Starting phenix.real_space_refine
on Sun Apr  5 01:30:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xn4_33310/04_2026/7xn4_33310.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xn4_33310/04_2026/7xn4_33310.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xn4_33310/04_2026/7xn4_33310.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xn4_33310/04_2026/7xn4_33310.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xn4_33310/04_2026/7xn4_33310.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xn4_33310/04_2026/7xn4_33310.cif"
  }
  resolution = 3.35
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      38      5.16       5
     C    4335      2.51       5
     N    1209      2.21       5
     O    1275      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6859
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1706
          Classifications: {'peptide': 210}
          Link IDs: {'PTRANS': 6, 'TRANS': 203}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 3256
          Classifications: {'peptide': 422}
          Link IDs: {'PTRANS': 13, 'TRANS': 408}
    Chain: "C"
      Number of atoms: 1387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1387
          Classifications: {'peptide': 169}
          Link IDs: {'PTRANS': 5, 'TRANS': 163}
          Chain breaks: 5
    Chain: "D"
      Number of atoms: 466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 466
          Classifications: {'peptide': 58}
          Link IDs: {'TRANS': 57}
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'NAD': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.57, per 1000 atoms: 0.23
  Number of scatterers: 6859
  At special positions: 0
  Unit cell: (110.302, 95.988, 74.096, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P       2     15.00
     O    1275      8.00
     N    1209      7.00
     C    4335      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 264.3 milliseconds
  

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1602

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      43.4% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing helix  chain 'A' and resid 67 through 82
      removed outlier: 3.598A  pdb=" N   ALA A  71 " --> pdb=" O   THR A  67 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU A  81 " --> pdb=" O   THR A  77 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   LYS A  82 " --> pdb=" O   PHE A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 105
      removed outlier: 3.528A  pdb=" N   ILE A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 4.267A  pdb=" N   VAL A  97 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   LYS A 105 " --> pdb=" O   ARG A 101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 142
      removed outlier: 3.576A  pdb=" N   THR A 140 " --> pdb=" O   LEU A 136 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   PHE A 142 " --> pdb=" O   LYS A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 227
      removed outlier: 4.298A  pdb=" N   GLN A 225 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 246
      removed outlier: 3.962A  pdb=" N   ARG A 238 " --> pdb=" O   HIS A 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 74
      removed outlier: 4.025A  pdb=" N   ILE B  55 " --> pdb=" O   ALA B  51 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   GLN B  66 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   SER B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR B  68 " --> pdb=" O   ALA B  64 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   MET B  71 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 81
    Processing helix  chain 'B' and resid 93 through 114
      removed outlier: 3.729A  pdb=" N   LEU B  99 " --> pdb=" O   ALA B  95 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASP B 100 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG B 105 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL B 110 " --> pdb=" O   ASN B 106 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LEU B 114 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 129
      removed outlier: 4.414A  pdb=" N   ARG B 127 " --> pdb=" O   GLY B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 160
      removed outlier: 3.925A  pdb=" N   GLU B 160 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 224
      removed outlier: 3.635A  pdb=" N   ARG B 222 " --> pdb=" O   PRO B 219 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   HIS B 223 " --> pdb=" O   ALA B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 249
    Processing helix  chain 'B' and resid 256 through 261
      removed outlier: 4.538A  pdb=" N   ARG B 260 " --> pdb=" O   ALA B 256 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   TRP B 261 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 256 through 261'
    Processing helix  chain 'B' and resid 278 through 293
      removed outlier: 3.894A  pdb=" N   VAL B 283 " --> pdb=" O   MET B 279 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ALA B 284 " --> pdb=" O   LYS B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 302
      removed outlier: 3.680A  pdb=" N   TYR B 302 " --> pdb=" O   ALA B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 322
      removed outlier: 3.521A  pdb=" N   SER B 320 " --> pdb=" O   ARG B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 348 through 353
    Processing helix  chain 'B' and resid 355 through 363
    Processing helix  chain 'B' and resid 365 through 378
      removed outlier: 3.533A  pdb=" N   ASP B 378 " --> pdb=" O   TRP B 374 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 392
      removed outlier: 3.524A  pdb=" N   GLY B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN B 391 " --> pdb=" O   HIS B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 401
      removed outlier: 3.865A  pdb=" N   ALA B 400 " --> pdb=" O   GLY B 397 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   SER B 401 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 397 through 401'
    Processing helix  chain 'B' and resid 409 through 415
      removed outlier: 3.620A  pdb=" N   SER B 415 " --> pdb=" O   ASN B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 420 through 429
      removed outlier: 3.561A  pdb=" N   LEU B 424 " --> pdb=" O   SER B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 455
      removed outlier: 3.677A  pdb=" N   ASN B 451 " --> pdb=" O   THR B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 457 through 468
      removed outlier: 3.648A  pdb=" N   ALA B 463 " --> pdb=" O   GLU B 459 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 81
      removed outlier: 3.703A  pdb=" N   LEU C  81 " --> pdb=" O   THR C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 96 through 102
      removed outlier: 4.354A  pdb=" N   MET C 100 " --> pdb=" O   ILE C  96 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 103 through 106
      removed outlier: 3.568A  pdb=" N   GLU C 106 " --> pdb=" O   VAL C 103 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 103 through 106'
    Processing helix  chain 'C' and resid 107 through 111
      removed outlier: 4.095A  pdb=" N   LYS C 110 " --> pdb=" O   ASP C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 136 through 141
      removed outlier: 3.509A  pdb=" N   ASN C 141 " --> pdb=" O   LYS C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 142 through 144
      No H-bonds generated for 'chain 'C' and resid 142 through 144'
    Processing helix  chain 'C' and resid 213 through 227
      removed outlier: 3.663A  pdb=" N   ALA C 227 " --> pdb=" O   LEU C 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 246
      removed outlier: 3.520A  pdb=" N   ALA C 244 " --> pdb=" O   ASN C 240 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 86 through 91
    Processing helix  chain 'D' and resid 104 through 112
      removed outlier: 3.747A  pdb=" N   ASN D 111 " --> pdb=" O   HIS D 107 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 117 through 127
      removed outlier: 4.066A  pdb=" N   GLU D 123 " --> pdb=" O   GLU D 119 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLU D 127 " --> pdb=" O   GLU D 123 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 142
      removed outlier: 4.040A  pdb=" N   GLU D 140 " --> pdb=" O   ASN D 137 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE D 141 " --> pdb=" O   TYR D 138 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL D 142 " --> pdb=" O   GLU D 139 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89
      removed outlier: 5.983A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   VAL A 117 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ILE A  48 " --> pdb=" O   VAL A 117 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   LEU A 119 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   ILE A  50 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   CYS A 116 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   GLN A 161 " --> pdb=" O   CYS A 116 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   LEU A 118 " --> pdb=" O   GLN A 161 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER C 267 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   TYR C 197 " --> pdb=" O   CYS C 264 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128
    Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 226
    Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152
    Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 88
      removed outlier: 6.739A  pdb=" N   CYS C  47 " --> pdb=" O   ARG C  86 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   LYS C  88 " --> pdb=" O   CYS C  47 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ILE C  49 " --> pdb=" O   LYS C  88 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   LEU C  46 " --> pdb=" O   VAL C 115 " (cutoff:3.500A)
      removed outlier: 7.592A  pdb=" N   VAL C 117 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   ILE C  48 " --> pdb=" O   VAL C 117 " (cutoff:3.500A)
      removed outlier: 7.161A  pdb=" N   LEU C 119 " --> pdb=" O   ILE C  48 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   ILE C  50 " --> pdb=" O   LEU C 119 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   GLN C 161 " --> pdb=" O   CYS C 116 " (cutoff:3.500A)
      removed outlier: 6.828A  pdb=" N   LEU C 118 " --> pdb=" O   GLN C 161 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    218 hydrogen bonds defined for protein.
    615 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: 0.95

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1144
        1.29 -     1.42: 1886
        1.42 -     1.55: 3903
        1.55 -     1.68: 5
        1.68 -     1.81: 64
  Bond restraints: 7002
  Sorted by residual:
  bond pdb=" CA  ASN B 355 "
       pdb=" C   ASN B 355 "
    ideal  model  delta    sigma   weight residual
    1.526  1.438  0.087 1.08e-02 8.57e+03 6.53e+01
  bond pdb=" CA  LYS B 454 "
       pdb=" C   LYS B 454 "
    ideal  model  delta    sigma   weight residual
    1.524  1.443  0.081 1.26e-02 6.30e+03 4.09e+01
  bond pdb=" C   ASN B 443 "
       pdb=" O   ASN B 443 "
    ideal  model  delta    sigma   weight residual
    1.235  1.162  0.073 1.26e-02 6.30e+03 3.37e+01
  bond pdb=" C   VAL B 442 "
       pdb=" N   ASN B 443 "
    ideal  model  delta    sigma   weight residual
    1.332  1.253  0.079 1.40e-02 5.10e+03 3.21e+01
  bond pdb=" N   GLU A 272 "
       pdb=" CA  GLU A 272 "
    ideal  model  delta    sigma   weight residual
    1.454  1.389  0.065 1.16e-02 7.43e+03 3.14e+01
  ... (remaining 6997 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.38: 9342
        3.38 -     6.76: 73
        6.76 -    10.14: 10
       10.14 -    13.52: 4
       13.52 -    16.90: 1
  Bond angle restraints: 9430
  Sorted by residual:
  angle pdb=" N   GLU D 123 "
        pdb=" CA  GLU D 123 "
        pdb=" C   GLU D 123 "
      ideal   model   delta    sigma   weight residual
     112.23  104.22    8.01 1.26e+00 6.30e-01 4.04e+01
  angle pdb=" O   VAL B 442 "
        pdb=" C   VAL B 442 "
        pdb=" N   ASN B 443 "
      ideal   model   delta    sigma   weight residual
     123.03  117.08    5.95 1.05e+00 9.07e-01 3.21e+01
  angle pdb=" C   ASN B 355 "
        pdb=" CA  ASN B 355 "
        pdb=" CB  ASN B 355 "
      ideal   model   delta    sigma   weight residual
     111.23  103.22    8.01 1.42e+00 4.96e-01 3.18e+01
  angle pdb=" O1A NAD B1001 "
        pdb=" PA  NAD B1001 "
        pdb=" O2A NAD B1001 "
      ideal   model   delta    sigma   weight residual
     122.64  105.74   16.90 3.00e+00 1.11e-01 3.17e+01
  angle pdb=" N   LEU A 230 "
        pdb=" CA  LEU A 230 "
        pdb=" C   LEU A 230 "
      ideal   model   delta    sigma   weight residual
     111.81  119.28   -7.47 1.54e+00 4.22e-01 2.35e+01
  ... (remaining 9425 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.17: 3659
       16.17 -    32.34: 401
       32.34 -    48.50: 123
       48.50 -    64.67: 22
       64.67 -    80.84: 8
  Dihedral angle restraints: 4213
    sinusoidal: 1731
      harmonic: 2482
  Sorted by residual:
  dihedral pdb=" C   ASN B 355 "
           pdb=" N   ASN B 355 "
           pdb=" CA  ASN B 355 "
           pdb=" CB  ASN B 355 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.59  -14.01     0      2.50e+00 1.60e-01 3.14e+01
  dihedral pdb=" CA  PRO B 329 "
           pdb=" C   PRO B 329 "
           pdb=" N   ARG B 330 "
           pdb=" CA  ARG B 330 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.54  -22.46     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  GLN B 253 "
           pdb=" C   GLN B 253 "
           pdb=" N   MET B 254 "
           pdb=" CA  MET B 254 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.64   22.36     0      5.00e+00 4.00e-02 2.00e+01
  ... (remaining 4210 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 896
       0.065 -    0.131: 99
       0.131 -    0.196: 10
       0.196 -    0.261: 2
       0.261 -    0.326: 2
  Chirality restraints: 1009
  Sorted by residual:
  chirality pdb=" CA  ASN B 443 "
            pdb=" N   ASN B 443 "
            pdb=" C   ASN B 443 "
            pdb=" CB  ASN B 443 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" C2B NAD B1001 "
            pdb=" C1B NAD B1001 "
            pdb=" C3B NAD B1001 "
            pdb=" O2B NAD B1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.84    0.31 2.00e-01 2.50e+01 2.33e+00
  chirality pdb=" CA  GLN B  66 "
            pdb=" N   GLN B  66 "
            pdb=" C   GLN B  66 "
            pdb=" CB  GLN B  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1006 not shown)

  Planarity restraints: 1218
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 442 "    0.025 2.00e-02 2.50e+03   4.77e-02 2.28e+01
        pdb=" C   VAL B 442 "   -0.083 2.00e-02 2.50e+03
        pdb=" O   VAL B 442 "    0.029 2.00e-02 2.50e+03
        pdb=" N   ASN B 443 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG D 126 "    0.018 2.00e-02 2.50e+03   3.70e-02 1.37e+01
        pdb=" C   ARG D 126 "   -0.064 2.00e-02 2.50e+03
        pdb=" O   ARG D 126 "    0.024 2.00e-02 2.50e+03
        pdb=" N   GLU D 127 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D 122 "    0.015 2.00e-02 2.50e+03   2.96e-02 8.77e+00
        pdb=" C   ASP D 122 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ASP D 122 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLU D 123 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1215 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1142
        2.76 -     3.29: 6485
        3.29 -     3.83: 10573
        3.83 -     4.36: 13299
        4.36 -     4.90: 22625
  Nonbonded interactions: 54124
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN B 253 "
            pdb=" O   LYS B 295 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O2B NAD B1001 "
            pdb=" O3B NAD B1001 "
     model   vdw
     2.261 2.432
  nonbonded pdb=" O   GLY B 171 "
            pdb=" N   LEU B 175 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" OD1 ASN D  97 "
            pdb=" N   GLY D  98 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OG  SER B 429 "
            pdb=" ND1 HIS B 467 "
     model   vdw
     2.296 3.120
  ... (remaining 54119 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:             3.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.660
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
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   0.102   7002  Z= 0.318
  Angle     :  0.795  16.897   9430  Z= 0.404
  Chirality :  0.047   0.326   1009
  Planarity :  0.005   0.068   1218
  Dihedral  : 15.383  80.840   2611
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.80 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  0.70 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.12 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.93 (0.28), residues: 837
  helix: -1.71 (0.26), residues: 305
  sheet: -2.94 (0.48), residues: 115
  loop : -1.72 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  79 
 TYR   0.022   0.001   TYR A  37 
 PHE   0.020   0.001   PHE B 233 
 TRP   0.013   0.001   TRP C 214 
 HIS   0.005   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 7002)
  covalent geometry    : angle       0.79483 ( 9430)
  hydrogen bonds       : bond        0.25600 (  218)
  hydrogen bonds       : angle       8.27879 (  615)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 150
  time to evaluate  : 0.327 
Fit side-chains
REVERT: A  102 ASP cc_start: 0.7355 (m-30) cc_final: 0.7034 (m-30)
REVERT: A  135 ASP cc_start: 0.6982 (p0) cc_final: 0.6332 (t70)
REVERT: C  107 ASP cc_start: 0.7442 (t70) cc_final: 0.7105 (t0)
REVERT: D   85 ILE cc_start: 0.8045 (pt) cc_final: 0.7838 (mt)
REVERT: D  130 ILE cc_start: 0.5948 (mm) cc_final: 0.5373 (tp)
  outliers start: 5
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0965
  time to fit residues: 19.2337
Evaluate side-chains
  125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0170
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
B 244 HIS
C 161 GLN
D 107 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.142135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.115367 restraints weight = 11613.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.61
r_work: 0.3440 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7002  Z= 0.128
  Angle     :  0.614  14.299   9430  Z= 0.315
  Chirality :  0.042   0.175   1009
  Planarity :  0.005   0.048   1218
  Dihedral  :  7.425  49.030    988
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  8.11 %
    Favored  : 91.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.48 (0.28), residues: 837
  helix: -1.03 (0.27), residues: 312
  sheet: -2.75 (0.44), residues: 129
  loop : -1.65 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  75 
 TYR   0.015   0.001   TYR A  37 
 PHE   0.009   0.001   PHE B 233 
 TRP   0.012   0.001   TRP A 214 
 HIS   0.017   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7002)
  covalent geometry    : angle       0.61433 ( 9430)
  hydrogen bonds       : bond        0.04353 (  218)
  hydrogen bonds       : angle       5.09160 (  615)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 137
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  102 ASP cc_start: 0.7722 (m-30) cc_final: 0.7302 (m-30)
REVERT: A  135 ASP cc_start: 0.7213 (p0) cc_final: 0.6579 (t70)
REVERT: B  302 TYR cc_start: 0.6559 (OUTLIER) cc_final: 0.5825 (t80)
REVERT: B  448 MET cc_start: 0.8177 (mtt) cc_final: 0.7885 (mtt)
REVERT: C   76 GLU cc_start: 0.7754 (tp30) cc_final: 0.7553 (tp30)
REVERT: C  240 ASN cc_start: 0.8461 (t0) cc_final: 0.8239 (t0)
REVERT: C  268 MET cc_start: 0.8586 (mtm) cc_final: 0.8303 (mtt)
  outliers start: 6
  outliers final: 1
  residues processed: 139
  average time/residue: 0.0896
  time to fit residues: 16.6040
Evaluate side-chains
  126 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue  302 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 83 optimal weight:    0.0870
   chunk 11 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0070
   overall best weight:    0.9378

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

Flipped N/Q/H residues before XYZ refinement:
D 107 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.139032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.111315 restraints weight = 11354.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 2.67
r_work: 0.3358 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7002  Z= 0.153
  Angle     :  0.592   9.255   9430  Z= 0.307
  Chirality :  0.042   0.165   1009
  Planarity :  0.004   0.053   1218
  Dihedral  :  6.971  58.387    988
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 11.89 %
    Favored  : 87.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.28), residues: 837
  helix: -0.91 (0.27), residues: 324
  sheet: -2.70 (0.45), residues: 127
  loop : -1.88 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  79 
 TYR   0.011   0.001   TYR B 225 
 PHE   0.014   0.001   PHE B  78 
 TRP   0.008   0.001   TRP A 214 
 HIS   0.005   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7002)
  covalent geometry    : angle       0.59246 ( 9430)
  hydrogen bonds       : bond        0.03807 (  218)
  hydrogen bonds       : angle       4.65738 (  615)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 129
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  102 ASP cc_start: 0.7758 (m-30) cc_final: 0.7325 (m-30)
REVERT: A  135 ASP cc_start: 0.7360 (p0) cc_final: 0.6719 (t70)
REVERT: B  302 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.5879 (t80)
REVERT: B  448 MET cc_start: 0.8477 (mtt) cc_final: 0.8260 (mtt)
REVERT: C   70 ASP cc_start: 0.8593 (p0) cc_final: 0.8219 (p0)
  outliers start: 7
  outliers final: 4
  residues processed: 132
  average time/residue: 0.0796
  time to fit residues: 14.3722
Evaluate side-chains
  131 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 126
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue   55 ILE
Chi-restraints excluded: chain B residue  302 TYR
Chi-restraints excluded: chain B residue  308 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 79 optimal weight:    0.6980
   chunk 52 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
D 107 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.141413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.114454 restraints weight = 11518.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.59
r_work: 0.3427 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7002  Z= 0.136
  Angle     :  0.584  16.114   9430  Z= 0.296
  Chirality :  0.042   0.158   1009
  Planarity :  0.004   0.051   1218
  Dihedral  :  6.731  59.702    988
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.96 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 14.13 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.37 (0.28), residues: 837
  helix: -0.78 (0.28), residues: 328
  sheet: -2.56 (0.45), residues: 127
  loop : -1.84 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  79 
 TYR   0.011   0.001   TYR B 225 
 PHE   0.011   0.001   PHE B 299 
 TRP   0.004   0.001   TRP B 261 
 HIS   0.006   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7002)
  covalent geometry    : angle       0.58377 ( 9430)
  hydrogen bonds       : bond        0.03323 (  218)
  hydrogen bonds       : angle       4.42321 (  615)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  102 ASP cc_start: 0.7716 (m-30) cc_final: 0.7320 (m-30)
REVERT: A  135 ASP cc_start: 0.7268 (p0) cc_final: 0.6751 (t70)
REVERT: B  167 ASN cc_start: 0.7831 (m-40) cc_final: 0.7576 (m110)
REVERT: B  302 TYR cc_start: 0.6498 (OUTLIER) cc_final: 0.5782 (t80)
REVERT: B  308 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8062 (ptt)
REVERT: C   70 ASP cc_start: 0.8517 (p0) cc_final: 0.8118 (p0)
REVERT: C  268 MET cc_start: 0.8515 (mtm) cc_final: 0.8301 (mtt)
  outliers start: 12
  outliers final: 7
  residues processed: 134
  average time/residue: 0.0854
  time to fit residues: 15.5618
Evaluate side-chains
  134 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  226 TYR
Chi-restraints excluded: chain B residue   55 ILE
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  302 TYR
Chi-restraints excluded: chain B residue  308 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   chunk 70 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 23 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0170
   chunk 72 optimal weight:    0.9980
   chunk 83 optimal weight:    7.9990
   overall best weight:    1.0220

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 107 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.138580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.110591 restraints weight = 11433.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.68
r_work: 0.3345 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7002  Z= 0.160
  Angle     :  0.593  12.485   9430  Z= 0.305
  Chirality :  0.042   0.162   1009
  Planarity :  0.004   0.053   1218
  Dihedral  :  6.587  52.425    988
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.52 %
    Favored  : 82.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.29), residues: 837
  helix: -0.73 (0.28), residues: 326
  sheet: -2.60 (0.45), residues: 127
  loop : -1.90 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  79 
 TYR   0.011   0.001   TYR B 225 
 PHE   0.013   0.001   PHE B  78 
 TRP   0.004   0.001   TRP B 261 
 HIS   0.005   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 7002)
  covalent geometry    : angle       0.59293 ( 9430)
  hydrogen bonds       : bond        0.03464 (  218)
  hydrogen bonds       : angle       4.39188 (  615)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 130
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  102 ASP cc_start: 0.7742 (m-30) cc_final: 0.7330 (m-30)
REVERT: A  135 ASP cc_start: 0.7357 (p0) cc_final: 0.6841 (t70)
REVERT: B  167 ASN cc_start: 0.7799 (m-40) cc_final: 0.7434 (m110)
REVERT: B  302 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.5794 (t80)
REVERT: D   97 ASN cc_start: 0.8318 (t0) cc_final: 0.8080 (t0)
  outliers start: 12
  outliers final: 8
  residues processed: 135
  average time/residue: 0.0751
  time to fit residues: 14.0310
Evaluate side-chains
  137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  226 TYR
Chi-restraints excluded: chain B residue   55 ILE
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  302 TYR
Chi-restraints excluded: chain B residue  308 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
** A 141 ASN ** 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 = 0.3887 r_free = 0.3887 target = 0.139341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.113298 restraints weight = 11511.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.54
r_work: 0.3387 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7002  Z= 0.182
  Angle     :  0.624  14.409   9430  Z= 0.317
  Chirality :  0.043   0.161   1009
  Planarity :  0.004   0.052   1218
  Dihedral  :  6.623  46.549    988
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.80 %
    Favored  : 90.20 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.50 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.28), residues: 837
  helix: -0.76 (0.28), residues: 326
  sheet: -2.72 (0.44), residues: 127
  loop : -1.92 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 260 
 TYR   0.013   0.001   TYR D 138 
 PHE   0.015   0.001   PHE B  78 
 TRP   0.004   0.001   TRP B 261 
 HIS   0.006   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 7002)
  covalent geometry    : angle       0.62426 ( 9430)
  hydrogen bonds       : bond        0.03600 (  218)
  hydrogen bonds       : angle       4.45823 (  615)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 130
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  102 ASP cc_start: 0.7732 (m-30) cc_final: 0.7321 (m-30)
REVERT: A  135 ASP cc_start: 0.7228 (p0) cc_final: 0.6780 (t70)
REVERT: B  302 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.5757 (t80)
REVERT: B  448 MET cc_start: 0.8219 (mtt) cc_final: 0.7940 (mtt)
REVERT: C  157 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.9015 (mt)
REVERT: D   97 ASN cc_start: 0.8251 (t0) cc_final: 0.8030 (t0)
  outliers start: 13
  outliers final: 11
  residues processed: 134
  average time/residue: 0.0738
  time to fit residues: 13.7358
Evaluate side-chains
  137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  226 TYR
Chi-restraints excluded: chain B residue   55 ILE
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  302 TYR
Chi-restraints excluded: chain B residue  308 MET
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain C residue  157 LEU
Chi-restraints excluded: chain C residue  246 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 70 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.138563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.112424 restraints weight = 11391.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 2.55
r_work: 0.3387 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7002  Z= 0.174
  Angle     :  0.633  14.954   9430  Z= 0.321
  Chirality :  0.043   0.160   1009
  Planarity :  0.004   0.053   1218
  Dihedral  :  6.574  47.135    988
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.44 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.34 %
    Favored  : 80.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.46 (0.28), residues: 837
  helix: -0.72 (0.28), residues: 326
  sheet: -2.72 (0.44), residues: 127
  loop : -1.98 (0.31), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 260 
 TYR   0.013   0.001   TYR D 138 
 PHE   0.014   0.001   PHE B  78 
 TRP   0.004   0.001   TRP B 261 
 HIS   0.006   0.001   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 7002)
  covalent geometry    : angle       0.63270 ( 9430)
  hydrogen bonds       : bond        0.03529 (  218)
  hydrogen bonds       : angle       4.42929 (  615)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  102 ASP cc_start: 0.7735 (m-30) cc_final: 0.7321 (m-30)
REVERT: B  302 TYR cc_start: 0.6555 (OUTLIER) cc_final: 0.5703 (t80)
REVERT: B  336 ASP cc_start: 0.8227 (t0) cc_final: 0.7930 (t0)
REVERT: B  448 MET cc_start: 0.8291 (mtt) cc_final: 0.8073 (mtt)
REVERT: D   97 ASN cc_start: 0.8256 (t0) cc_final: 0.7987 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 131
  average time/residue: 0.0767
  time to fit residues: 13.8498
Evaluate side-chains
  135 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  226 TYR
Chi-restraints excluded: chain B residue   55 ILE
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  302 TYR
Chi-restraints excluded: chain B residue  308 MET
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain C residue  246 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 70 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 40 optimal weight:    0.1980
   chunk 45 optimal weight:    2.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.135094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.108926 restraints weight = 11644.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 2.53
r_work: 0.3335 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051   7002  Z= 0.285
  Angle     :  0.729  14.888   9430  Z= 0.373
  Chirality :  0.047   0.219   1009
  Planarity :  0.005   0.053   1218
  Dihedral  :  7.211  49.576    988
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.63 %
    Favored  : 89.37 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.90 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.79 (0.28), residues: 837
  helix: -1.04 (0.27), residues: 325
  sheet: -2.96 (0.42), residues: 130
  loop : -2.07 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 260 
 TYR   0.014   0.002   TYR B 225 
 PHE   0.027   0.002   PHE A 128 
 TRP   0.006   0.001   TRP B 432 
 HIS   0.008   0.002   HIS B 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00683 ( 7002)
  covalent geometry    : angle       0.72902 ( 9430)
  hydrogen bonds       : bond        0.04412 (  218)
  hydrogen bonds       : angle       4.76655 (  615)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  102 ASP cc_start: 0.7774 (m-30) cc_final: 0.7382 (m-30)
REVERT: B  302 TYR cc_start: 0.6571 (OUTLIER) cc_final: 0.5643 (t80)
REVERT: D   97 ASN cc_start: 0.8264 (t0) cc_final: 0.7955 (t0)
  outliers start: 14
  outliers final: 10
  residues processed: 128
  average time/residue: 0.0826
  time to fit residues: 14.3908
Evaluate side-chains
  131 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASP
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain B residue   55 ILE
Chi-restraints excluded: chain B residue  145 ASP
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  302 TYR
Chi-restraints excluded: chain B residue  377 ILE
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain C residue  246 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.140865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.114349 restraints weight = 11455.007|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.58
r_work: 0.3403 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7002  Z= 0.138
  Angle     :  0.625  16.139   9430  Z= 0.314
  Chirality :  0.042   0.204   1009
  Planarity :  0.004   0.052   1218
  Dihedral  :  6.584  55.856    988
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 19.16 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.44 (0.28), residues: 837
  helix: -0.66 (0.29), residues: 325
  sheet: -2.81 (0.43), residues: 127
  loop : -1.96 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 136 
 TYR   0.009   0.001   TYR B 225 
 PHE   0.010   0.001   PHE B  78 
 TRP   0.005   0.001   TRP A 206 
 HIS   0.008   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7002)
  covalent geometry    : angle       0.62453 ( 9430)
  hydrogen bonds       : bond        0.03200 (  218)
  hydrogen bonds       : angle       4.42237 (  615)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  102 ASP cc_start: 0.7749 (m-30) cc_final: 0.7354 (m-30)
REVERT: B  302 TYR cc_start: 0.6495 (OUTLIER) cc_final: 0.5587 (t80)
REVERT: B  336 ASP cc_start: 0.8216 (t0) cc_final: 0.7932 (t0)
REVERT: D   97 ASN cc_start: 0.8293 (t0) cc_final: 0.7965 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 127
  average time/residue: 0.0780
  time to fit residues: 13.6530
Evaluate side-chains
  127 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  131 ASN
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  226 TYR
Chi-restraints excluded: chain B residue   55 ILE
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  302 TYR
Chi-restraints excluded: chain B residue  449 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0020
   chunk 23 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0270
   chunk 24 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.4846

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

Flipped N/Q/H residues before XYZ refinement:
** A  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 121 HIS
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.141818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.115118 restraints weight = 11497.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.59
r_work: 0.3434 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7002  Z= 0.117
  Angle     :  0.610  16.227   9430  Z= 0.306
  Chirality :  0.041   0.199   1009
  Planarity :  0.004   0.051   1218
  Dihedral  :  6.319  56.559    988
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  8.24 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 19.02 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.29), residues: 837
  helix: -0.46 (0.29), residues: 327
  sheet: -2.64 (0.43), residues: 127
  loop : -1.84 (0.32), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 122 
 TYR   0.008   0.001   TYR B 225 
 PHE   0.010   0.001   PHE B 233 
 TRP   0.006   0.001   TRP A 206 
 HIS   0.012   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7002)
  covalent geometry    : angle       0.60953 ( 9430)
  hydrogen bonds       : bond        0.02808 (  218)
  hydrogen bonds       : angle       4.28707 (  615)

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

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

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1674 Ramachandran restraints generated.
    837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  102 ASP cc_start: 0.7718 (m-30) cc_final: 0.7355 (m-30)
REVERT: B  302 TYR cc_start: 0.6399 (OUTLIER) cc_final: 0.5628 (t80)
REVERT: B  336 ASP cc_start: 0.8190 (t0) cc_final: 0.7973 (t0)
REVERT: D   97 ASN cc_start: 0.8269 (t0) cc_final: 0.7976 (t0)
REVERT: D  112 LEU cc_start: 0.8447 (mt) cc_final: 0.8175 (mt)
  outliers start: 10
  outliers final: 6
  residues processed: 131
  average time/residue: 0.0748
  time to fit residues: 13.4363
Evaluate side-chains
  133 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 126
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  226 TYR
Chi-restraints excluded: chain B residue   55 ILE
Chi-restraints excluded: chain B residue  204 THR
Chi-restraints excluded: chain B residue  302 TYR
Chi-restraints excluded: chain B residue  449 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 46 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 121 HIS
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 161 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.134394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.108191 restraints weight = 11549.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.52
r_work: 0.3337 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.2370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.059   7002  Z= 0.328
  Angle     :  0.772  14.877   9430  Z= 0.397
  Chirality :  0.049   0.211   1009
  Planarity :  0.005   0.054   1218
  Dihedral  :  7.319  52.974    988
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  : 10.87 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 19.58 %
    Favored  : 79.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.80 (0.28), residues: 837
  helix: -1.00 (0.27), residues: 319
  sheet: -2.97 (0.42), residues: 130
  loop : -2.10 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 260 
 TYR   0.017   0.002   TYR A 197 
 PHE   0.022   0.002   PHE B  78 
 TRP   0.012   0.002   TRP A 214 
 HIS   0.011   0.002   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00776 ( 7002)
  covalent geometry    : angle       0.77191 ( 9430)
  hydrogen bonds       : bond        0.04594 (  218)
  hydrogen bonds       : angle       4.79757 (  615)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1634.69 seconds
wall clock time: 28 minutes 44.53 seconds (1724.53 seconds total)