Starting phenix.real_space_refine
on Tue Mar  3 19:29:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hik_34819/03_2026/8hik_34819.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hik_34819/03_2026/8hik_34819.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hik_34819/03_2026/8hik_34819.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hik_34819/03_2026/8hik_34819.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hik_34819/03_2026/8hik_34819.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hik_34819/03_2026/8hik_34819.map"
  }
  resolution = 3.72
  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=   0.016
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       2      5.49       5
     S      27      5.16       5
     C    5296      2.51       5
     N    1376      2.21       5
     O    1537      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8238
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 498, 3969
          Classifications: {'peptide': 498}
          Link IDs: {'PTRANS': 17, 'TRANS': 480}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1686
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1686
          Classifications: {'peptide': 225}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211}
    Chain: "N"
      Number of atoms: 925
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 925
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 1632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1632
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201}
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Unusual residues: {'TPP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.71, per 1000 atoms: 0.21
  Number of scatterers: 8238
  At special positions: 0
  Unit cell: (66.34, 99.51, 148.73, 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      27     16.00
     P       2     15.00
     O    1537      8.00
     N    1376      7.00
     C    5296      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  25 " - pdb=" SG  CYS H  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 154 " - pdb=" SG  CYS H 210 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  24 " - pdb=" SG  CYS L  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 136 " - pdb=" SG  CYS L 196 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 321.9 milliseconds
  

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1972

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 14 sheets defined
      39.7% alpha, 23.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid -80 through -64
      removed outlier: 3.672A  pdb=" N   LYS A -64 " --> pdb=" O   LYS A -68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -57 through -43
      removed outlier: 3.598A  pdb=" N   ALA A -43 " --> pdb=" O   ALA A -47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -38 through -33
      removed outlier: 4.020A  pdb=" N   ASP A -33 " --> pdb=" O   PRO A -37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -25 through -3
      removed outlier: 3.702A  pdb=" N   LEU A  -5 " --> pdb=" O   ASP A  -9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2 through 18
      removed outlier: 3.694A  pdb=" N   ALA A   6 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 19 through 23
    Processing helix  chain 'A' and resid 27 through 39
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 66
    Processing helix  chain 'A' and resid 68 through 81
    Processing helix  chain 'A' and resid 82 through 90
      removed outlier: 4.114A  pdb=" N   LEU A  86 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 112
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.884A  pdb=" N   MET A 119 " --> pdb=" O   SER A 115 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   VAL A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   THR A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 144
      removed outlier: 4.115A  pdb=" N   SER A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 176
    Processing helix  chain 'A' and resid 181 through 202
    Processing helix  chain 'A' and resid 251 through 259
    Processing helix  chain 'A' and resid 260 through 262
      No H-bonds generated for 'chain 'A' and resid 260 through 262'
    Processing helix  chain 'A' and resid 264 through 296
      removed outlier: 3.936A  pdb=" N   TYR A 287 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   HIS A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   ILE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP A 296 " --> pdb=" O   TRP A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 323
    Processing helix  chain 'A' and resid 335 through 355
    Processing helix  chain 'A' and resid 361 through 375
    Processing helix  chain 'A' and resid 379 through 389
      removed outlier: 3.718A  pdb=" N   ILE A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   SER A 389 " --> pdb=" O   PHE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 418
    Processing helix  chain 'A' and resid 427 through 451
    Processing helix  chain 'H' and resid 90 through 94
      removed outlier: 3.532A  pdb=" N   ASP H  93 " --> pdb=" O   ARG H  90 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   THR H  94 " --> pdb=" O   ALA H  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 90 through 94'
    Processing helix  chain 'H' and resid 107 through 112
      removed outlier: 3.631A  pdb=" N   LYS H 112 " --> pdb=" O   GLU H 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 80 through 84
      removed outlier: 4.097A  pdb=" N   PHE L  84 " --> pdb=" O   PRO L  81 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 184 through 188
    Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10
    Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15
      removed outlier: 3.588A  pdb=" N   VAL H  15 " --> pdb=" O   THR H 124 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   LEU H  37 " --> pdb=" O   TYR H  53 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   TYR H  53 " --> pdb=" O   LEU H  37 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   TRP H  39 " --> pdb=" O   VAL H  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 134 through 138
      removed outlier: 6.145A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 134 through 138
      removed outlier: 6.145A  pdb=" N   TYR H 190 " --> pdb=" O   ASP H 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 164 through 167
      removed outlier: 4.332A  pdb=" N   TYR H 208 " --> pdb=" O   VAL H 225 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.735A  pdb=" N   SER N   7 " --> pdb=" O   SER N  21 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   SER N  21 " --> pdb=" O   SER N   7 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.833A  pdb=" N   THR N 118 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR N 115 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR N  94 " --> pdb=" O   THR N 115 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   MET N  34 " --> pdb=" O   VAL N  50 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   VAL N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'N' and resid 10 through 12
      removed outlier: 3.833A  pdb=" N   THR N 118 " --> pdb=" O   GLY N  10 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR N 115 " --> pdb=" O   TYR N  94 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR N  94 " --> pdb=" O   THR N 115 " (cutoff:3.500A)
      removed outlier: 4.826A  pdb=" N   TYR N 110 " --> pdb=" O   ILE N  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6
    Processing sheet with id=AB1, first strand: chain 'L' and resid 13 through 14
    Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55
      removed outlier: 3.941A  pdb=" N   TYR L  50 " --> pdb=" O   SER L  54 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN L  91 " --> pdb=" O   THR L  99 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   THR L  99 " --> pdb=" O   GLN L  91 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55
      removed outlier: 3.941A  pdb=" N   TYR L  50 " --> pdb=" O   SER L  54 " (cutoff:3.500A)
      removed outlier: 5.870A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 116 through 120
      removed outlier: 5.961A  pdb=" N   TYR L 175 " --> pdb=" O   ASN L 140 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 147 through 148

    446 hydrogen bonds defined for protein.
    1248 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: 1.48

  Time building geometry restraints manager: 1.04 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2562
        1.34 -     1.46: 2030
        1.46 -     1.58: 3807
        1.58 -     1.70: 3
        1.70 -     1.81: 38
  Bond restraints: 8440
  Sorted by residual:
  bond pdb=" C5  TPP A 601 "
       pdb=" S1  TPP A 601 "
    ideal  model  delta    sigma   weight residual
    1.727  1.510  0.217 1.00e-02 1.00e+04 4.69e+02
  bond pdb=" C2  TPP A 601 "
       pdb=" S1  TPP A 601 "
    ideal  model  delta    sigma   weight residual
    1.675  1.544  0.131 1.00e-02 1.00e+04 1.71e+02
  bond pdb=" C4' TPP A 601 "
       pdb=" N4' TPP A 601 "
    ideal  model  delta    sigma   weight residual
    1.337  1.454 -0.117 1.10e-02 8.26e+03 1.13e+02
  bond pdb=" C2  TPP A 601 "
       pdb=" N3  TPP A 601 "
    ideal  model  delta    sigma   weight residual
    1.318  1.424 -0.106 1.30e-02 5.92e+03 6.66e+01
  bond pdb=" O3A TPP A 601 "
       pdb=" PB  TPP A 601 "
    ideal  model  delta    sigma   weight residual
    1.587  1.662 -0.075 1.10e-02 8.26e+03 4.66e+01
  ... (remaining 8435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.25: 11372
        3.25 -     6.49: 91
        6.49 -     9.74: 18
        9.74 -    12.98: 2
       12.98 -    16.23: 1
  Bond angle restraints: 11484
  Sorted by residual:
  angle pdb=" PA  TPP A 601 "
        pdb=" O3A TPP A 601 "
        pdb=" PB  TPP A 601 "
      ideal   model   delta    sigma   weight residual
     139.87  123.64   16.23 1.00e+00 1.00e+00 2.63e+02
  angle pdb=" C2  TPP A 601 "
        pdb=" S1  TPP A 601 "
        pdb=" C5  TPP A 601 "
      ideal   model   delta    sigma   weight residual
      91.33  104.13  -12.80 1.00e+00 1.00e+00 1.64e+02
  angle pdb=" C7  TPP A 601 "
        pdb=" O7  TPP A 601 "
        pdb=" PA  TPP A 601 "
      ideal   model   delta    sigma   weight residual
     124.29  118.57    5.72 1.00e+00 1.00e+00 3.27e+01
  angle pdb=" N1' TPP A 601 "
        pdb=" C2' TPP A 601 "
        pdb=" N3' TPP A 601 "
      ideal   model   delta    sigma   weight residual
     125.71  119.88    5.83 1.07e+00 8.80e-01 2.99e+01
  angle pdb=" N3  TPP A 601 "
        pdb=" C2  TPP A 601 "
        pdb=" S1  TPP A 601 "
      ideal   model   delta    sigma   weight residual
     112.34  107.32    5.02 1.00e+00 1.00e+00 2.52e+01
  ... (remaining 11479 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.52: 4807
       16.52 -    33.03: 110
       33.03 -    49.54: 38
       49.54 -    66.06: 1
       66.06 -    82.57: 11
  Dihedral angle restraints: 4967
    sinusoidal: 1890
      harmonic: 3077
  Sorted by residual:
  dihedral pdb=" CB  CYS H 154 "
           pdb=" SG  CYS H 154 "
           pdb=" SG  CYS H 210 "
           pdb=" CB  CYS H 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  175.57  -82.57     1      1.00e+01 1.00e-02 8.36e+01
  dihedral pdb=" CB  CYS L 136 "
           pdb=" SG  CYS L 136 "
           pdb=" SG  CYS L 196 "
           pdb=" CB  CYS L 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -120.31   34.31     1      1.00e+01 1.00e-02 1.67e+01
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   TYR A  92 "
           pdb=" CA  TYR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.67   20.33     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 4964 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 957
       0.049 -    0.097: 267
       0.097 -    0.146: 64
       0.146 -    0.195: 7
       0.195 -    0.243: 1
  Chirality restraints: 1296
  Sorted by residual:
  chirality pdb=" CA  THR A  69 "
            pdb=" N   THR A  69 "
            pdb=" C   THR A  69 "
            pdb=" CB  THR A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CB  THR A  69 "
            pdb=" CA  THR A  69 "
            pdb=" OG1 THR A  69 "
            pdb=" CG2 THR A  69 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.13e-01
  chirality pdb=" CA  TYR N 104 "
            pdb=" N   TYR N 104 "
            pdb=" C   TYR N 104 "
            pdb=" CB  TYR N 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.80e-01
  ... (remaining 1293 not shown)

  Planarity restraints: 1437
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 102 "   -0.016 2.00e-02 2.50e+03   1.51e-02 5.66e+00
        pdb=" CG  TRP H 102 "    0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 102 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 102 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 102 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 102 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 102 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 102 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 102 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 102 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP H 105 "    0.038 5.00e-02 4.00e+02   5.76e-02 5.31e+00
        pdb=" N   PRO H 106 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO H 106 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO H 106 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 108 "   -0.035 5.00e-02 4.00e+02   5.18e-02 4.29e+00
        pdb=" N   PRO H 109 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO H 109 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO H 109 "   -0.030 5.00e-02 4.00e+02
  ... (remaining 1434 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2236
        2.81 -     3.33: 7133
        3.33 -     3.85: 13492
        3.85 -     4.38: 15090
        4.38 -     4.90: 26545
  Nonbonded interactions: 64496
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 168 "
            pdb=" O   GLY A 307 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG  SER L  64 "
            pdb=" OG1 THR L  75 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   GLU A -26 "
            pdb=" OH  TYR A  22 "
     model   vdw
     2.336 3.040
  nonbonded pdb=" NE  ARG A -49 "
            pdb=" O   LEU L  93 "
     model   vdw
     2.340 3.120
  nonbonded pdb=" O   TRP H 111 "
            pdb=" OH  TYR L  92 "
     model   vdw
     2.345 3.040
  ... (remaining 64491 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:             2.950
  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:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.150
  Find NCS groups from input model:        0.040
  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:1.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6165
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      :  0.005   0.217   8445  Z= 0.385
  Angle     :  0.821  16.228  11494  Z= 0.473
  Chirality :  0.047   0.243   1296
  Planarity :  0.006   0.058   1437
  Dihedral  :  9.567  75.327   2980
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 are not related in a simple way.
  whole: -3.54 (0.21), residues: 1045
  helix: -1.96 (0.20), residues: 380
  sheet: -1.92 (0.29), residues: 241
  loop : -2.84 (0.25), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG L  62 
 TYR   0.023   0.002   TYR H  53 
 PHE   0.029   0.002   PHE A 103 
 TRP   0.041   0.002   TRP H 102 
 HIS   0.006   0.002   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 ( 8440)
  covalent geometry    : angle       0.82034 (11484)
  SS BOND              : bond        0.00134 (    5)
  SS BOND              : angle       1.34217 (   10)
  hydrogen bonds       : bond        0.11935 (  420)
  hydrogen bonds       : angle       6.64327 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -51 LYS cc_start: 0.7460 (tttt) cc_final: 0.7258 (mtmm)
REVERT: A  -50 MET cc_start: 0.6246 (mmm) cc_final: 0.5921 (mmm)
REVERT: A  -22 PHE cc_start: 0.7319 (t80) cc_final: 0.6815 (t80)
REVERT: A   27 HIS cc_start: 0.5170 (m90) cc_final: 0.4851 (m-70)
REVERT: A   73 SER cc_start: 0.6585 (m) cc_final: 0.6353 (t)
REVERT: A  140 ILE cc_start: 0.7951 (mt) cc_final: 0.7742 (tp)
REVERT: A  281 TYR cc_start: 0.6510 (t80) cc_final: 0.6203 (t80)
REVERT: A  304 VAL cc_start: 0.7185 (t) cc_final: 0.5917 (m)
REVERT: A  386 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7062 (tm-30)
REVERT: A  387 ILE cc_start: 0.7155 (mt) cc_final: 0.6955 (mt)
REVERT: H   86 MET cc_start: 0.6378 (mtm) cc_final: 0.6146 (mtm)
REVERT: H   99 CYS cc_start: 0.5632 (t) cc_final: 0.5367 (t)
REVERT: H  112 LYS cc_start: 0.7716 (mttt) cc_final: 0.7507 (ttmm)
REVERT: H  119 GLN cc_start: 0.6958 (mt0) cc_final: 0.6698 (mt0)
REVERT: H  135 VAL cc_start: 0.7872 (t) cc_final: 0.7591 (m)
REVERT: H  136 PHE cc_start: 0.7526 (m-80) cc_final: 0.7085 (m-80)
REVERT: N   34 MET cc_start: 0.6441 (mtp) cc_final: 0.6214 (mtp)
REVERT: L   32 SER cc_start: 0.7747 (t) cc_final: 0.7452 (p)
REVERT: L   37 TYR cc_start: 0.8262 (m-10) cc_final: 0.7689 (m-80)
REVERT: L   43 LYS cc_start: 0.8431 (mttt) cc_final: 0.8095 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.0837
  time to fit residues: 25.2553
Evaluate side-chains
  184 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0070
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
A -77 ASN
A -42 GLN
A  27 HIS
A 120 GLN
A 293 ASN
A 358 HIS
H 178 HIS
H 214 HIS
L  28 GLN
L  39 GLN
L  90 GLN
L 162 GLN
L 191 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.169684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.150897 restraints weight = 13127.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.154712 restraints weight = 7267.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.157250 restraints weight = 4578.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.158867 restraints weight = 3213.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.160078 restraints weight = 2465.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6428
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.101   8445  Z= 0.225
  Angle     :  0.661   7.472  11494  Z= 0.345
  Chirality :  0.043   0.169   1296
  Planarity :  0.005   0.050   1437
  Dihedral  :  5.473  52.060   1163
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  9.41 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 are not related in a simple way.
  whole: -2.14 (0.24), residues: 1045
  helix: -0.35 (0.25), residues: 389
  sheet: -1.49 (0.31), residues: 241
  loop : -2.33 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A -49 
 TYR   0.032   0.002   TYR A 126 
 PHE   0.020   0.002   PHE L 211 
 TRP   0.039   0.003   TRP H 102 
 HIS   0.006   0.002   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 8440)
  covalent geometry    : angle       0.65667 (11484)
  SS BOND              : bond        0.01333 (    5)
  SS BOND              : angle       2.64777 (   10)
  hydrogen bonds       : bond        0.04041 (  420)
  hydrogen bonds       : angle       5.54287 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 227
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -51 LYS cc_start: 0.7718 (tttt) cc_final: 0.7342 (mtmm)
REVERT: A  -50 MET cc_start: 0.6526 (mmm) cc_final: 0.6315 (mmm)
REVERT: A   27 HIS cc_start: 0.5825 (m-70) cc_final: 0.5595 (m-70)
REVERT: A   67 GLU cc_start: 0.7682 (tt0) cc_final: 0.7340 (tt0)
REVERT: A   73 SER cc_start: 0.7616 (m) cc_final: 0.7224 (t)
REVERT: A   99 GLN cc_start: 0.7844 (tt0) cc_final: 0.7422 (tt0)
REVERT: A  294 GLU cc_start: 0.6915 (tt0) cc_final: 0.6642 (tt0)
REVERT: A  386 GLN cc_start: 0.7459 (mm-40) cc_final: 0.7092 (tm-30)
REVERT: A  387 ILE cc_start: 0.7194 (mt) cc_final: 0.6918 (mt)
REVERT: A  405 PHE cc_start: 0.6977 (t80) cc_final: 0.6724 (t80)
REVERT: H    7 LEU cc_start: 0.7579 (mm) cc_final: 0.7344 (mt)
REVERT: H   46 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8161 (mmmm)
REVERT: H   63 TYR cc_start: 0.7711 (m-10) cc_final: 0.7384 (m-10)
REVERT: H   86 MET cc_start: 0.6741 (mtm) cc_final: 0.6523 (mtm)
REVERT: H  135 VAL cc_start: 0.7878 (t) cc_final: 0.7638 (m)
REVERT: H  197 THR cc_start: 0.7180 (p) cc_final: 0.6960 (p)
REVERT: N   39 GLN cc_start: 0.5882 (mp10) cc_final: 0.3863 (mp10)
REVERT: N   59 PHE cc_start: 0.7114 (m-80) cc_final: 0.6858 (m-80)
REVERT: L   36 TRP cc_start: 0.8180 (m100) cc_final: 0.7838 (m100)
REVERT: L   37 TYR cc_start: 0.8299 (m-10) cc_final: 0.8072 (m-80)
REVERT: L   43 LYS cc_start: 0.8640 (mttt) cc_final: 0.8359 (mmmm)
REVERT: L   47 LEU cc_start: 0.8593 (tp) cc_final: 0.8309 (tt)
REVERT: L  104 THR cc_start: 0.7829 (p) cc_final: 0.7619 (p)
REVERT: L  117 VAL cc_start: 0.8267 (t) cc_final: 0.7995 (p)
REVERT: L  137 LEU cc_start: 0.8103 (tp) cc_final: 0.7830 (tt)
REVERT: L  166 THR cc_start: 0.8507 (t) cc_final: 0.8062 (m)
  outliers start: 23
  outliers final: 10
  residues processed: 234
  average time/residue: 0.0767
  time to fit residues: 25.5578
Evaluate side-chains
  212 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 202
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue   91 ARG
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 86 optimal weight:    0.7980
   chunk 16 optimal weight:    0.5980
   chunk 89 optimal weight:    0.0010
   chunk 55 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
A -20 HIS
** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 377 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.168316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.149664 restraints weight = 13005.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.153420 restraints weight = 7170.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.155928 restraints weight = 4498.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.157603 restraints weight = 3144.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.158759 restraints weight = 2392.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.4008
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6460
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   8445  Z= 0.180
  Angle     :  0.618   7.292  11494  Z= 0.314
  Chirality :  0.042   0.155   1296
  Planarity :  0.005   0.087   1437
  Dihedral  :  5.248  48.170   1163
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 12.32 %
    Favored  : 85.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 are not related in a simple way.
  whole: -1.61 (0.25), residues: 1045
  helix:  0.18 (0.26), residues: 387
  sheet: -1.19 (0.31), residues: 243
  loop : -2.15 (0.30), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A -49 
 TYR   0.024   0.002   TYR A 126 
 PHE   0.018   0.001   PHE A 212 
 TRP   0.023   0.002   TRP H 102 
 HIS   0.003   0.001   HIS H  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 8440)
  covalent geometry    : angle       0.61670 (11484)
  SS BOND              : bond        0.00525 (    5)
  SS BOND              : angle       1.57562 (   10)
  hydrogen bonds       : bond        0.03866 (  420)
  hydrogen bonds       : angle       5.27854 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 205
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.7775 (m) cc_final: 0.7339 (t)
REVERT: A   99 GLN cc_start: 0.7602 (tt0) cc_final: 0.7098 (tt0)
REVERT: A  264 ARG cc_start: 0.4952 (ttp-110) cc_final: 0.4354 (mtm110)
REVERT: A  294 GLU cc_start: 0.6887 (tt0) cc_final: 0.6604 (tt0)
REVERT: A  386 GLN cc_start: 0.7332 (mm-40) cc_final: 0.6888 (tm-30)
REVERT: A  387 ILE cc_start: 0.7099 (mt) cc_final: 0.6898 (mt)
REVERT: A  405 PHE cc_start: 0.7094 (t80) cc_final: 0.6869 (t80)
REVERT: H   63 TYR cc_start: 0.7737 (m-10) cc_final: 0.7390 (m-10)
REVERT: H  116 TYR cc_start: 0.7480 (m-10) cc_final: 0.7279 (m-80)
REVERT: H  135 VAL cc_start: 0.7854 (t) cc_final: 0.7561 (m)
REVERT: H  136 PHE cc_start: 0.7539 (m-80) cc_final: 0.7277 (m-80)
REVERT: L   36 TRP cc_start: 0.8125 (m100) cc_final: 0.7785 (m100)
REVERT: L   43 LYS cc_start: 0.8672 (mttt) cc_final: 0.8386 (mtpp)
REVERT: L   48 LEU cc_start: 0.7975 (tp) cc_final: 0.7475 (tp)
REVERT: L   87 TYR cc_start: 0.8494 (m-80) cc_final: 0.8049 (m-10)
  outliers start: 22
  outliers final: 13
  residues processed: 214
  average time/residue: 0.0824
  time to fit residues: 24.8799
Evaluate side-chains
  210 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 197
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   66 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    0.0370
   chunk 59 optimal weight:    0.6980
   chunk 31 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0170
   chunk 91 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
A 293 ASN
H 169 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.167657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.149170 restraints weight = 13318.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.152876 restraints weight = 7263.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.155360 restraints weight = 4569.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.157018 restraints weight = 3195.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.158171 restraints weight = 2430.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.4003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6461
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   8445  Z= 0.144
  Angle     :  0.587   8.021  11494  Z= 0.295
  Chirality :  0.041   0.144   1296
  Planarity :  0.004   0.071   1437
  Dihedral  :  5.050  54.289   1163
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.89 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 are not related in a simple way.
  whole: -1.27 (0.26), residues: 1045
  helix:  0.46 (0.26), residues: 387
  sheet: -1.06 (0.32), residues: 245
  loop : -1.91 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A -49 
 TYR   0.021   0.002   TYR A 126 
 PHE   0.033   0.001   PHE H 160 
 TRP   0.015   0.002   TRP H 102 
 HIS   0.003   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 8440)
  covalent geometry    : angle       0.58613 (11484)
  SS BOND              : bond        0.00281 (    5)
  SS BOND              : angle       1.01479 (   10)
  hydrogen bonds       : bond        0.03611 (  420)
  hydrogen bonds       : angle       5.03605 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 200
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 VAL cc_start: 0.7395 (m) cc_final: 0.7147 (p)
REVERT: A   73 SER cc_start: 0.7907 (m) cc_final: 0.7439 (t)
REVERT: A   99 GLN cc_start: 0.7615 (tt0) cc_final: 0.7129 (tt0)
REVERT: A  294 GLU cc_start: 0.6882 (tt0) cc_final: 0.6588 (tt0)
REVERT: A  386 GLN cc_start: 0.7412 (mm-40) cc_final: 0.7006 (tm-30)
REVERT: A  387 ILE cc_start: 0.7155 (mt) cc_final: 0.6940 (mt)
REVERT: H   20 SER cc_start: 0.8040 (m) cc_final: 0.7648 (p)
REVERT: H  116 TYR cc_start: 0.7389 (m-10) cc_final: 0.7185 (m-80)
REVERT: H  135 VAL cc_start: 0.7863 (t) cc_final: 0.7591 (m)
REVERT: H  136 PHE cc_start: 0.7629 (m-80) cc_final: 0.7386 (m-80)
REVERT: N   95 TYR cc_start: 0.6071 (m-10) cc_final: 0.5782 (m-10)
REVERT: L   32 SER cc_start: 0.8239 (t) cc_final: 0.7834 (p)
REVERT: L   36 TRP cc_start: 0.8122 (m100) cc_final: 0.7748 (m100)
REVERT: L   37 TYR cc_start: 0.8259 (m-80) cc_final: 0.7982 (m-80)
REVERT: L   43 LYS cc_start: 0.8662 (mttt) cc_final: 0.8369 (mtpp)
REVERT: L   48 LEU cc_start: 0.7948 (tp) cc_final: 0.7494 (tp)
REVERT: L   87 TYR cc_start: 0.8485 (m-80) cc_final: 0.8026 (m-10)
REVERT: L   88 TYR cc_start: 0.8314 (m-80) cc_final: 0.7437 (m-80)
  outliers start: 22
  outliers final: 16
  residues processed: 211
  average time/residue: 0.0816
  time to fit residues: 24.3984
Evaluate side-chains
  211 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 195
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   75 THR
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 56 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 91 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 84 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A   5 GLN
** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.163777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.145063 restraints weight = 13124.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.148969 restraints weight = 7014.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.151520 restraints weight = 4320.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.153222 restraints weight = 2980.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.154313 restraints weight = 2254.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6560
moved from start:          0.4789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.093   8445  Z= 0.218
  Angle     :  0.656   8.530  11494  Z= 0.334
  Chirality :  0.043   0.178   1296
  Planarity :  0.005   0.070   1437
  Dihedral  :  5.182  44.090   1163
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.68 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 are not related in a simple way.
  whole: -1.32 (0.26), residues: 1045
  helix:  0.37 (0.26), residues: 387
  sheet: -1.03 (0.32), residues: 245
  loop : -1.92 (0.31), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N  52 
 TYR   0.022   0.002   TYR A 126 
 PHE   0.015   0.001   PHE L 211 
 TRP   0.015   0.002   TRP H 117 
 HIS   0.005   0.001   HIS A  27 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 8440)
  covalent geometry    : angle       0.65552 (11484)
  SS BOND              : bond        0.00588 (    5)
  SS BOND              : angle       1.08114 (   10)
  hydrogen bonds       : bond        0.04068 (  420)
  hydrogen bonds       : angle       5.30863 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 212
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -76 TRP cc_start: 0.6225 (t-100) cc_final: 0.5956 (t-100)
REVERT: A  -50 MET cc_start: 0.6454 (mmm) cc_final: 0.6056 (tmm)
REVERT: A   53 LEU cc_start: 0.6235 (mp) cc_final: 0.5806 (mt)
REVERT: A   71 VAL cc_start: 0.7451 (m) cc_final: 0.7133 (p)
REVERT: A   73 SER cc_start: 0.8006 (m) cc_final: 0.7616 (t)
REVERT: A   77 LEU cc_start: 0.7806 (tp) cc_final: 0.7598 (tt)
REVERT: A  122 MET cc_start: 0.7138 (tmm) cc_final: 0.6050 (tmm)
REVERT: A  294 GLU cc_start: 0.6953 (tt0) cc_final: 0.6699 (tt0)
REVERT: A  300 ASN cc_start: 0.5991 (t0) cc_final: 0.5773 (t0)
REVERT: A  386 GLN cc_start: 0.7340 (mm-40) cc_final: 0.6936 (tt0)
REVERT: A  387 ILE cc_start: 0.7186 (mt) cc_final: 0.6950 (mt)
REVERT: H   20 SER cc_start: 0.8167 (m) cc_final: 0.7793 (p)
REVERT: H   63 TYR cc_start: 0.7821 (m-10) cc_final: 0.7422 (m-10)
REVERT: H  117 TRP cc_start: 0.8088 (m100) cc_final: 0.7878 (m100)
REVERT: H  135 VAL cc_start: 0.7883 (t) cc_final: 0.7634 (m)
REVERT: N   95 TYR cc_start: 0.5985 (m-10) cc_final: 0.5759 (m-10)
REVERT: L    7 GLN cc_start: 0.7347 (tt0) cc_final: 0.6891 (tt0)
REVERT: L   36 TRP cc_start: 0.8300 (m100) cc_final: 0.7773 (m100)
REVERT: L   43 LYS cc_start: 0.8720 (mttt) cc_final: 0.8414 (mtpp)
REVERT: L   48 LEU cc_start: 0.7951 (tp) cc_final: 0.7593 (tp)
REVERT: L   92 TYR cc_start: 0.8295 (p90) cc_final: 0.7925 (p90)
REVERT: L  142 TYR cc_start: 0.7634 (t80) cc_final: 0.7130 (t80)
REVERT: L  166 THR cc_start: 0.8610 (t) cc_final: 0.8220 (m)
  outliers start: 27
  outliers final: 22
  residues processed: 223
  average time/residue: 0.0840
  time to fit residues: 26.1560
Evaluate side-chains
  223 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 201
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   26 ARG
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  194 SER
Chi-restraints excluded: chain H residue  200 SER
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 18 optimal weight:    0.3980
   chunk 75 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 52 optimal weight:    0.5980
   chunk 73 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A  27 HIS
A 289 HIS
** N  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.162523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.144589 restraints weight = 13006.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.148184 restraints weight = 7107.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.150598 restraints weight = 4417.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.152206 restraints weight = 3055.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.153349 restraints weight = 2315.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3940
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6560
moved from start:          0.5093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   8445  Z= 0.197
  Angle     :  0.654  10.427  11494  Z= 0.328
  Chirality :  0.042   0.147   1296
  Planarity :  0.004   0.070   1437
  Dihedral  :  5.088  40.939   1163
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 17.92 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 are not related in a simple way.
  whole: -1.25 (0.26), residues: 1045
  helix:  0.41 (0.26), residues: 390
  sheet: -0.95 (0.33), residues: 239
  loop : -1.91 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  52 
 TYR   0.027   0.002   TYR A 126 
 PHE   0.024   0.002   PHE H 136 
 TRP   0.016   0.002   TRP H 117 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 8440)
  covalent geometry    : angle       0.65370 (11484)
  SS BOND              : bond        0.00443 (    5)
  SS BOND              : angle       0.90401 (   10)
  hydrogen bonds       : bond        0.03962 (  420)
  hydrogen bonds       : angle       5.23348 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 204
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -50 MET cc_start: 0.6516 (mmm) cc_final: 0.6268 (tmm)
REVERT: A   53 LEU cc_start: 0.6350 (mp) cc_final: 0.5908 (mt)
REVERT: A   71 VAL cc_start: 0.7433 (m) cc_final: 0.7105 (p)
REVERT: A   73 SER cc_start: 0.7913 (m) cc_final: 0.7588 (t)
REVERT: A   99 GLN cc_start: 0.7622 (tt0) cc_final: 0.7071 (tt0)
REVERT: A  128 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7774 (p)
REVERT: A  294 GLU cc_start: 0.6936 (tt0) cc_final: 0.6680 (tt0)
REVERT: A  300 ASN cc_start: 0.5998 (t0) cc_final: 0.5797 (t0)
REVERT: A  386 GLN cc_start: 0.7285 (mm-40) cc_final: 0.6934 (tt0)
REVERT: A  387 ILE cc_start: 0.7202 (mt) cc_final: 0.6972 (mt)
REVERT: H   20 SER cc_start: 0.8179 (m) cc_final: 0.7783 (p)
REVERT: H   63 TYR cc_start: 0.7823 (m-10) cc_final: 0.7558 (m-10)
REVERT: H  136 PHE cc_start: 0.7288 (m-80) cc_final: 0.7017 (m-80)
REVERT: N   95 TYR cc_start: 0.6037 (m-10) cc_final: 0.5808 (m-10)
REVERT: L   32 SER cc_start: 0.8231 (t) cc_final: 0.7782 (p)
REVERT: L   36 TRP cc_start: 0.8245 (m100) cc_final: 0.7872 (m100)
REVERT: L   43 LYS cc_start: 0.8722 (mttt) cc_final: 0.8375 (mtpp)
REVERT: L   92 TYR cc_start: 0.8358 (p90) cc_final: 0.7960 (p90)
REVERT: L  142 TYR cc_start: 0.7583 (t80) cc_final: 0.7085 (t80)
REVERT: L  166 THR cc_start: 0.8572 (t) cc_final: 0.8178 (m)
  outliers start: 26
  outliers final: 21
  residues processed: 217
  average time/residue: 0.0816
  time to fit residues: 24.7294
Evaluate side-chains
  218 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 196
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   19 ILE
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  200 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   21 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   89 CYS
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 103 optimal weight:    0.6980
   chunk 59 optimal weight:    0.1980
   chunk 100 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 40 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
L 160 ASN
** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.162463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.144504 restraints weight = 13109.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.148108 restraints weight = 7091.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.150464 restraints weight = 4411.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.152057 restraints weight = 3073.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.153103 restraints weight = 2342.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6559
moved from start:          0.5269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8445  Z= 0.175
  Angle     :  0.644   8.665  11494  Z= 0.321
  Chirality :  0.042   0.148   1296
  Planarity :  0.005   0.065   1437
  Dihedral  :  5.030  36.856   1163
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 17.92 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 are not related in a simple way.
  whole: -1.15 (0.26), residues: 1045
  helix:  0.52 (0.26), residues: 389
  sheet: -0.97 (0.33), residues: 239
  loop : -1.83 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  52 
 TYR   0.026   0.002   TYR H  53 
 PHE   0.022   0.001   PHE H 136 
 TRP   0.018   0.002   TRP H 168 
 HIS   0.004   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 8440)
  covalent geometry    : angle       0.64394 (11484)
  SS BOND              : bond        0.00285 (    5)
  SS BOND              : angle       0.81640 (   10)
  hydrogen bonds       : bond        0.03840 (  420)
  hydrogen bonds       : angle       5.10461 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 208
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 LEU cc_start: 0.6365 (mp) cc_final: 0.5920 (mt)
REVERT: A   71 VAL cc_start: 0.7462 (m) cc_final: 0.7123 (p)
REVERT: A   73 SER cc_start: 0.7879 (m) cc_final: 0.7521 (t)
REVERT: A   99 GLN cc_start: 0.7649 (tt0) cc_final: 0.7112 (tt0)
REVERT: A  128 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7813 (p)
REVERT: A  294 GLU cc_start: 0.6945 (tt0) cc_final: 0.6680 (tt0)
REVERT: A  300 ASN cc_start: 0.5990 (t0) cc_final: 0.5789 (t0)
REVERT: A  366 TYR cc_start: 0.6984 (m-80) cc_final: 0.6650 (m-80)
REVERT: A  386 GLN cc_start: 0.7277 (mm-40) cc_final: 0.6906 (tt0)
REVERT: A  387 ILE cc_start: 0.7197 (mt) cc_final: 0.6959 (mt)
REVERT: H    7 LEU cc_start: 0.7469 (mm) cc_final: 0.7236 (mt)
REVERT: H   20 SER cc_start: 0.8209 (m) cc_final: 0.7802 (p)
REVERT: H   37 LEU cc_start: 0.7915 (mm) cc_final: 0.7588 (mt)
REVERT: H   63 TYR cc_start: 0.7810 (m-10) cc_final: 0.7562 (m-10)
REVERT: N   95 TYR cc_start: 0.6076 (m-10) cc_final: 0.5853 (m-10)
REVERT: L   32 SER cc_start: 0.8142 (t) cc_final: 0.7700 (p)
REVERT: L   39 GLN cc_start: 0.8291 (tt0) cc_final: 0.8075 (tt0)
REVERT: L   43 LYS cc_start: 0.8711 (mttt) cc_final: 0.8403 (mtpp)
REVERT: L   92 TYR cc_start: 0.8320 (p90) cc_final: 0.7958 (p90)
REVERT: L  142 TYR cc_start: 0.7565 (t80) cc_final: 0.7091 (t80)
REVERT: L  166 THR cc_start: 0.8574 (t) cc_final: 0.8158 (m)
  outliers start: 27
  outliers final: 20
  residues processed: 224
  average time/residue: 0.0833
  time to fit residues: 25.9366
Evaluate side-chains
  223 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 202
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   26 ARG
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 30 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 35 optimal weight:    0.8980
   chunk 52 optimal weight:    0.5980
   chunk 102 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 293 ASN
** N  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 160 ASN
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.159452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.140761 restraints weight = 13212.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.144577 restraints weight = 7187.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.147090 restraints weight = 4488.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.148745 restraints weight = 3101.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.149912 restraints weight = 2349.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6612
moved from start:          0.5672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.085   8445  Z= 0.227
  Angle     :  0.686   7.700  11494  Z= 0.348
  Chirality :  0.043   0.155   1296
  Planarity :  0.005   0.066   1437
  Dihedral  :  5.238  33.533   1163
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.25 %
    Favored  : 78.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 are not related in a simple way.
  whole: -1.28 (0.26), residues: 1045
  helix:  0.35 (0.26), residues: 394
  sheet: -1.04 (0.33), residues: 236
  loop : -1.84 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  42 
 TYR   0.033   0.002   TYR H  53 
 PHE   0.026   0.002   PHE H 136 
 TRP   0.028   0.002   TRP H 168 
 HIS   0.005   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 8440)
  covalent geometry    : angle       0.68507 (11484)
  SS BOND              : bond        0.00300 (    5)
  SS BOND              : angle       1.15425 (   10)
  hydrogen bonds       : bond        0.04200 (  420)
  hydrogen bonds       : angle       5.36983 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 203
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -50 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6101 (tmm)
REVERT: A  -49 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7575 (tpp80)
REVERT: A    3 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6832 (mm-30)
REVERT: A   46 SER cc_start: 0.7973 (m) cc_final: 0.7450 (t)
REVERT: A   53 LEU cc_start: 0.6385 (mp) cc_final: 0.5951 (mt)
REVERT: A   71 VAL cc_start: 0.7560 (m) cc_final: 0.7242 (p)
REVERT: A   73 SER cc_start: 0.8148 (m) cc_final: 0.7797 (t)
REVERT: A   99 GLN cc_start: 0.7715 (tt0) cc_final: 0.7160 (tt0)
REVERT: A  122 MET cc_start: 0.7330 (tmm) cc_final: 0.6460 (tmm)
REVERT: A  294 GLU cc_start: 0.6990 (tt0) cc_final: 0.6716 (tt0)
REVERT: A  300 ASN cc_start: 0.6000 (t0) cc_final: 0.5796 (t0)
REVERT: A  366 TYR cc_start: 0.7181 (m-80) cc_final: 0.6900 (m-80)
REVERT: A  386 GLN cc_start: 0.7251 (mm-40) cc_final: 0.6714 (tm-30)
REVERT: A  387 ILE cc_start: 0.7214 (mt) cc_final: 0.6970 (mt)
REVERT: H  110 TRP cc_start: 0.8349 (t60) cc_final: 0.7025 (t60)
REVERT: L   32 SER cc_start: 0.8204 (t) cc_final: 0.7797 (p)
REVERT: L   43 LYS cc_start: 0.8714 (mttt) cc_final: 0.8387 (mtpp)
REVERT: L   92 TYR cc_start: 0.8471 (p90) cc_final: 0.8043 (p90)
REVERT: L  142 TYR cc_start: 0.7629 (t80) cc_final: 0.7144 (t80)
REVERT: L  166 THR cc_start: 0.8571 (t) cc_final: 0.8163 (m)
  outliers start: 31
  outliers final: 24
  residues processed: 216
  average time/residue: 0.0841
  time to fit residues: 25.2586
Evaluate side-chains
  228 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 202
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -49 ARG
Chi-restraints excluded: chain A residue  -26 GLU
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  200 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0970
   chunk 64 optimal weight:    0.2980
   chunk 68 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 100 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** N  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 160 ASN
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.161512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.143096 restraints weight = 13218.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.146904 restraints weight = 7179.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.149363 restraints weight = 4450.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.151007 restraints weight = 3093.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.151927 restraints weight = 2340.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6583
moved from start:          0.5707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8445  Z= 0.180
  Angle     :  0.667   9.857  11494  Z= 0.332
  Chirality :  0.042   0.149   1296
  Planarity :  0.005   0.065   1437
  Dihedral  :  5.092  29.479   1163
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.37 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 are not related in a simple way.
  whole: -1.16 (0.26), residues: 1045
  helix:  0.44 (0.26), residues: 390
  sheet: -0.94 (0.33), residues: 246
  loop : -1.78 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  52 
 TYR   0.036   0.002   TYR A 149 
 PHE   0.024   0.001   PHE H 136 
 TRP   0.031   0.002   TRP H 168 
 HIS   0.005   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 8440)
  covalent geometry    : angle       0.66629 (11484)
  SS BOND              : bond        0.00242 (    5)
  SS BOND              : angle       1.04212 (   10)
  hydrogen bonds       : bond        0.03970 (  420)
  hydrogen bonds       : angle       5.15921 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 204
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -50 MET cc_start: 0.6481 (OUTLIER) cc_final: 0.6046 (tmm)
REVERT: A  -49 ARG cc_start: 0.7950 (tpp80) cc_final: 0.7563 (tpp80)
REVERT: A    3 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6745 (mm-30)
REVERT: A   46 SER cc_start: 0.7962 (m) cc_final: 0.7432 (t)
REVERT: A   53 LEU cc_start: 0.6418 (mp) cc_final: 0.5988 (mt)
REVERT: A   71 VAL cc_start: 0.7550 (m) cc_final: 0.7237 (p)
REVERT: A   73 SER cc_start: 0.7949 (m) cc_final: 0.7600 (t)
REVERT: A   99 GLN cc_start: 0.7655 (tt0) cc_final: 0.7136 (tt0)
REVERT: A  122 MET cc_start: 0.7294 (tmm) cc_final: 0.6552 (tmm)
REVERT: A  294 GLU cc_start: 0.6949 (tt0) cc_final: 0.6672 (tt0)
REVERT: A  300 ASN cc_start: 0.6008 (t0) cc_final: 0.5797 (t0)
REVERT: A  366 TYR cc_start: 0.7107 (m-80) cc_final: 0.6863 (m-80)
REVERT: A  386 GLN cc_start: 0.7134 (mm-40) cc_final: 0.6741 (tm-30)
REVERT: A  387 ILE cc_start: 0.7203 (mt) cc_final: 0.6990 (mt)
REVERT: H  110 TRP cc_start: 0.8312 (t60) cc_final: 0.6992 (t60)
REVERT: L   32 SER cc_start: 0.8155 (t) cc_final: 0.7757 (p)
REVERT: L   43 LYS cc_start: 0.8698 (mttt) cc_final: 0.8369 (mtpp)
REVERT: L   92 TYR cc_start: 0.8412 (p90) cc_final: 0.7995 (p90)
REVERT: L  142 TYR cc_start: 0.7537 (t80) cc_final: 0.7052 (t80)
REVERT: L  166 THR cc_start: 0.8574 (t) cc_final: 0.8178 (m)
  outliers start: 25
  outliers final: 23
  residues processed: 219
  average time/residue: 0.0825
  time to fit residues: 25.0248
Evaluate side-chains
  234 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 210
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  160 PHE
Chi-restraints excluded: chain H residue  193 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 25 optimal weight:    0.3980
   chunk 53 optimal weight:    0.8980
   chunk 101 optimal weight:    0.6980
   chunk 91 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 60 optimal weight:    0.1980
   chunk 48 optimal weight:    0.0870
   chunk 93 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.3958

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
L 160 ASN
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.162510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.144169 restraints weight = 13173.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.147888 restraints weight = 7152.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.150398 restraints weight = 4475.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.152012 restraints weight = 3087.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.153109 restraints weight = 2341.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.5716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8445  Z= 0.159
  Angle     :  0.670  11.920  11494  Z= 0.329
  Chirality :  0.042   0.146   1296
  Planarity :  0.005   0.064   1437
  Dihedral  :  4.998  28.274   1163
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.16 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 are not related in a simple way.
  whole: -1.02 (0.26), residues: 1045
  helix:  0.54 (0.26), residues: 390
  sheet: -0.94 (0.33), residues: 253
  loop : -1.62 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  52 
 TYR   0.038   0.002   TYR A 149 
 PHE   0.023   0.002   PHE H 136 
 TRP   0.036   0.002   TRP H 168 
 HIS   0.005   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 8440)
  covalent geometry    : angle       0.67012 (11484)
  SS BOND              : bond        0.00225 (    5)
  SS BOND              : angle       0.92704 (   10)
  hydrogen bonds       : bond        0.03855 (  420)
  hydrogen bonds       : angle       5.05200 ( 1248)

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

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

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2090 Ramachandran restraints generated.
    1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 201
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  -50 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5936 (tmm)
REVERT: A  -49 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7558 (tpp80)
REVERT: A    0 LYS cc_start: 0.7265 (mtmm) cc_final: 0.7048 (ptpp)
REVERT: A   46 SER cc_start: 0.7993 (m) cc_final: 0.7457 (t)
REVERT: A   53 LEU cc_start: 0.6428 (mp) cc_final: 0.5986 (mt)
REVERT: A   71 VAL cc_start: 0.7488 (m) cc_final: 0.7196 (p)
REVERT: A   73 SER cc_start: 0.8088 (m) cc_final: 0.7728 (t)
REVERT: A   99 GLN cc_start: 0.7676 (tt0) cc_final: 0.7082 (tt0)
REVERT: A  122 MET cc_start: 0.7259 (tmm) cc_final: 0.6639 (tmm)
REVERT: A  294 GLU cc_start: 0.6923 (tt0) cc_final: 0.6647 (tt0)
REVERT: A  300 ASN cc_start: 0.6009 (t0) cc_final: 0.5792 (t0)
REVERT: A  366 TYR cc_start: 0.7058 (m-80) cc_final: 0.6823 (m-80)
REVERT: A  386 GLN cc_start: 0.7160 (mm-40) cc_final: 0.6673 (tm-30)
REVERT: A  387 ILE cc_start: 0.7123 (mt) cc_final: 0.6908 (mt)
REVERT: H   20 SER cc_start: 0.8233 (m) cc_final: 0.7855 (p)
REVERT: H  110 TRP cc_start: 0.8289 (t60) cc_final: 0.6974 (t60)
REVERT: H  198 VAL cc_start: 0.8658 (p) cc_final: 0.8428 (m)
REVERT: L   32 SER cc_start: 0.8088 (t) cc_final: 0.7688 (p)
REVERT: L   43 LYS cc_start: 0.8682 (mttt) cc_final: 0.8354 (mtpp)
REVERT: L   92 TYR cc_start: 0.8390 (p90) cc_final: 0.8002 (p90)
REVERT: L  142 TYR cc_start: 0.7540 (t80) cc_final: 0.7081 (t80)
REVERT: L  166 THR cc_start: 0.8562 (t) cc_final: 0.8157 (m)
  outliers start: 24
  outliers final: 20
  residues processed: 212
  average time/residue: 0.0844
  time to fit residues: 24.5067
Evaluate side-chains
  222 residues out of total 893 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 200
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -69 LEU
Chi-restraints excluded: chain A residue  -50 MET
Chi-restraints excluded: chain A residue  -49 ARG
Chi-restraints excluded: chain A residue  -18 PHE
Chi-restraints excluded: chain A residue  -11 ILE
Chi-restraints excluded: chain A residue   -7 LEU
Chi-restraints excluded: chain A residue   69 THR
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain H residue   62 SER
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain H residue  121 THR
Chi-restraints excluded: chain H residue  160 PHE
Chi-restraints excluded: chain H residue  193 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   46 GLU
Chi-restraints excluded: chain L residue    3 ILE
Chi-restraints excluded: chain L residue   12 LEU
Chi-restraints excluded: chain L residue   16 VAL
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   51 SER
Chi-restraints excluded: chain L residue   64 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 58 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 102 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** H  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 160 ASN
** L 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.160530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.142101 restraints weight = 13233.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.145988 restraints weight = 7146.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.148455 restraints weight = 4397.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.150125 restraints weight = 3041.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.151187 restraints weight = 2296.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
moved from start:          0.5975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   8445  Z= 0.212
  Angle     :  0.692   9.351  11494  Z= 0.347
  Chirality :  0.043   0.142   1296
  Planarity :  0.005   0.065   1437
  Dihedral  :  5.197  28.832   1163
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 20.27 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.98 %
    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 are not related in a simple way.
  whole: -1.09 (0.26), residues: 1045
  helix:  0.40 (0.25), residues: 396
  sheet: -0.86 (0.33), residues: 251
  loop : -1.70 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  42 
 TYR   0.038   0.002   TYR A 149 
 PHE   0.023   0.002   PHE H 136 
 TRP   0.048   0.002   TRP H 168 
 HIS   0.005   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 8440)
  covalent geometry    : angle       0.69145 (11484)
  SS BOND              : bond        0.00269 (    5)
  SS BOND              : angle       1.02140 (   10)
  hydrogen bonds       : bond        0.04092 (  420)
  hydrogen bonds       : angle       5.24558 ( 1248)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1463.71 seconds
wall clock time: 25 minutes 58.87 seconds (1558.87 seconds total)