angle       3.41816 (  805)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 68
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 22
  outliers final: 13
  residues processed: 83
  average time/residue: 0.0640
  time to fit residues: 7.8674
Evaluate side-chains
  77 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  284 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0060
   chunk 58 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 10 optimal weight:    8.9990
   chunk 46 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    2.6004

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
B 120 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.161891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.134462 restraints weight = 10703.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.137078 restraints weight = 6565.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.138858 restraints weight = 4866.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.139952 restraints weight = 4026.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.140638 restraints weight = 3583.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7326  Z= 0.175
  Angle     :  0.586   7.462  10390  Z= 0.298
  Chirality :  0.038   0.199   1230
  Planarity :  0.006   0.058    954
  Dihedral  : 22.715 177.581   2178
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 16.29 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.47 (0.34), residues: 590
  helix:  0.59 (0.27), residues: 344
  sheet:  None (None), residues: 0
  loop :  0.09 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B   4 
 TYR   0.008   0.001   TYR B  11 
 PHE   0.015   0.002   PHE A 289 
 TRP   0.007   0.001   TRP A 299 
 HIS   0.002   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 7326)
  covalent geometry    : angle       0.58575 (10390)
  hydrogen bonds       : bond        0.05834 (  311)
  hydrogen bonds       : angle       3.50289 (  805)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  276 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7435 (mp)
  outliers start: 22
  outliers final: 16
  residues processed: 79
  average time/residue: 0.0695
  time to fit residues: 7.9963
Evaluate side-chains
  80 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  287 MET
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  287 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 29 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 30 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN
B 120 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.162200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.134924 restraints weight = 10705.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.137478 restraints weight = 6589.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.139267 restraints weight = 4917.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.140439 restraints weight = 4069.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.141144 restraints weight = 3598.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7326  Z= 0.156
  Angle     :  0.568   7.503  10390  Z= 0.288
  Chirality :  0.037   0.196   1230
  Planarity :  0.006   0.059    954
  Dihedral  : 22.695 177.701   2178
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.35 %
    Favored  : 78.65 %
  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:  0.58 (0.35), residues: 590
  helix:  0.72 (0.27), residues: 344
  sheet:  None (None), residues: 0
  loop :  0.07 (0.42), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  62 
 TYR   0.007   0.001   TYR B  11 
 PHE   0.014   0.001   PHE A 289 
 TRP   0.006   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7326)
  covalent geometry    : angle       0.56776 (10390)
  hydrogen bonds       : bond        0.05581 (  311)
  hydrogen bonds       : angle       3.44072 (  805)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 63
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 15
  residues processed: 74
  average time/residue: 0.0536
  time to fit residues: 5.9784
Evaluate side-chains
  77 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 THR
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  287 MET
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  287 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 16 optimal weight:    0.0470
   chunk 51 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 1 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 47 optimal weight:    5.9990
   chunk 13 optimal weight:   10.0000
   overall best weight:    1.5884

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

Flipped N/Q/H residues before XYZ refinement:
A 120 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.164397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.137138 restraints weight = 10778.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.139839 restraints weight = 6554.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.141526 restraints weight = 4830.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.142684 restraints weight = 4011.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.143354 restraints weight = 3559.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7326  Z= 0.130
  Angle     :  0.534   7.674  10390  Z= 0.270
  Chirality :  0.035   0.193   1230
  Planarity :  0.006   0.060    954
  Dihedral  : 22.566 178.638   2178
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.79 %
    Favored  : 79.03 %
  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:  0.84 (0.35), residues: 590
  helix:  0.98 (0.28), residues: 344
  sheet:  None (None), residues: 0
  loop :  0.12 (0.43), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 237 
 TYR   0.007   0.001   TYR B 249 
 PHE   0.011   0.001   PHE A 289 
 TRP   0.006   0.001   TRP A 220 
 HIS   0.002   0.001   HIS B 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7326)
  covalent geometry    : angle       0.53408 (10390)
  hydrogen bonds       : bond        0.04909 (  311)
  hydrogen bonds       : angle       3.33960 (  805)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 12
  residues processed: 81
  average time/residue: 0.0715
  time to fit residues: 8.4401
Evaluate side-chains
  77 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  239 ILE
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  287 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:   10.0000
   chunk 17 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   overall best weight:    1.7386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.164066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.136673 restraints weight = 10620.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.139376 restraints weight = 6437.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.141077 restraints weight = 4734.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.142215 restraints weight = 3931.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.142870 restraints weight = 3496.494|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7326  Z= 0.136
  Angle     :  0.541   7.721  10390  Z= 0.273
  Chirality :  0.035   0.194   1230
  Planarity :  0.005   0.062    954
  Dihedral  : 22.485 179.326   2178
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 18.91 %
    Favored  : 78.46 %
  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 (0.35), residues: 590
  helix:  1.00 (0.27), residues: 344
  sheet:  None (None), residues: 0
  loop :  0.09 (0.43), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 237 
 TYR   0.007   0.001   TYR A 249 
 PHE   0.012   0.001   PHE A 289 
 TRP   0.006   0.001   TRP A 220 
 HIS   0.002   0.001   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7326)
  covalent geometry    : angle       0.54076 (10390)
  hydrogen bonds       : bond        0.05100 (  311)
  hydrogen bonds       : angle       3.33753 (  805)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 13
  residues processed: 75
  average time/residue: 0.0639
  time to fit residues: 7.0803
Evaluate side-chains
  78 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  287 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 37 optimal weight:    0.7980
   chunk 54 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    3.8786

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

Flipped N/Q/H residues before XYZ refinement:
B 120 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.159075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.131426 restraints weight = 10676.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.133995 restraints weight = 6582.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.135688 restraints weight = 4885.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.136805 restraints weight = 4066.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.137452 restraints weight = 3617.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   7326  Z= 0.242
  Angle     :  0.651   7.420  10390  Z= 0.332
  Chirality :  0.040   0.208   1230
  Planarity :  0.006   0.065    954
  Dihedral  : 22.592 177.502   2178
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.10 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.09 (0.33), residues: 590
  helix:  0.51 (0.26), residues: 346
  sheet:  None (None), residues: 0
  loop : -0.47 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  83 
 TYR   0.009   0.002   TYR B  11 
 PHE   0.020   0.002   PHE A 289 
 TRP   0.010   0.002   TRP A 220 
 HIS   0.003   0.001   HIS A 216 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 ( 7326)
  covalent geometry    : angle       0.65142 (10390)
  hydrogen bonds       : bond        0.06742 (  311)
  hydrogen bonds       : angle       3.68634 (  805)

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

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

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1180 Ramachandran restraints generated.
    590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 13
  residues processed: 78
  average time/residue: 0.0694
  time to fit residues: 7.6868
Evaluate side-chains
  76 residues out of total 534 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  181 THR
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  284 ILE
Chi-restraints excluded: chain A residue  287 MET
Chi-restraints excluded: chain B residue   13 SER
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  219 VAL
Chi-restraints excluded: chain B residue  259 LEU
Chi-restraints excluded: chain B residue  284 ILE
Chi-restraints excluded: chain B residue  287 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   chunk 53 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0870
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0050
   chunk 18 optimal weight:    5.9990
   chunk 33 optimal weight:    0.1980
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.4372

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.168395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.141598 restraints weight = 10715.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.144319 restraints weight = 6496.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.146057 restraints weight = 4766.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.147238 restraints weight = 3942.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.147903 restraints weight = 3489.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   7326  Z= 0.104
  Angle     :  0.512   7.758  10390  Z= 0.256
  Chirality :  0.034   0.188   1230
  Planarity :  0.005   0.061    954
  Dihedral  : 22.409 178.490   2178
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 20.60 %
    Favored  : 77.90 %
  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:  1.03 (0.35), residues: 590
  helix:  1.18 (0.28), residues: 348
  sheet:  None (None), residues: 0
  loop :  0.08 (0.43), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  83 
 TYR   0.009   0.001   TYR B 249 
 PHE   0.006   0.001   PHE A 289 
 TRP   0.008   0.001   TRP A 114 
 HIS   0.001   0.000   HIS B 148 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 7326)
  covalent geometry    : angle       0.51246 (10390)
  hydrogen bonds       : bond        0.04034 (  311)
  hydrogen bonds       : angle       3.23372 (  805)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1105.35 seconds
wall clock time: 19 minutes 52.02 seconds (1192.02 seconds total)