Starting phenix.real_space_refine
on Tue Jan 14 16:10:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yso_34078/01_2025/7yso_34078.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yso_34078/01_2025/7yso_34078.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yso_34078/01_2025/7yso_34078.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yso_34078/01_2025/7yso_34078.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yso_34078/01_2025/7yso_34078.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yso_34078/01_2025/7yso_34078.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
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       5      5.49       5
     S      48      5.16       5
     C    4278      2.51       5
     N    1162      2.21       5
     O    1317      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 6810
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3374
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3376
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 409}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.15, per 1000 atoms: 0.61
  Number of scatterers: 6810
  At special positions: 0
  Unit cell: (111.28, 71.904, 67.624, 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      48     16.00
     P       5     15.00
     O    1317      8.00
     N    1162      7.00
     C    4278      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: 1.83
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1594

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      50.8% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 28
    Processing helix  chain 'A' and resid 48 through 52
      removed outlier: 4.203A  pdb=" N   PHE A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 48 through 52'
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 111 through 127
      removed outlier: 4.295A  pdb=" N   ASP A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   LEU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 161
      removed outlier: 4.439A  pdb=" N   THR A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 195
    Processing helix  chain 'A' and resid 206 through 216
    Processing helix  chain 'A' and resid 223 through 244
      removed outlier: 4.911A  pdb=" N   SER A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   LEU A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 259
    Processing helix  chain 'A' and resid 277 through 281
    Processing helix  chain 'A' and resid 287 through 296
      removed outlier: 4.304A  pdb=" N   PHE A 296 " --> pdb=" O   THR A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 337
      removed outlier: 3.582A  pdb=" N   THR A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 400
      removed outlier: 4.022A  pdb=" N   TRP A 388 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.861A  pdb=" N   TYR A 408 " --> pdb=" O   PHE A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 436
      removed outlier: 3.933A  pdb=" N   PHE A 418 " --> pdb=" O   GLU A 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 28
    Processing helix  chain 'B' and resid 41 through 48
      removed outlier: 4.163A  pdb=" N   ARG B  48 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 71 through 81
      removed outlier: 3.815A  pdb=" N   MET B  75 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 92
    Processing helix  chain 'B' and resid 103 through 109
    Processing helix  chain 'B' and resid 111 through 129
      removed outlier: 3.585A  pdb=" N   ASP B 116 " --> pdb=" O   ALA B 112 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   SER B 117 " --> pdb=" O   GLU B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 161
    Processing helix  chain 'B' and resid 182 through 198
      removed outlier: 4.132A  pdb=" N   ASN B 186 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 216
    Processing helix  chain 'B' and resid 223 through 239
      removed outlier: 3.812A  pdb=" N   LEU B 230 " --> pdb=" O   ASP B 226 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   THR B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 240 through 243
    Processing helix  chain 'B' and resid 251 through 260
    Processing helix  chain 'B' and resid 287 through 295
      removed outlier: 3.601A  pdb=" N   LEU B 291 " --> pdb=" O   THR B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 310
    Processing helix  chain 'B' and resid 324 through 340
      removed outlier: 4.033A  pdb=" N   VAL B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 343
      No H-bonds generated for 'chain 'B' and resid 341 through 343'
    Processing helix  chain 'B' and resid 384 through 400
      removed outlier: 3.843A  pdb=" N   PHE B 388 " --> pdb=" O   ILE B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 4.539A  pdb=" N   TYR B 408 " --> pdb=" O   PHE B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 437
      removed outlier: 3.812A  pdb=" N   PHE B 418 " --> pdb=" O   ASP B 414 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68
      removed outlier: 7.113A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 68
      removed outlier: 7.113A  pdb=" N   SER A   6 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   VAL A  68 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   HIS A   8 " --> pdb=" O   VAL A  68 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   SER A 140 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   PHE A 169 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   VAL A 137 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   HIS A 139 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55
    Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 273
      removed outlier: 4.014A  pdb=" N   ASN A 380 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   ALA A 314 " --> pdb=" O   ASN A 380 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 67
      removed outlier: 8.694A  pdb=" N   ILE B  66 " --> pdb=" O   ILE B   4 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   HIS B   6 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   VAL B   5 " --> pdb=" O   GLN B 136 " (cutoff:3.500A)
      removed outlier: 7.982A  pdb=" N   THR B 138 " --> pdb=" O   VAL B   5 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ILE B   7 " --> pdb=" O   THR B 138 " (cutoff:3.500A)
      removed outlier: 8.744A  pdb=" N   SER B 140 " --> pdb=" O   ILE B   7 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   PHE B 135 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 7.444A  pdb=" N   PHE B 169 " --> pdb=" O   PHE B 135 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   LEU B 137 " --> pdb=" O   PHE B 169 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   VAL B 171 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.432A  pdb=" N   HIS B 139 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   GLU B 200 " --> pdb=" O   MET B 166 " (cutoff:3.500A)
      removed outlier: 7.977A  pdb=" N   ASP B 205 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
      removed outlier: 12.071A  pdb=" N   PHE B 272 " --> pdb=" O   ASP B 205 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   PHE B 267 " --> pdb=" O   SER B 381 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   SER B 381 " --> pdb=" O   PHE B 267 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLY B 379 " --> pdb=" O   MET B 269 " (cutoff:3.500A)
      removed outlier: 8.767A  pdb=" N   LYS B 352 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
      removed outlier: 6.278A  pdb=" N   VAL B 315 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
      removed outlier: 8.075A  pdb=" N   ALA B 354 " --> pdb=" O   VAL B 315 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ALA B 317 " --> pdb=" O   ALA B 354 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   CYS B 356 " --> pdb=" O   ALA B 317 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   PHE B 319 " --> pdb=" O   CYS B 356 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 55

    330 hydrogen bonds defined for protein.
    960 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: 1.89

  Time building geometry restraints manager: 2.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2274
        1.34 -     1.46: 1532
        1.46 -     1.58: 3073
        1.58 -     1.69: 11
        1.69 -     1.81: 76
  Bond restraints: 6966
  Sorted by residual:
  bond pdb=" C6  GTP A 501 "
       pdb=" O6  GTP A 501 "
    ideal  model  delta    sigma   weight residual
    1.230  1.463 -0.233 2.00e-02 2.50e+03 1.36e+02
  bond pdb=" C2' GTP A 501 "
       pdb=" C3' GTP A 501 "
    ideal  model  delta    sigma   weight residual
    1.524  1.332  0.192 2.00e-02 2.50e+03 9.17e+01
  bond pdb=" C3' GDP B 501 "
       pdb=" C2' GDP B 501 "
    ideal  model  delta    sigma   weight residual
    1.524  1.334  0.190 2.00e-02 2.50e+03 9.03e+01
  bond pdb=" C4' GDP B 501 "
       pdb=" O4' GDP B 501 "
    ideal  model  delta    sigma   weight residual
    1.426  1.600 -0.174 2.00e-02 2.50e+03 7.54e+01
  bond pdb=" C4' GTP A 501 "
       pdb=" O4' GTP A 501 "
    ideal  model  delta    sigma   weight residual
    1.410  1.566 -0.156 2.00e-02 2.50e+03 6.08e+01
  ... (remaining 6961 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 9305
        2.35 -     4.71: 122
        4.71 -     7.06: 23
        7.06 -     9.42: 11
        9.42 -    11.77: 1
  Bond angle restraints: 9462
  Sorted by residual:
  angle pdb=" N   VAL A 182 "
        pdb=" CA  VAL A 182 "
        pdb=" C   VAL A 182 "
      ideal   model   delta    sigma   weight residual
     112.29  107.43    4.86 9.40e-01 1.13e+00 2.67e+01
  angle pdb=" C   GLN A  35 "
        pdb=" N   MET A  36 "
        pdb=" CA  MET A  36 "
      ideal   model   delta    sigma   weight residual
     121.83  128.91   -7.08 1.56e+00 4.11e-01 2.06e+01
  angle pdb=" CB  MET B 235 "
        pdb=" CG  MET B 235 "
        pdb=" SD  MET B 235 "
      ideal   model   delta    sigma   weight residual
     112.70  124.47  -11.77 3.00e+00 1.11e-01 1.54e+01
  angle pdb=" N   SER B 324 "
        pdb=" CA  SER B 324 "
        pdb=" C   SER B 324 "
      ideal   model   delta    sigma   weight residual
     110.65  105.75    4.90 1.26e+00 6.30e-01 1.51e+01
  angle pdb=" CG  ARG B  79 "
        pdb=" CD  ARG B  79 "
        pdb=" NE  ARG B  79 "
      ideal   model   delta    sigma   weight residual
     112.00  103.76    8.24 2.20e+00 2.07e-01 1.40e+01
  ... (remaining 9457 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.56: 4044
       33.56 -    67.12: 84
       67.12 -   100.68: 14
      100.68 -   134.25: 1
      134.25 -   167.81: 1
  Dihedral angle restraints: 4144
    sinusoidal: 1659
      harmonic: 2485
  Sorted by residual:
  dihedral pdb=" C8  GTP A 501 "
           pdb=" C1' GTP A 501 "
           pdb=" N9  GTP A 501 "
           pdb=" O4' GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -87.60 -167.81     1      2.00e+01 2.50e-03 4.75e+01
  dihedral pdb=" C5' GTP A 501 "
           pdb=" O5' GTP A 501 "
           pdb=" PA  GTP A 501 "
           pdb=" O3A GTP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -164.21 -126.53     1      2.00e+01 2.50e-03 3.83e+01
  dihedral pdb=" CA  VAL B  93 "
           pdb=" C   VAL B  93 "
           pdb=" N   PHE B  94 "
           pdb=" CA  PHE B  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.98  -24.02     0      5.00e+00 4.00e-02 2.31e+01
  ... (remaining 4141 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 712
       0.041 -    0.082: 237
       0.082 -    0.122: 76
       0.122 -    0.163: 7
       0.163 -    0.204: 2
  Chirality restraints: 1034
  Sorted by residual:
  chirality pdb=" CB  THR B 221 "
            pdb=" CA  THR B 221 "
            pdb=" OG1 THR B 221 "
            pdb=" CG2 THR B 221 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" C4' GTP A 501 "
            pdb=" C3' GTP A 501 "
            pdb=" C5' GTP A 501 "
            pdb=" O4' GTP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.66    0.19 2.00e-01 2.50e+01 9.16e-01
  chirality pdb=" CA  GLU B 127 "
            pdb=" N   GLU B 127 "
            pdb=" C   GLU B 127 "
            pdb=" CB  GLU B 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.58e-01
  ... (remaining 1031 not shown)

  Planarity restraints: 1233
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  94 "    0.014 2.00e-02 2.50e+03   1.46e-02 3.75e+00
        pdb=" CG  PHE B  94 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  94 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  94 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  94 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  94 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  94 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 123 "   -0.009 2.00e-02 2.50e+03   1.71e-02 2.94e+00
        pdb=" C   ARG B 123 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ARG B 123 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LYS B 124 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 297 "   -0.027 5.00e-02 4.00e+02   4.12e-02 2.71e+00
        pdb=" N   PRO A 298 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 298 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 298 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1230 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 780
        2.74 -     3.28: 7718
        3.28 -     3.82: 12458
        3.82 -     4.36: 14576
        4.36 -     4.90: 23901
  Nonbonded interactions: 59433
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 320 "
            pdb=" O   GLN A 358 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" NE2 GLN B  11 "
            pdb=" O2A GDP B 501 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OG  SER A 241 "
            pdb=" O   VAL A 250 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OG  SER B 170 "
            pdb=" O   TYR B 202 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OH  TYR B 185 "
            pdb=" O   ALA B 403 "
     model   vdw
     2.278 3.040
  ... (remaining 59428 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.250
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.980
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
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      :  0.008   0.233   6966  Z= 0.540
  Angle     :  0.702  11.770   9462  Z= 0.348
  Chirality :  0.044   0.204   1034
  Planarity :  0.004   0.041   1233
  Dihedral  : 15.403 167.807   2550
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 19.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.29), residues: 854
  helix:  0.49 (0.26), residues: 379
  sheet: -0.07 (0.47), residues: 130
  loop : -0.13 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 103 
 HIS   0.003   0.001   HIS B  28 
 PHE   0.033   0.002   PHE B  94 
 TYR   0.011   0.001   TYR A 432 
 ARG   0.001   0.000   ARG B 322 

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 HIS cc_start: 0.8840 (m-70) cc_final: 0.8390 (m90)
REVERT: A  102 ASN cc_start: 0.9042 (t0) cc_final: 0.8264 (t0)
REVERT: B   76 ASP cc_start: 0.9031 (m-30) cc_final: 0.8549 (m-30)
REVERT: B  149 MET cc_start: 0.8699 (mmp) cc_final: 0.8269 (mmp)
REVERT: B  204 ILE cc_start: 0.7638 (mm) cc_final: 0.7406 (mm)
REVERT: B  329 ASP cc_start: 0.8832 (m-30) cc_final: 0.8582 (m-30)
REVERT: B  353 THR cc_start: 0.8106 (p) cc_final: 0.7679 (p)
REVERT: B  406 HIS cc_start: 0.9266 (m90) cc_final: 0.9056 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1629
  time to fit residues: 32.1655
Evaluate side-chains
  111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:   20.0000
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   chunk 26 optimal weight:    6.9990
   chunk 40 optimal weight:    6.9990
   chunk 50 optimal weight:    8.9990
   chunk 78 optimal weight:    9.9990
   overall best weight:    4.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.108562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.082962 restraints weight = 18575.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.086469 restraints weight = 10848.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.088905 restraints weight = 7579.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   6966  Z= 0.328
  Angle     :  0.682   7.147   9462  Z= 0.356
  Chirality :  0.047   0.187   1034
  Planarity :  0.005   0.045   1233
  Dihedral  :  9.646 179.857    959
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 18.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.82 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.28), residues: 854
  helix:  0.21 (0.25), residues: 385
  sheet: -0.26 (0.45), residues: 122
  loop : -0.15 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 103 
 HIS   0.007   0.002   HIS B 229 
 PHE   0.027   0.002   PHE B  94 
 TYR   0.007   0.001   TYR A 103 
 ARG   0.007   0.001   ARG B 158 

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: A   69 ASP cc_start: 0.8721 (p0) cc_final: 0.8414 (p0)
REVERT: A   71 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7627 (tm-30)
REVERT: A  102 ASN cc_start: 0.9123 (t0) cc_final: 0.8462 (t0)
REVERT: A  238 ILE cc_start: 0.9314 (mt) cc_final: 0.9105 (mt)
REVERT: A  434 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8649 (pp20)
REVERT: B   92 PHE cc_start: 0.8836 (m-80) cc_final: 0.8613 (m-80)
REVERT: B  139 HIS cc_start: 0.8583 (p-80) cc_final: 0.8336 (p-80)
REVERT: B  149 MET cc_start: 0.8727 (mmp) cc_final: 0.8395 (mmt)
REVERT: B  166 MET cc_start: 0.8494 (tmm) cc_final: 0.7817 (tmm)
REVERT: B  235 MET cc_start: 0.8751 (tmm) cc_final: 0.8085 (tmm)
REVERT: B  301 MET cc_start: 0.9205 (tpp) cc_final: 0.8949 (tpp)
REVERT: B  329 ASP cc_start: 0.8916 (m-30) cc_final: 0.8660 (m-30)
REVERT: B  406 HIS cc_start: 0.9269 (m90) cc_final: 0.9046 (m90)
  outliers start: 6
  outliers final: 6
  residues processed: 128
  average time/residue: 0.1499
  time to fit residues: 27.4566
Evaluate side-chains
  117 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 67 optimal weight:    0.0970
   chunk 11 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   chunk 48 optimal weight:   10.0000
   chunk 49 optimal weight:    6.9990
   chunk 43 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   overall best weight:    2.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 329 ASN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.110642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.084582 restraints weight = 18288.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.088275 restraints weight = 10671.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.090844 restraints weight = 7391.701|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6966  Z= 0.221
  Angle     :  0.616   7.384   9462  Z= 0.316
  Chirality :  0.045   0.164   1034
  Planarity :  0.004   0.041   1233
  Dihedral  :  9.298 175.975    959
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 13.10 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.28), residues: 854
  helix:  0.29 (0.25), residues: 385
  sheet: -0.39 (0.45), residues: 121
  loop : -0.18 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 103 
 HIS   0.004   0.001   HIS B 229 
 PHE   0.016   0.001   PHE A 255 
 TYR   0.007   0.001   TYR A 282 
 ARG   0.003   0.000   ARG B 158 

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7803 (tmm) cc_final: 0.7598 (tmm)
REVERT: A   69 ASP cc_start: 0.8658 (p0) cc_final: 0.8395 (p0)
REVERT: A   71 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7647 (tm-30)
REVERT: A  102 ASN cc_start: 0.9072 (t0) cc_final: 0.8299 (t0)
REVERT: A  238 ILE cc_start: 0.9284 (mt) cc_final: 0.9058 (mt)
REVERT: B   75 MET cc_start: 0.8621 (ppp) cc_final: 0.8379 (ppp)
REVERT: B   94 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6457 (t80)
REVERT: B  139 HIS cc_start: 0.8533 (p-80) cc_final: 0.8217 (p-80)
REVERT: B  149 MET cc_start: 0.8756 (mmp) cc_final: 0.8513 (mmt)
REVERT: B  166 MET cc_start: 0.8449 (tmm) cc_final: 0.7715 (tmm)
REVERT: B  197 ASN cc_start: 0.8052 (t0) cc_final: 0.7758 (t0)
REVERT: B  210 TYR cc_start: 0.9120 (t80) cc_final: 0.8913 (t80)
REVERT: B  235 MET cc_start: 0.8680 (tmm) cc_final: 0.7980 (tmm)
REVERT: B  329 ASP cc_start: 0.8875 (m-30) cc_final: 0.8653 (m-30)
REVERT: B  406 HIS cc_start: 0.9264 (m90) cc_final: 0.9053 (m90)
  outliers start: 13
  outliers final: 7
  residues processed: 132
  average time/residue: 0.1486
  time to fit residues: 28.0710
Evaluate side-chains
  120 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  138 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  387 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9990
   chunk 78 optimal weight:    0.0570
   chunk 57 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.9904

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

Flipped N/Q/H residues before XYZ refinement:
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 426 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.113618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.089619 restraints weight = 18179.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.093371 restraints weight = 10368.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.096089 restraints weight = 7000.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6966  Z= 0.170
  Angle     :  0.611   8.205   9462  Z= 0.307
  Chirality :  0.044   0.159   1034
  Planarity :  0.004   0.040   1233
  Dihedral  :  9.030 172.667    959
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 14.46 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.28), residues: 854
  helix:  0.45 (0.25), residues: 386
  sheet: -0.22 (0.46), residues: 115
  loop : -0.29 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 103 
 HIS   0.004   0.001   HIS A 283 
 PHE   0.013   0.001   PHE B 377 
 TYR   0.007   0.001   TYR B 161 
 ARG   0.005   0.000   ARG B 369 

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7789 (tmm) cc_final: 0.7528 (tmm)
REVERT: A   69 ASP cc_start: 0.8710 (p0) cc_final: 0.8415 (p0)
REVERT: A   71 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7610 (tm-30)
REVERT: A  102 ASN cc_start: 0.9023 (t0) cc_final: 0.8194 (t0)
REVERT: A  202 PHE cc_start: 0.8696 (m-80) cc_final: 0.8446 (m-80)
REVERT: A  238 ILE cc_start: 0.9264 (mt) cc_final: 0.9044 (mt)
REVERT: B   75 MET cc_start: 0.8734 (ppp) cc_final: 0.8499 (ppp)
REVERT: B  139 HIS cc_start: 0.8560 (p-80) cc_final: 0.8311 (p-80)
REVERT: B  149 MET cc_start: 0.8736 (mmp) cc_final: 0.8436 (mmt)
REVERT: B  156 LYS cc_start: 0.9425 (mmtm) cc_final: 0.9200 (mmtm)
REVERT: B  166 MET cc_start: 0.8486 (tmm) cc_final: 0.7592 (tmm)
REVERT: B  235 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8039 (tmm)
REVERT: B  272 PHE cc_start: 0.9020 (t80) cc_final: 0.8538 (t80)
REVERT: B  325 MET cc_start: 0.8444 (ppp) cc_final: 0.7589 (ppp)
REVERT: B  329 ASP cc_start: 0.8870 (m-30) cc_final: 0.8541 (m-30)
REVERT: B  406 HIS cc_start: 0.9212 (m90) cc_final: 0.9005 (m90)
REVERT: B  416 MET cc_start: 0.9692 (ppp) cc_final: 0.9426 (ppp)
  outliers start: 15
  outliers final: 9
  residues processed: 131
  average time/residue: 0.1480
  time to fit residues: 27.8202
Evaluate side-chains
  130 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  387 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 4 optimal weight:   10.0000
   chunk 80 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 12 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 67 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 57 optimal weight:   30.0000
   overall best weight:    3.3584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.110073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.083645 restraints weight = 18324.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.087270 restraints weight = 10845.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.089828 restraints weight = 7619.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6966  Z= 0.268
  Angle     :  0.637   8.988   9462  Z= 0.324
  Chirality :  0.045   0.155   1034
  Planarity :  0.004   0.042   1233
  Dihedral  :  8.929 165.177    959
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.19 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.28), residues: 854
  helix:  0.40 (0.25), residues: 385
  sheet: -0.96 (0.47), residues: 108
  loop : -0.17 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 103 
 HIS   0.004   0.001   HIS B 229 
 PHE   0.013   0.002   PHE A 255 
 TYR   0.014   0.001   TYR B 210 
 ARG   0.007   0.000   ARG B  79 

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7805 (tmm) cc_final: 0.7541 (tmm)
REVERT: A   69 ASP cc_start: 0.8663 (p0) cc_final: 0.8463 (p0)
REVERT: A   71 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7674 (tm-30)
REVERT: A  102 ASN cc_start: 0.9157 (t0) cc_final: 0.8504 (t0)
REVERT: A  238 ILE cc_start: 0.9335 (mt) cc_final: 0.9111 (mt)
REVERT: A  425 MET cc_start: 0.8918 (mmm) cc_final: 0.8512 (mmm)
REVERT: B   75 MET cc_start: 0.8843 (ppp) cc_final: 0.8333 (ppp)
REVERT: B   79 ARG cc_start: 0.8719 (mtm180) cc_final: 0.8233 (tpm170)
REVERT: B   94 PHE cc_start: 0.6852 (t80) cc_final: 0.6482 (t80)
REVERT: B  139 HIS cc_start: 0.8651 (p-80) cc_final: 0.8242 (p-80)
REVERT: B  149 MET cc_start: 0.8746 (mmp) cc_final: 0.8359 (mmp)
REVERT: B  166 MET cc_start: 0.8414 (tmm) cc_final: 0.7593 (tmm)
REVERT: B  235 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8096 (tmm)
REVERT: B  272 PHE cc_start: 0.8993 (t80) cc_final: 0.8579 (t80)
REVERT: B  325 MET cc_start: 0.8453 (ppp) cc_final: 0.7959 (ppp)
REVERT: B  329 ASP cc_start: 0.8869 (m-30) cc_final: 0.8615 (m-30)
REVERT: B  406 HIS cc_start: 0.9291 (m90) cc_final: 0.9080 (m90)
REVERT: B  416 MET cc_start: 0.9720 (ppp) cc_final: 0.9503 (ppp)
  outliers start: 19
  outliers final: 13
  residues processed: 125
  average time/residue: 0.1480
  time to fit residues: 26.5077
Evaluate side-chains
  124 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  387 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 40 optimal weight:    9.9990
   chunk 79 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0370
   chunk 72 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 65 optimal weight:    0.9990
   chunk 73 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    3.0066

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.109742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.083885 restraints weight = 18283.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.087538 restraints weight = 10699.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.090093 restraints weight = 7408.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6966  Z= 0.252
  Angle     :  0.655   9.626   9462  Z= 0.326
  Chirality :  0.045   0.154   1034
  Planarity :  0.004   0.044   1233
  Dihedral  :  8.957 164.959    959
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 16.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 18.14 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.28), residues: 854
  helix:  0.32 (0.25), residues: 386
  sheet: -1.04 (0.47), residues: 108
  loop : -0.09 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 103 
 HIS   0.003   0.001   HIS B 229 
 PHE   0.016   0.002   PHE B 388 
 TYR   0.013   0.001   TYR A 224 
 ARG   0.004   0.000   ARG B 264 

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7801 (tmm) cc_final: 0.7542 (tmm)
REVERT: A   69 ASP cc_start: 0.8638 (p0) cc_final: 0.8333 (p0)
REVERT: A   71 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7579 (tm-30)
REVERT: A  102 ASN cc_start: 0.9130 (t0) cc_final: 0.8424 (t0)
REVERT: B   75 MET cc_start: 0.8903 (ppp) cc_final: 0.8368 (ppp)
REVERT: B   79 ARG cc_start: 0.8827 (mtm180) cc_final: 0.8326 (tpm170)
REVERT: B   94 PHE cc_start: 0.6772 (t80) cc_final: 0.6474 (t80)
REVERT: B  139 HIS cc_start: 0.8643 (p-80) cc_final: 0.8193 (p-80)
REVERT: B  149 MET cc_start: 0.8726 (mmp) cc_final: 0.8328 (mmp)
REVERT: B  166 MET cc_start: 0.8457 (tmm) cc_final: 0.7639 (tmm)
REVERT: B  235 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8173 (tmm)
REVERT: B  272 PHE cc_start: 0.8979 (t80) cc_final: 0.8479 (t80)
REVERT: B  325 MET cc_start: 0.8529 (ppp) cc_final: 0.8026 (ppp)
REVERT: B  329 ASP cc_start: 0.8859 (m-30) cc_final: 0.8570 (m-30)
REVERT: B  406 HIS cc_start: 0.9273 (m90) cc_final: 0.9062 (m90)
  outliers start: 15
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1537
  time to fit residues: 27.5708
Evaluate side-chains
  128 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  328 VAL
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  387 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 57 optimal weight:    7.9990
   chunk 66 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0970
   chunk 54 optimal weight:    6.9990
   chunk 3 optimal weight:    8.9990
   chunk 44 optimal weight:   10.0000
   chunk 67 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 41 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    4.8186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.107552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.081369 restraints weight = 18700.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.084986 restraints weight = 10918.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.087519 restraints weight = 7624.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6966  Z= 0.361
  Angle     :  0.723  10.596   9462  Z= 0.367
  Chirality :  0.047   0.194   1034
  Planarity :  0.005   0.047   1233
  Dihedral  :  9.138 166.648    959
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 19.10 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.28), residues: 854
  helix:  0.07 (0.25), residues: 386
  sheet: -1.25 (0.47), residues: 108
  loop : -0.10 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 103 
 HIS   0.005   0.001   HIS B 266 
 PHE   0.017   0.002   PHE A 169 
 TYR   0.015   0.002   TYR A 224 
 ARG   0.004   0.001   ARG B  79 

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7709 (tmm) cc_final: 0.7386 (tmm)
REVERT: A   71 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7770 (tt0)
REVERT: A  102 ASN cc_start: 0.9209 (t0) cc_final: 0.8557 (t0)
REVERT: A  425 MET cc_start: 0.8919 (mmm) cc_final: 0.8616 (mmm)
REVERT: B   26 ASP cc_start: 0.8867 (t70) cc_final: 0.8625 (t70)
REVERT: B   75 MET cc_start: 0.8959 (ppp) cc_final: 0.8409 (ppp)
REVERT: B   79 ARG cc_start: 0.8837 (mtm180) cc_final: 0.8372 (tpm170)
REVERT: B   94 PHE cc_start: 0.6452 (OUTLIER) cc_final: 0.6207 (t80)
REVERT: B  139 HIS cc_start: 0.8675 (p-80) cc_final: 0.8283 (p-80)
REVERT: B  149 MET cc_start: 0.8794 (mmp) cc_final: 0.8386 (mmp)
REVERT: B  166 MET cc_start: 0.8464 (tmm) cc_final: 0.7723 (tmm)
REVERT: B  235 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8279 (tmm)
REVERT: B  272 PHE cc_start: 0.9000 (t80) cc_final: 0.8568 (t80)
REVERT: B  329 ASP cc_start: 0.8877 (m-30) cc_final: 0.8632 (m-30)
REVERT: B  388 PHE cc_start: 0.8114 (m-80) cc_final: 0.7834 (m-80)
REVERT: B  406 HIS cc_start: 0.9303 (m90) cc_final: 0.9088 (m90)
  outliers start: 20
  outliers final: 12
  residues processed: 128
  average time/residue: 0.1624
  time to fit residues: 29.2072
Evaluate side-chains
  132 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 CYS
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  198 THR
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  387 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0060
   chunk 65 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    1.8002

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.110905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.084629 restraints weight = 18220.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.088352 restraints weight = 10748.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.090940 restraints weight = 7501.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6966  Z= 0.210
  Angle     :  0.709  10.107   9462  Z= 0.348
  Chirality :  0.046   0.242   1034
  Planarity :  0.005   0.055   1233
  Dihedral  :  8.959 165.983    959
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 20.46 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.28), residues: 854
  helix:  0.23 (0.25), residues: 385
  sheet: -1.14 (0.49), residues: 107
  loop : -0.13 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 103 
 HIS   0.003   0.001   HIS A 283 
 PHE   0.026   0.002   PHE A 135 
 TYR   0.009   0.001   TYR B 432 
 ARG   0.003   0.000   ARG B  79 

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.822 
Fit side-chains
   revert: symmetry clash
REVERT: A   36 MET cc_start: 0.7590 (tmm) cc_final: 0.7350 (tmm)
REVERT: A   71 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7587 (tm-30)
REVERT: A  102 ASN cc_start: 0.9091 (t0) cc_final: 0.8379 (t0)
REVERT: B   75 MET cc_start: 0.8968 (ppp) cc_final: 0.8709 (ppp)
REVERT: B   94 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.6207 (t80)
REVERT: B  149 MET cc_start: 0.8749 (mmp) cc_final: 0.8362 (mmp)
REVERT: B  166 MET cc_start: 0.8518 (tmm) cc_final: 0.7665 (tmm)
REVERT: B  235 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8213 (tmm)
REVERT: B  272 PHE cc_start: 0.8987 (t80) cc_final: 0.8501 (t80)
REVERT: B  329 ASP cc_start: 0.8858 (m-30) cc_final: 0.8570 (m-30)
REVERT: B  388 PHE cc_start: 0.8068 (m-80) cc_final: 0.7799 (m-80)
REVERT: B  406 HIS cc_start: 0.9286 (m90) cc_final: 0.9071 (m90)
  outliers start: 17
  outliers final: 11
  residues processed: 129
  average time/residue: 0.1634
  time to fit residues: 29.7184
Evaluate side-chains
  134 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 VAL
Chi-restraints excluded: chain A residue   71 GLU
Chi-restraints excluded: chain A residue   88 HIS
Chi-restraints excluded: chain A residue  262 TYR
Chi-restraints excluded: chain A residue  398 MET
Chi-restraints excluded: chain B residue   94 PHE
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  221 THR
Chi-restraints excluded: chain B residue  235 MET
Chi-restraints excluded: chain B residue  275 LEU
Chi-restraints excluded: chain B residue  305 CYS
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  387 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 58.1467 > 50:
  distance: 17 - 19:  14.526
  distance: 19 - 20:  20.522
  distance: 20 - 21:  31.739
  distance: 20 - 23:  21.491
  distance: 21 - 22:  32.601
  distance: 21 - 27:  21.943
  distance: 23 - 24:  22.954
  distance: 23 - 25:  26.387
  distance: 24 - 26:  13.983
  distance: 27 - 28:  21.427
  distance: 28 - 29:  17.063
  distance: 28 - 31:  10.790
  distance: 29 - 30:   8.853
  distance: 29 - 36:  14.935
  distance: 31 - 32:  36.204
  distance: 32 - 33:  11.396
  distance: 33 - 34:  30.114
  distance: 33 - 35:  15.588
  distance: 36 - 37:   8.634
  distance: 36 - 42:  13.342
  distance: 37 - 38:  12.475
  distance: 37 - 40:  13.495
  distance: 38 - 39:  15.570
  distance: 38 - 43:  15.716
  distance: 40 - 41:  22.236
  distance: 41 - 42:  23.526
  distance: 43 - 44:   9.178
  distance: 44 - 45:   4.295
  distance: 44 - 47:   8.161
  distance: 45 - 46:   5.218
  distance: 45 - 51:  17.215
  distance: 47 - 48:  19.189
  distance: 48 - 49:  10.982
  distance: 48 - 50:  10.387
  distance: 51 - 52:   5.151
  distance: 52 - 53:  24.096
  distance: 53 - 54:   6.089
  distance: 53 - 55:  17.077
  distance: 55 - 56:  10.216
  distance: 56 - 57:   6.972
  distance: 56 - 59:   6.381
  distance: 57 - 58:   6.771
  distance: 57 - 64:   4.326
  distance: 59 - 60:  26.939
  distance: 60 - 61:  15.244
  distance: 61 - 62:   8.351
  distance: 61 - 63:   9.336
  distance: 64 - 65:  30.922
  distance: 65 - 66:  31.722
  distance: 65 - 68:  29.357
  distance: 66 - 67:  22.199
  distance: 66 - 72:  12.276
  distance: 68 - 69:   9.099
  distance: 69 - 70:  40.519
  distance: 72 - 73:  12.619
  distance: 72 - 78:  26.786
  distance: 73 - 74:  20.627
  distance: 73 - 76:  24.360
  distance: 74 - 75:  31.135
  distance: 76 - 77:  16.898
  distance: 77 - 78:  19.285
  distance: 79 - 80:  12.497
  distance: 80 - 81:  14.793
  distance: 80 - 83:   9.782
  distance: 81 - 82:  15.370
  distance: 81 - 87:   7.407
  distance: 83 - 84:   7.794
  distance: 84 - 85:  10.730
  distance: 84 - 86:   9.321
  distance: 87 - 88:  18.420
  distance: 88 - 89:  19.133
  distance: 88 - 91:  11.143
  distance: 89 - 90:  20.474
  distance: 89 - 95:  12.836
  distance: 91 - 92:  15.038
  distance: 92 - 94:  11.455