Starting phenix.real_space_refine
on Wed Feb  4 01:38:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9klk_62407/02_2026/9klk_62407.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9klk_62407/02_2026/9klk_62407.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9klk_62407/02_2026/9klk_62407.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9klk_62407/02_2026/9klk_62407.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9klk_62407/02_2026/9klk_62407.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9klk_62407/02_2026/9klk_62407.map"
  }
  resolution = 2.9
  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=   0.001
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: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5166      2.51       5
     N    1392      2.21       5
     O    1538      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8153
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1045
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1045
          Classifications: {'peptide': 130}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 125}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2094
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2094
          Classifications: {'peptide': 269}
          Link IDs: {'PTRANS': 15, 'TRANS': 253}
    Chain: "C"
      Number of atoms: 5007
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 641, 5007
          Classifications: {'peptide': 641}
          Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 608}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'GR2': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GR2:plan-1': 1, 'GR2:plan-2': 1}
          Unresolved non-hydrogen planarities: 12
  Time building chain proxies: 1.78, per 1000 atoms: 0.22
  Number of scatterers: 8153
  At special positions: 0
  Unit cell: (76.65, 89.06, 125.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O    1538      8.00
     N    1392      7.00
     C    5166      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 311.0 milliseconds
  

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1962

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 3 sheets defined
      45.4% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'B' and resid 21 through 25
    Processing helix  chain 'B' and resid 26 through 32
    Processing helix  chain 'B' and resid 49 through 62
    Processing helix  chain 'B' and resid 84 through 90
    Processing helix  chain 'B' and resid 94 through 106
    Processing helix  chain 'B' and resid 110 through 122
      removed outlier: 4.346A  pdb=" N   THR B 120 " --> pdb=" O   LEU B 116 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   VAL B 121 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 126
    Processing helix  chain 'B' and resid 129 through 137
    Processing helix  chain 'B' and resid 144 through 156
    Processing helix  chain 'A' and resid 2 through 9
    Processing helix  chain 'A' and resid 29 through 34
    Processing helix  chain 'A' and resid 36 through 41
      removed outlier: 3.573A  pdb=" N   LEU A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 68
      removed outlier: 3.787A  pdb=" N   SER A  68 " --> pdb=" O   ASP A  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 65 through 68'
    Processing helix  chain 'A' and resid 69 through 84
      removed outlier: 4.120A  pdb=" N   TYR A  73 " --> pdb=" O   SER A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 108
    Processing helix  chain 'A' and resid 135 through 155
      removed outlier: 3.906A  pdb=" N   GLU A 141 " --> pdb=" O   LYS A 137 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   THR A 142 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 166
    Processing helix  chain 'A' and resid 170 through 175
    Processing helix  chain 'A' and resid 176 through 180
      removed outlier: 3.582A  pdb=" N   PHE A 179 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 195
    Processing helix  chain 'A' and resid 199 through 205
      removed outlier: 3.639A  pdb=" N   LEU A 202 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
      removed outlier: 4.204A  pdb=" N   GLY A 203 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 232
      removed outlier: 4.107A  pdb=" N   GLU A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 252
    Processing helix  chain 'A' and resid 252 through 266
      Proline residue:  A 258  - end of helix
    Processing helix  chain 'C' and resid 36 through 40
    Processing helix  chain 'C' and resid 41 through 51
      removed outlier: 3.578A  pdb=" N   GLY C  51 " --> pdb=" O   ASN C  47 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 62
    Processing helix  chain 'C' and resid 65 through 76
    Processing helix  chain 'C' and resid 87 through 91
    Processing helix  chain 'C' and resid 118 through 120
      No H-bonds generated for 'chain 'C' and resid 118 through 120'
    Processing helix  chain 'C' and resid 121 through 132
      removed outlier: 4.089A  pdb=" N   GLY C 125 " --> pdb=" O   SER C 121 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   HIS C 126 " --> pdb=" O   ALA C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 144 through 152
      removed outlier: 3.681A  pdb=" N   ILE C 148 " --> pdb=" O   ASP C 144 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 155
      No H-bonds generated for 'chain 'C' and resid 153 through 155'
    Processing helix  chain 'C' and resid 176 through 181
      removed outlier: 3.582A  pdb=" N   LEU C 181 " --> pdb=" O   ASP C 177 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 209
    Processing helix  chain 'C' and resid 211 through 217
    Processing helix  chain 'C' and resid 233 through 244
    Processing helix  chain 'C' and resid 265 through 276
    Processing helix  chain 'C' and resid 288 through 291
    Processing helix  chain 'C' and resid 293 through 298
      removed outlier: 4.160A  pdb=" N   PHE C 297 " --> pdb=" O   ALA C 293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 313 through 323
    Processing helix  chain 'C' and resid 341 through 352
      removed outlier: 3.567A  pdb=" N   ASN C 349 " --> pdb=" O   LEU C 345 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   SER C 350 " --> pdb=" O   GLU C 346 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 375 through 380
    Processing helix  chain 'C' and resid 395 through 406
    Processing helix  chain 'C' and resid 421 through 432
    Processing helix  chain 'C' and resid 448 through 456
    Processing helix  chain 'C' and resid 548 through 553
      removed outlier: 3.603A  pdb=" N   GLY C 553 " --> pdb=" O   LEU C 549 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 583 through 590
      removed outlier: 3.505A  pdb=" N   ASN C 589 " --> pdb=" O   THR C 586 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 616 through 626
      removed outlier: 3.904A  pdb=" N   TRP C 620 " --> pdb=" O   ASP C 616 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 652 through 661
      removed outlier: 3.626A  pdb=" N   GLU C 661 " --> pdb=" O   GLY C 657 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 675 through 680
    Processing helix  chain 'C' and resid 681 through 685
    Processing helix  chain 'C' and resid 710 through 722
    Processing sheet with id=AA1, first strand: chain 'B' and resid 7 through 9
    Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 14
      removed outlier: 6.567A  pdb=" N   CYS A  89 " --> pdb=" O   LYS A 114 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   VAL A 116 " --> pdb=" O   CYS A  89 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   TYR A  91 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
      removed outlier: 7.749A  pdb=" N   ILE A 118 " --> pdb=" O   TYR A  91 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   GLY A  93 " --> pdb=" O   ILE A 118 " (cutoff:3.500A)
      removed outlier: 8.766A  pdb=" N   HIS A 210 " --> pdb=" O   HIS A 113 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   LEU A 115 " --> pdb=" O   HIS A 210 " (cutoff:3.500A)
      removed outlier: 7.539A  pdb=" N   ILE A 212 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   MET A 117 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   SER A 214 " --> pdb=" O   MET A 117 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 78 through 80
      removed outlier: 6.777A  pdb=" N   LEU C 161 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 5.678A  pdb=" N   LEU C 194 " --> pdb=" O   LEU C 161 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   LEU C 163 " --> pdb=" O   LEU C 194 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   SER C 196 " --> pdb=" O   LEU C 163 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER C 253 " --> pdb=" O   LEU C 223 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   PHE C 250 " --> pdb=" O   HIS C 283 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   ALA C 285 " --> pdb=" O   PHE C 250 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ALA C 252 " --> pdb=" O   ALA C 285 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   CYS C 335 " --> pdb=" O   ASP C 286 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   PHE C 363 " --> pdb=" O   LEU C 334 " (cutoff:3.500A)
      removed outlier: 10.700A  pdb=" N   ASN C 336 " --> pdb=" O   PHE C 363 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASP C 469 " --> pdb=" O   ILE C 441 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   LEU C 466 " --> pdb=" O   SER C 537 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   TRP C 539 " --> pdb=" O   LEU C 466 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   ILE C 468 " --> pdb=" O   TRP C 539 " (cutoff:3.500A)
      removed outlier: 8.976A  pdb=" N   PHE C 541 " --> pdb=" O   ILE C 468 " (cutoff:3.500A)
      removed outlier: 4.765A  pdb=" N   GLY C 601 " --> pdb=" O   VAL C 567 " (cutoff:3.500A)
      removed outlier: 7.885A  pdb=" N   GLY C 569 " --> pdb=" O   GLY C 601 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ILE C 603 " --> pdb=" O   GLY C 569 " (cutoff:3.500A)

    330 hydrogen bonds defined for protein.
    912 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: 1.08

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1377
        1.31 -     1.43: 2090
        1.43 -     1.56: 4766
        1.56 -     1.69: 0
        1.69 -     1.81: 84
  Bond restraints: 8317
  Sorted by residual:
  bond pdb=" C14 GR2 A 301 "
       pdb=" C15 GR2 A 301 "
    ideal  model  delta    sigma   weight residual
    1.327  1.438 -0.111 2.00e-02 2.50e+03 3.08e+01
  bond pdb=" C16 GR2 A 301 "
       pdb=" O5  GR2 A 301 "
    ideal  model  delta    sigma   weight residual
    1.350  1.416 -0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" C13 GR2 A 301 "
       pdb=" O5  GR2 A 301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.476 -0.063 2.00e-02 2.50e+03 9.86e+00
  bond pdb=" C15 GR2 A 301 "
       pdb=" C17 GR2 A 301 "
    ideal  model  delta    sigma   weight residual
    1.482  1.523 -0.041 2.00e-02 2.50e+03 4.16e+00
  bond pdb=" C   LEU B  44 "
       pdb=" N   PRO B  45 "
    ideal  model  delta    sigma   weight residual
    1.332  1.342 -0.010 8.20e-03 1.49e+04 1.43e+00
  ... (remaining 8312 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.39: 10932
        1.39 -     2.79: 270
        2.79 -     4.18: 64
        4.18 -     5.58: 14
        5.58 -     6.97: 2
  Bond angle restraints: 11282
  Sorted by residual:
  angle pdb=" N   VAL B  63 "
        pdb=" CA  VAL B  63 "
        pdb=" C   VAL B  63 "
      ideal   model   delta    sigma   weight residual
     113.71  109.07    4.64 9.50e-01 1.11e+00 2.39e+01
  angle pdb=" N   THR B 120 "
        pdb=" CA  THR B 120 "
        pdb=" C   THR B 120 "
      ideal   model   delta    sigma   weight residual
     113.18  106.83    6.35 1.33e+00 5.65e-01 2.28e+01
  angle pdb=" N   VAL B 121 "
        pdb=" CA  VAL B 121 "
        pdb=" C   VAL B 121 "
      ideal   model   delta    sigma   weight residual
     112.04  107.53    4.51 1.40e+00 5.10e-01 1.04e+01
  angle pdb=" N   GLN B 119 "
        pdb=" CA  GLN B 119 "
        pdb=" C   GLN B 119 "
      ideal   model   delta    sigma   weight residual
     113.20  108.99    4.21 1.36e+00 5.41e-01 9.56e+00
  angle pdb=" CA  THR B 120 "
        pdb=" C   THR B 120 "
        pdb=" N   VAL B 121 "
      ideal   model   delta    sigma   weight residual
     118.22  115.51    2.71 1.03e+00 9.43e-01 6.94e+00
  ... (remaining 11277 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 4702
       17.56 -    35.11: 265
       35.11 -    52.67: 56
       52.67 -    70.23: 19
       70.23 -    87.78: 10
  Dihedral angle restraints: 5052
    sinusoidal: 2027
      harmonic: 3025
  Sorted by residual:
  dihedral pdb=" CA  VAL B  42 "
           pdb=" C   VAL B  42 "
           pdb=" N   PRO B  43 "
           pdb=" CA  PRO B  43 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.38  -20.62     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  GLN C 642 "
           pdb=" C   GLN C 642 "
           pdb=" N   ASP C 643 "
           pdb=" CA  ASP C 643 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.07   17.93     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CB  GLU A 148 "
           pdb=" CG  GLU A 148 "
           pdb=" CD  GLU A 148 "
           pdb=" OE1 GLU A 148 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.78  -87.78     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 5049 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 716
       0.031 -    0.061: 380
       0.061 -    0.092: 135
       0.092 -    0.122: 55
       0.122 -    0.152: 9
  Chirality restraints: 1295
  Sorted by residual:
  chirality pdb=" CA  THR C 547 "
            pdb=" N   THR C 547 "
            pdb=" C   THR C 547 "
            pdb=" CB  THR C 547 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 5.81e-01
  chirality pdb=" CA  PRO A 183 "
            pdb=" N   PRO A 183 "
            pdb=" C   PRO A 183 "
            pdb=" CB  PRO A 183 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.14 2.00e-01 2.50e+01 5.20e-01
  chirality pdb=" CA  ILE C 603 "
            pdb=" N   ILE C 603 "
            pdb=" C   ILE C 603 "
            pdb=" CB  ILE C 603 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  ... (remaining 1292 not shown)

  Planarity restraints: 1450
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 182 "    0.031 5.00e-02 4.00e+02   4.62e-02 3.42e+00
        pdb=" N   PRO A 183 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A 183 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 183 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  44 "    0.028 5.00e-02 4.00e+02   4.32e-02 2.98e+00
        pdb=" N   PRO B  45 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B  45 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  45 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 698 "   -0.027 5.00e-02 4.00e+02   4.06e-02 2.63e+00
        pdb=" N   PRO C 699 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO C 699 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 699 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 1447 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 156
        2.69 -     3.24: 7959
        3.24 -     3.79: 12952
        3.79 -     4.35: 18129
        4.35 -     4.90: 29184
  Nonbonded interactions: 68380
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  67 "
            pdb=" OD2 ASP A  76 "
     model   vdw
     2.137 3.040
  nonbonded pdb=" OD2 ASP C 300 "
            pdb=" NZ  LYS C 418 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" OD1 ASP C 333 "
            pdb=" NH2 ARG C 389 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OG1 THR C 673 "
            pdb=" OE2 GLU C 708 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   LEU B 113 "
            pdb=" OG1 THR B 117 "
     model   vdw
     2.273 3.040
  ... (remaining 68375 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 individual isotropic
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:             3.310
  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:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.780
  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:6.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
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   0.111   8318  Z= 0.217
  Angle     :  0.583   6.970  11282  Z= 0.320
  Chirality :  0.044   0.152   1295
  Planarity :  0.004   0.046   1450
  Dihedral  : 12.962  87.785   3090
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.70 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  :  7.94 %
    Favored  : 90.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.12 (0.27), residues: 1028
  helix:  0.11 (0.26), residues: 434
  sheet: -0.05 (0.42), residues: 174
  loop : -0.07 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 426 
 TYR   0.009   0.002   TYR C 590 
 PHE   0.014   0.002   PHE C 582 
 TRP   0.007   0.001   TRP C 620 
 HIS   0.005   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 8317)
  covalent geometry    : angle       0.58346 (11282)
  hydrogen bonds       : bond        0.16381 (  330)
  hydrogen bonds       : angle       6.46020 (  912)
  Misc. bond           : bond        0.00094 (    1)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.372 
Fit side-chains
REVERT: B    8 LEU cc_start: 0.3348 (OUTLIER) cc_final: 0.3095 (mm)
REVERT: B  124 MET cc_start: 0.8452 (mtp) cc_final: 0.8127 (mtp)
REVERT: A   15 SER cc_start: 0.8273 (p) cc_final: 0.7960 (m)
REVERT: A   45 LYS cc_start: 0.8299 (ttmt) cc_final: 0.8023 (ttmm)
REVERT: A  153 LEU cc_start: 0.8611 (tp) cc_final: 0.8294 (tm)
REVERT: A  201 TYR cc_start: 0.8242 (m-80) cc_final: 0.8028 (m-10)
REVERT: C  143 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8572 (tpt90)
REVERT: C  248 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7733 (ttp-110)
REVERT: C  354 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8377 (mppt)
REVERT: C  413 GLU cc_start: 0.8322 (tt0) cc_final: 0.7911 (mt-10)
REVERT: C  418 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8682 (mttp)
REVERT: C  433 ARG cc_start: 0.8310 (ptp90) cc_final: 0.7746 (ptm-80)
REVERT: C  457 GLU cc_start: 0.8652 (tt0) cc_final: 0.8173 (mt-10)
REVERT: C  462 ARG cc_start: 0.8106 (mtt90) cc_final: 0.7584 (mtm180)
REVERT: C  528 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7476 (mmtp)
REVERT: C  581 GLU cc_start: 0.8280 (pt0) cc_final: 0.7912 (tt0)
REVERT: C  644 ARG cc_start: 0.8234 (ttm-80) cc_final: 0.7942 (mtm110)
REVERT: C  723 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7720 (mtm110)
  outliers start: 18
  outliers final: 6
  residues processed: 134
  average time/residue: 0.6539
  time to fit residues: 92.4832
Evaluate side-chains
  121 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain C residue  143 ARG
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain C residue  609 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0270
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0570
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
B 112 ASN
B 119 GLN
B 141 ASN
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 GLN
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.114523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.084445 restraints weight = 11747.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 2.04
r_work: 0.2791 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2661 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.0864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8318  Z= 0.119
  Angle     :  0.518   6.473  11282  Z= 0.271
  Chirality :  0.042   0.147   1295
  Planarity :  0.004   0.044   1450
  Dihedral  :  5.077  57.991   1143
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 10.36 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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:  0.06 (0.28), residues: 1028
  helix:  0.37 (0.26), residues: 442
  sheet: -0.05 (0.44), residues: 165
  loop : -0.08 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 710 
 TYR   0.013   0.001   TYR A  44 
 PHE   0.010   0.001   PHE C 297 
 TRP   0.007   0.001   TRP C 639 
 HIS   0.003   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8317)
  covalent geometry    : angle       0.51827 (11282)
  hydrogen bonds       : bond        0.03873 (  330)
  hydrogen bonds       : angle       4.98159 (  912)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 123
  time to evaluate  : 0.273 
Fit side-chains
REVERT: B    8 LEU cc_start: 0.3546 (OUTLIER) cc_final: 0.3282 (mm)
REVERT: B   97 THR cc_start: 0.8031 (OUTLIER) cc_final: 0.7748 (t)
REVERT: B  124 MET cc_start: 0.8507 (mtp) cc_final: 0.8135 (mtp)
REVERT: A   15 SER cc_start: 0.8229 (p) cc_final: 0.7927 (m)
REVERT: A   45 LYS cc_start: 0.8422 (ttmt) cc_final: 0.8125 (ttmm)
REVERT: A  153 LEU cc_start: 0.8649 (tp) cc_final: 0.8332 (tm)
REVERT: A  201 TYR cc_start: 0.8173 (m-80) cc_final: 0.7929 (m-80)
REVERT: C  129 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7025 (tpp-160)
REVERT: C  248 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7904 (ttp-110)
REVERT: C  333 ASP cc_start: 0.8472 (t0) cc_final: 0.8212 (t70)
REVERT: C  339 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6662 (mtp85)
REVERT: C  354 LYS cc_start: 0.8649 (mmmm) cc_final: 0.8366 (mppt)
REVERT: C  413 GLU cc_start: 0.8326 (tt0) cc_final: 0.7962 (mt-10)
REVERT: C  433 ARG cc_start: 0.8215 (ptp90) cc_final: 0.7746 (ptm-80)
REVERT: C  457 GLU cc_start: 0.8660 (tt0) cc_final: 0.8159 (mt-10)
REVERT: C  528 LYS cc_start: 0.7631 (mtmt) cc_final: 0.7392 (mmtp)
REVERT: C  581 GLU cc_start: 0.8249 (pt0) cc_final: 0.7818 (tt0)
REVERT: C  644 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.7976 (mtm110)
REVERT: C  723 ARG cc_start: 0.7971 (ttp-170) cc_final: 0.7577 (mtm-85)
  outliers start: 20
  outliers final: 8
  residues processed: 139
  average time/residue: 0.5523
  time to fit residues: 81.4022
Evaluate side-chains
  124 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  129 ARG
Chi-restraints excluded: chain C residue  233 LYS
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain C residue  339 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  384 GLU
Chi-restraints excluded: chain C residue  434 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   chunk 95 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0980
   chunk 64 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
B 119 GLN
B 141 ASN
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 GLN
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.115490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.085692 restraints weight = 11667.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.03
r_work: 0.2814 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2684 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8637
moved from start:          0.1161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8318  Z= 0.099
  Angle     :  0.493   7.258  11282  Z= 0.256
  Chirality :  0.042   0.147   1295
  Planarity :  0.004   0.048   1450
  Dihedral  :  4.465  42.689   1136
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 11.03 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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:  0.26 (0.28), residues: 1028
  helix:  0.67 (0.27), residues: 442
  sheet: -0.17 (0.43), residues: 162
  loop : -0.04 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 229 
 TYR   0.010   0.001   TYR A  44 
 PHE   0.010   0.001   PHE C 297 
 TRP   0.008   0.001   TRP C 639 
 HIS   0.004   0.001   HIS A 210 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 8317)
  covalent geometry    : angle       0.49293 (11282)
  hydrogen bonds       : bond        0.03257 (  330)
  hydrogen bonds       : angle       4.60765 (  912)
  Misc. bond           : bond        0.00015 (    1)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.260 
Fit side-chains
REVERT: B    8 LEU cc_start: 0.3698 (OUTLIER) cc_final: 0.3418 (mm)
REVERT: B  124 MET cc_start: 0.8463 (mtp) cc_final: 0.8083 (mtp)
REVERT: B  126 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8023 (tppt)
REVERT: A   15 SER cc_start: 0.8224 (p) cc_final: 0.7918 (m)
REVERT: A   45 LYS cc_start: 0.8441 (ttmt) cc_final: 0.8154 (ttmm)
REVERT: A   63 ASP cc_start: 0.7869 (t0) cc_final: 0.7589 (t0)
REVERT: A  153 LEU cc_start: 0.8645 (tp) cc_final: 0.8344 (tm)
REVERT: C  129 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7095 (tpp-160)
REVERT: C  248 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7868 (ttp-110)
REVERT: C  333 ASP cc_start: 0.8386 (t0) cc_final: 0.8109 (t70)
REVERT: C  339 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.6568 (mtp85)
REVERT: C  354 LYS cc_start: 0.8613 (mmmm) cc_final: 0.8349 (mppt)
REVERT: C  413 GLU cc_start: 0.8310 (tt0) cc_final: 0.7945 (mt-10)
REVERT: C  433 ARG cc_start: 0.8198 (ptp90) cc_final: 0.7722 (ptm-80)
REVERT: C  457 GLU cc_start: 0.8668 (tt0) cc_final: 0.8177 (mt-10)
REVERT: C  528 LYS cc_start: 0.7631 (mtmt) cc_final: 0.7383 (mmtp)
REVERT: C  581 GLU cc_start: 0.8267 (pt0) cc_final: 0.7886 (tt0)
REVERT: C  644 ARG cc_start: 0.8230 (ttm-80) cc_final: 0.7962 (mtm110)
  outliers start: 24
  outliers final: 10
  residues processed: 139
  average time/residue: 0.4868
  time to fit residues: 72.0258
Evaluate side-chains
  122 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    8 LEU
Chi-restraints excluded: chain B residue   31 HIS
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain C residue   85 ILE
Chi-restraints excluded: chain C residue  129 ARG
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain C residue  339 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  384 GLU
Chi-restraints excluded: chain C residue  434 LYS
Chi-restraints excluded: chain C residue  609 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 92 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
B 119 GLN
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 GLN
C 336 ASN
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.111449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.080737 restraints weight = 11960.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 2.13
r_work: 0.2733 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2603 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   8318  Z= 0.280
  Angle     :  0.652   7.837  11282  Z= 0.332
  Chirality :  0.048   0.220   1295
  Planarity :  0.005   0.048   1450
  Dihedral  :  4.909  36.875   1131
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 12.35 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.22 (0.27), residues: 1028
  helix:  0.20 (0.25), residues: 447
  sheet: -0.30 (0.44), residues: 154
  loop : -0.27 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 134 
 TYR   0.012   0.002   TYR C 624 
 PHE   0.015   0.002   PHE C 297 
 TRP   0.008   0.001   TRP C 620 
 HIS   0.006   0.002   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00664 ( 8317)
  covalent geometry    : angle       0.65155 (11282)
  hydrogen bonds       : bond        0.04527 (  330)
  hydrogen bonds       : angle       5.07583 (  912)
  Misc. bond           : bond        0.00123 (    1)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.376 
Fit side-chains
REVERT: B  124 MET cc_start: 0.8471 (mtp) cc_final: 0.8046 (mtp)
REVERT: B  126 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8232 (tppp)
REVERT: B  135 THR cc_start: 0.8730 (m) cc_final: 0.8303 (t)
REVERT: A   15 SER cc_start: 0.8276 (p) cc_final: 0.7953 (m)
REVERT: A   45 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8074 (ttmm)
REVERT: C   45 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7518 (mp)
REVERT: C  129 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6975 (tpp-160)
REVERT: C  143 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8576 (tpt90)
REVERT: C  248 ARG cc_start: 0.8135 (ttp80) cc_final: 0.7819 (ttp-110)
REVERT: C  333 ASP cc_start: 0.8482 (t0) cc_final: 0.8187 (t70)
REVERT: C  339 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.6708 (mtp85)
REVERT: C  354 LYS cc_start: 0.8747 (mmmm) cc_final: 0.8468 (mppt)
REVERT: C  397 MET cc_start: 0.8177 (mpp) cc_final: 0.7717 (mmm)
REVERT: C  413 GLU cc_start: 0.8356 (tt0) cc_final: 0.7998 (mt-10)
REVERT: C  433 ARG cc_start: 0.8347 (ptp90) cc_final: 0.7787 (ptm-80)
REVERT: C  457 GLU cc_start: 0.8680 (tt0) cc_final: 0.8227 (mt-10)
REVERT: C  462 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7518 (mtm180)
REVERT: C  528 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7520 (mmtp)
REVERT: C  581 GLU cc_start: 0.8323 (pt0) cc_final: 0.7932 (tt0)
REVERT: C  644 ARG cc_start: 0.8252 (ttm-80) cc_final: 0.7961 (mtm110)
  outliers start: 29
  outliers final: 11
  residues processed: 133
  average time/residue: 0.5552
  time to fit residues: 78.1324
Evaluate side-chains
  120 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  129 ARG
Chi-restraints excluded: chain C residue  143 ARG
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain C residue  339 ARG
Chi-restraints excluded: chain C residue  384 GLU
Chi-restraints excluded: chain C residue  434 LYS
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  609 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 42 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9980
   chunk 73 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   chunk 83 optimal weight:    0.0370
   chunk 14 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
B 119 GLN
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 GLN
A 216 ASN
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.114072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.084022 restraints weight = 11824.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 2.05
r_work: 0.2806 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2674 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8318  Z= 0.106
  Angle     :  0.525   7.924  11282  Z= 0.266
  Chirality :  0.042   0.151   1295
  Planarity :  0.004   0.051   1450
  Dihedral  :  4.292  17.680   1129
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 14.66 %
    Favored  : 83.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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:  0.02 (0.27), residues: 1028
  helix:  0.51 (0.26), residues: 448
  sheet: -0.29 (0.43), residues: 160
  loop : -0.22 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 229 
 TYR   0.006   0.001   TYR A  73 
 PHE   0.009   0.001   PHE C 297 
 TRP   0.008   0.001   TRP C 639 
 HIS   0.003   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8317)
  covalent geometry    : angle       0.52538 (11282)
  hydrogen bonds       : bond        0.03185 (  330)
  hydrogen bonds       : angle       4.60293 (  912)
  Misc. bond           : bond        0.00013 (    1)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.387 
Fit side-chains
REVERT: B   92 LYS cc_start: 0.7609 (mptp) cc_final: 0.7385 (mptt)
REVERT: B  124 MET cc_start: 0.8365 (mtp) cc_final: 0.8049 (mtp)
REVERT: B  126 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8048 (tppt)
REVERT: A   15 SER cc_start: 0.8303 (p) cc_final: 0.7984 (m)
REVERT: A   45 LYS cc_start: 0.8417 (ttmt) cc_final: 0.8103 (ttmm)
REVERT: A   63 ASP cc_start: 0.7921 (t0) cc_final: 0.7632 (t0)
REVERT: C   45 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7284 (mp)
REVERT: C  129 ARG cc_start: 0.7917 (OUTLIER) cc_final: 0.6990 (tpp-160)
REVERT: C  248 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7894 (ttp-110)
REVERT: C  333 ASP cc_start: 0.8441 (t0) cc_final: 0.8151 (t70)
REVERT: C  339 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6623 (mtp85)
REVERT: C  354 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8387 (mppt)
REVERT: C  397 MET cc_start: 0.8236 (mpp) cc_final: 0.7783 (mmm)
REVERT: C  413 GLU cc_start: 0.8350 (tt0) cc_final: 0.7955 (mt-10)
REVERT: C  433 ARG cc_start: 0.8237 (ptp90) cc_final: 0.7702 (ptm-80)
REVERT: C  457 GLU cc_start: 0.8671 (tt0) cc_final: 0.8203 (mt-10)
REVERT: C  462 ARG cc_start: 0.8079 (mtt90) cc_final: 0.7520 (mtm180)
REVERT: C  528 LYS cc_start: 0.7702 (mtmt) cc_final: 0.7456 (mmtp)
REVERT: C  581 GLU cc_start: 0.8218 (pt0) cc_final: 0.7883 (tt0)
REVERT: C  644 ARG cc_start: 0.8211 (ttm-80) cc_final: 0.7934 (mtm110)
  outliers start: 16
  outliers final: 9
  residues processed: 121
  average time/residue: 0.5787
  time to fit residues: 74.0538
Evaluate side-chains
  117 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 ILE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  129 ARG
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain C residue  339 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  384 GLU
Chi-restraints excluded: chain C residue  434 LYS
Chi-restraints excluded: chain C residue  609 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 76 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
B 119 GLN
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 GLN
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 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 = 0.3338 r_free = 0.3338 target = 0.111731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.081635 restraints weight = 11748.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 2.03
r_work: 0.2761 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2631 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8685
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   8318  Z= 0.241
  Angle     :  0.626  11.899  11282  Z= 0.316
  Chirality :  0.046   0.174   1295
  Planarity :  0.005   0.053   1450
  Dihedral  :  4.717  19.299   1129
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.45 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.24 (0.27), residues: 1028
  helix:  0.30 (0.26), residues: 447
  sheet: -0.34 (0.42), residues: 165
  loop : -0.40 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 649 
 TYR   0.011   0.002   TYR C 415 
 PHE   0.015   0.002   PHE C 297 
 TRP   0.007   0.001   TRP C 620 
 HIS   0.005   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 ( 8317)
  covalent geometry    : angle       0.62627 (11282)
  hydrogen bonds       : bond        0.04126 (  330)
  hydrogen bonds       : angle       4.90671 (  912)
  Misc. bond           : bond        0.00068 (    1)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.231 
Fit side-chains
REVERT: B  124 MET cc_start: 0.8445 (mtp) cc_final: 0.8074 (mtp)
REVERT: B  126 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8213 (tppp)
REVERT: A   15 SER cc_start: 0.8289 (p) cc_final: 0.7983 (m)
REVERT: A   43 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8455 (p0)
REVERT: A   45 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8105 (ttmm)
REVERT: C   40 LEU cc_start: 0.7531 (tp) cc_final: 0.7246 (tp)
REVERT: C   45 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7314 (mp)
REVERT: C  129 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.6963 (tpp-160)
REVERT: C  143 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8545 (tpt90)
REVERT: C  248 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7837 (ttp-110)
REVERT: C  333 ASP cc_start: 0.8447 (t0) cc_final: 0.8168 (t70)
REVERT: C  339 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6603 (mtp85)
REVERT: C  354 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8458 (mppt)
REVERT: C  413 GLU cc_start: 0.8359 (tt0) cc_final: 0.8003 (mt-10)
REVERT: C  433 ARG cc_start: 0.8360 (ptp90) cc_final: 0.7795 (ptm-80)
REVERT: C  457 GLU cc_start: 0.8669 (tt0) cc_final: 0.8224 (mt-10)
REVERT: C  462 ARG cc_start: 0.8107 (mtt90) cc_final: 0.7529 (mtm180)
REVERT: C  528 LYS cc_start: 0.7800 (mtmt) cc_final: 0.7537 (mmtp)
REVERT: C  581 GLU cc_start: 0.8269 (pt0) cc_final: 0.7908 (tt0)
REVERT: C  644 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7924 (mtm110)
  outliers start: 26
  outliers final: 15
  residues processed: 125
  average time/residue: 0.5333
  time to fit residues: 70.2374
Evaluate side-chains
  124 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   29 ILE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  129 ARG
Chi-restraints excluded: chain C residue  143 ARG
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain C residue  339 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  384 GLU
Chi-restraints excluded: chain C residue  434 LYS
Chi-restraints excluded: chain C residue  609 THR
Chi-restraints excluded: chain C residue  691 VAL
Chi-restraints excluded: chain C residue  723 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 94 optimal weight:    0.3980
   chunk 93 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 89 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 119 GLN
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 GLN
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 722 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.113464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.083219 restraints weight = 11991.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 2.07
r_work: 0.2793 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8318  Z= 0.133
  Angle     :  0.547  10.274  11282  Z= 0.277
  Chirality :  0.043   0.149   1295
  Planarity :  0.004   0.055   1450
  Dihedral  :  4.387  17.831   1129
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 14.66 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.05 (0.27), residues: 1028
  helix:  0.51 (0.26), residues: 447
  sheet: -0.36 (0.43), residues: 160
  loop : -0.32 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 229 
 TYR   0.007   0.001   TYR C 624 
 PHE   0.009   0.001   PHE C 582 
 TRP   0.008   0.001   TRP C 639 
 HIS   0.004   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 8317)
  covalent geometry    : angle       0.54677 (11282)
  hydrogen bonds       : bond        0.03295 (  330)
  hydrogen bonds       : angle       4.62543 (  912)
  Misc. bond           : bond        0.00043 (    1)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.256 
Fit side-chains
REVERT: B  124 MET cc_start: 0.8366 (mtp) cc_final: 0.8082 (mtp)
REVERT: B  126 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8043 (tppt)
REVERT: A   15 SER cc_start: 0.8287 (p) cc_final: 0.7972 (m)
REVERT: A   43 ASP cc_start: 0.8684 (OUTLIER) cc_final: 0.8481 (p0)
REVERT: A   45 LYS cc_start: 0.8409 (ttmt) cc_final: 0.8090 (ttmm)
REVERT: A   63 ASP cc_start: 0.8035 (t0) cc_final: 0.7756 (t70)
REVERT: C   45 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7287 (mp)
REVERT: C  129 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7002 (tpp-160)
REVERT: C  248 ARG cc_start: 0.8182 (ttp80) cc_final: 0.7896 (ttp-110)
REVERT: C  333 ASP cc_start: 0.8422 (t0) cc_final: 0.8138 (t70)
REVERT: C  339 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6566 (mtp85)
REVERT: C  354 LYS cc_start: 0.8666 (mmmm) cc_final: 0.8391 (mppt)
REVERT: C  397 MET cc_start: 0.8231 (mpp) cc_final: 0.7769 (mmm)
REVERT: C  413 GLU cc_start: 0.8345 (tt0) cc_final: 0.7989 (mt-10)
REVERT: C  433 ARG cc_start: 0.8315 (ptp90) cc_final: 0.7727 (ptm-80)
REVERT: C  457 GLU cc_start: 0.8675 (tt0) cc_final: 0.8213 (mt-10)
REVERT: C  462 ARG cc_start: 0.8065 (mtt90) cc_final: 0.7496 (mtm180)
REVERT: C  528 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7458 (mmtp)
REVERT: C  581 GLU cc_start: 0.8225 (pt0) cc_final: 0.7889 (tt0)
REVERT: C  644 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7939 (mtm110)
  outliers start: 20
  outliers final: 11
  residues processed: 121
  average time/residue: 0.4984
  time to fit residues: 63.8753
Evaluate side-chains
  117 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 ILE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  129 ARG
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain C residue  339 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  384 GLU
Chi-restraints excluded: chain C residue  434 LYS
Chi-restraints excluded: chain C residue  609 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 6 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B  31 HIS
B 119 GLN
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 GLN
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.111939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.081791 restraints weight = 11906.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 2.05
r_work: 0.2768 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2637 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.1434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8318  Z= 0.225
  Angle     :  0.639  18.751  11282  Z= 0.317
  Chirality :  0.046   0.170   1295
  Planarity :  0.005   0.052   1450
  Dihedral  :  4.701  19.153   1129
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 14.33 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.25 (0.27), residues: 1028
  helix:  0.30 (0.26), residues: 448
  sheet: -0.37 (0.42), residues: 165
  loop : -0.41 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 649 
 TYR   0.010   0.002   TYR C 415 
 PHE   0.013   0.002   PHE C 297 
 TRP   0.007   0.001   TRP C 620 
 HIS   0.005   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00532 ( 8317)
  covalent geometry    : angle       0.63859 (11282)
  hydrogen bonds       : bond        0.04012 (  330)
  hydrogen bonds       : angle       4.85504 (  912)
  Misc. bond           : bond        0.00083 (    1)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.197 
Fit side-chains
REVERT: B  124 MET cc_start: 0.8453 (mtp) cc_final: 0.8125 (mtp)
REVERT: B  126 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8236 (tppp)
REVERT: A   15 SER cc_start: 0.8305 (p) cc_final: 0.8004 (m)
REVERT: A   45 LYS cc_start: 0.8405 (ttmt) cc_final: 0.8127 (ttmm)
REVERT: C   45 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7395 (mp)
REVERT: C  129 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.6966 (tpp-160)
REVERT: C  143 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8542 (tpt90)
REVERT: C  248 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7851 (ttp-110)
REVERT: C  333 ASP cc_start: 0.8428 (t0) cc_final: 0.8140 (t70)
REVERT: C  339 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.6654 (mtp85)
REVERT: C  354 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8434 (mppt)
REVERT: C  397 MET cc_start: 0.8214 (mpp) cc_final: 0.7753 (mmm)
REVERT: C  413 GLU cc_start: 0.8364 (tt0) cc_final: 0.8020 (mt-10)
REVERT: C  433 ARG cc_start: 0.8327 (ptp90) cc_final: 0.7776 (ptm-80)
REVERT: C  457 GLU cc_start: 0.8687 (tt0) cc_final: 0.8238 (mt-10)
REVERT: C  462 ARG cc_start: 0.8105 (mtt90) cc_final: 0.7547 (mtm180)
REVERT: C  528 LYS cc_start: 0.7817 (mtmt) cc_final: 0.7569 (mmtp)
REVERT: C  581 GLU cc_start: 0.8259 (pt0) cc_final: 0.7912 (tt0)
REVERT: C  644 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7920 (mtm110)
  outliers start: 26
  outliers final: 14
  residues processed: 126
  average time/residue: 0.5079
  time to fit residues: 67.6782
Evaluate side-chains
  124 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   29 ILE
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  129 ARG
Chi-restraints excluded: chain C residue  143 ARG
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain C residue  339 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  384 GLU
Chi-restraints excluded: chain C residue  434 LYS
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  609 THR
Chi-restraints excluded: chain C residue  723 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 64 optimal weight:    3.9990
   chunk 90 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 101 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
B 119 GLN
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 GLN
** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 362 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 = 0.3357 r_free = 0.3357 target = 0.113183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.083145 restraints weight = 11759.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.01
r_work: 0.2784 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8318  Z= 0.153
  Angle     :  0.599  19.242  11282  Z= 0.295
  Chirality :  0.043   0.158   1295
  Planarity :  0.004   0.053   1450
  Dihedral  :  4.544  22.350   1129
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.11 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 14.44 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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: -0.14 (0.27), residues: 1028
  helix:  0.43 (0.26), residues: 446
  sheet: -0.41 (0.42), residues: 166
  loop : -0.35 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 134 
 TYR   0.009   0.001   TYR A  44 
 PHE   0.011   0.001   PHE C 297 
 TRP   0.007   0.001   TRP C 639 
 HIS   0.013   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 8317)
  covalent geometry    : angle       0.59901 (11282)
  hydrogen bonds       : bond        0.03538 (  330)
  hydrogen bonds       : angle       4.69731 (  912)
  Misc. bond           : bond        0.00041 (    1)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.241 
Fit side-chains
REVERT: B  124 MET cc_start: 0.8340 (mtp) cc_final: 0.8025 (mtp)
REVERT: B  126 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8240 (tppp)
REVERT: A   15 SER cc_start: 0.8292 (p) cc_final: 0.7994 (m)
REVERT: A   45 LYS cc_start: 0.8428 (ttmt) cc_final: 0.8122 (ttmm)
REVERT: A   63 ASP cc_start: 0.8050 (t0) cc_final: 0.7775 (t70)
REVERT: A  147 ASP cc_start: 0.8324 (m-30) cc_final: 0.8099 (m-30)
REVERT: C   45 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7388 (mp)
REVERT: C  129 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.6997 (tpp-160)
REVERT: C  143 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8509 (tpt90)
REVERT: C  248 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7877 (ttp-110)
REVERT: C  339 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6680 (mtp85)
REVERT: C  354 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8440 (mppt)
REVERT: C  397 MET cc_start: 0.8253 (mpp) cc_final: 0.7810 (mmm)
REVERT: C  413 GLU cc_start: 0.8342 (tt0) cc_final: 0.8011 (mt-10)
REVERT: C  433 ARG cc_start: 0.8301 (ptp90) cc_final: 0.7794 (ptm-80)
REVERT: C  457 GLU cc_start: 0.8656 (tt0) cc_final: 0.8219 (mt-10)
REVERT: C  462 ARG cc_start: 0.8090 (mtt90) cc_final: 0.7710 (mtm180)
REVERT: C  528 LYS cc_start: 0.7742 (mtmt) cc_final: 0.7497 (mmtp)
REVERT: C  581 GLU cc_start: 0.8218 (pt0) cc_final: 0.7901 (tt0)
REVERT: C  644 ARG cc_start: 0.8175 (ttm-80) cc_final: 0.7945 (mtm110)
  outliers start: 24
  outliers final: 18
  residues processed: 123
  average time/residue: 0.5502
  time to fit residues: 71.5147
Evaluate side-chains
  122 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   29 ILE
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  129 ARG
Chi-restraints excluded: chain C residue  143 ARG
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain C residue  339 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  384 GLU
Chi-restraints excluded: chain C residue  434 LYS
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  609 THR
Chi-restraints excluded: chain C residue  712 ASP
Chi-restraints excluded: chain C residue  723 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 56 optimal weight:    0.0270
   chunk 11 optimal weight:    0.0980
   chunk 12 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:    0.2980
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.3238

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 GLN
** C 362 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 = 0.3384 r_free = 0.3384 target = 0.115153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.085374 restraints weight = 11729.020|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.03
r_work: 0.2820 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2691 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8318  Z= 0.098
  Angle     :  0.558  20.107  11282  Z= 0.272
  Chirality :  0.042   0.150   1295
  Planarity :  0.004   0.052   1450
  Dihedral  :  4.217  25.597   1129
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.92 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.66 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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:  0.17 (0.27), residues: 1028
  helix:  0.78 (0.27), residues: 437
  sheet: -0.45 (0.42), residues: 167
  loop : -0.19 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 229 
 TYR   0.010   0.001   TYR A  44 
 PHE   0.008   0.001   PHE C 297 
 TRP   0.010   0.001   TRP C 639 
 HIS   0.006   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 8317)
  covalent geometry    : angle       0.55784 (11282)
  hydrogen bonds       : bond        0.02967 (  330)
  hydrogen bonds       : angle       4.41035 (  912)
  Misc. bond           : bond        0.00025 (    1)

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

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

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2056 Ramachandran restraints generated.
    1028 Oldfield, 0 Emsley, 1028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.205 
Fit side-chains
REVERT: B  126 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8054 (tppt)
REVERT: A   15 SER cc_start: 0.8260 (p) cc_final: 0.7956 (m)
REVERT: A   45 LYS cc_start: 0.8449 (ttmt) cc_final: 0.8155 (ttmm)
REVERT: A   63 ASP cc_start: 0.7937 (t0) cc_final: 0.7639 (t70)
REVERT: A  147 ASP cc_start: 0.8311 (m-30) cc_final: 0.8050 (m-30)
REVERT: C  129 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7510 (ttp80)
REVERT: C  144 ASP cc_start: 0.8305 (m-30) cc_final: 0.8044 (p0)
REVERT: C  248 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7929 (ttp-110)
REVERT: C  339 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.6615 (mtp85)
REVERT: C  354 LYS cc_start: 0.8620 (mmmm) cc_final: 0.8364 (mppt)
REVERT: C  397 MET cc_start: 0.8235 (mpp) cc_final: 0.7810 (mmm)
REVERT: C  413 GLU cc_start: 0.8321 (tt0) cc_final: 0.7991 (mt-10)
REVERT: C  433 ARG cc_start: 0.8230 (ptp90) cc_final: 0.7651 (ptm-80)
REVERT: C  457 GLU cc_start: 0.8689 (tt0) cc_final: 0.8228 (mt-10)
REVERT: C  462 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7490 (mtm180)
REVERT: C  528 LYS cc_start: 0.7724 (mtmt) cc_final: 0.7482 (mmtp)
REVERT: C  581 GLU cc_start: 0.8220 (pt0) cc_final: 0.7875 (tt0)
REVERT: C  644 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7936 (mtm110)
  outliers start: 22
  outliers final: 15
  residues processed: 124
  average time/residue: 0.4738
  time to fit residues: 62.3992
Evaluate side-chains
  120 residues out of total 907 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   42 VAL
Chi-restraints excluded: chain B residue   97 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  126 LYS
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain A residue   32 VAL
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain C residue  129 ARG
Chi-restraints excluded: chain C residue  261 ILE
Chi-restraints excluded: chain C residue  339 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  384 GLU
Chi-restraints excluded: chain C residue  434 LYS
Chi-restraints excluded: chain C residue  578 THR
Chi-restraints excluded: chain C residue  609 THR
Chi-restraints excluded: chain C residue  723 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 11 optimal weight:    0.5980
   chunk 102 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 56 optimal weight:    0.4980
   chunk 51 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0570
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 136 GLN
** C 362 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 = 0.3379 r_free = 0.3379 target = 0.114717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.084909 restraints weight = 11766.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 2.01
r_work: 0.2821 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2691 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8318  Z= 0.109
  Angle     :  0.576  19.572  11282  Z= 0.278
  Chirality :  0.042   0.154   1295
  Planarity :  0.004   0.053   1450
  Dihedral  :  4.198  23.722   1129
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.82 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.33 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.92 %
    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:  0.22 (0.28), residues: 1028
  helix:  0.81 (0.27), residues: 440
  sheet: -0.44 (0.43), residues: 161
  loop : -0.17 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 229 
 TYR   0.009   0.001   TYR A  44 
 PHE   0.009   0.001   PHE C 297 
 TRP   0.009   0.001   TRP C 639 
 HIS   0.008   0.001   HIS B  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8317)
  covalent geometry    : angle       0.57556 (11282)
  hydrogen bonds       : bond        0.03096 (  330)
  hydrogen bonds       : angle       4.38039 (  912)
  Misc. bond           : bond        0.00022 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2637.01 seconds
wall clock time: 45 minutes 34.90 seconds (2734.90 seconds total)