Starting phenix.real_space_refine
on Thu Jul  2 07:30:06 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8djm_27461/07_2026/8djm_27461.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8djm_27461/07_2026/8djm_27461.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8djm_27461/07_2026/8djm_27461.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8djm_27461/07_2026/8djm_27461.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8djm_27461/07_2026/8djm_27461.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8djm_27461/07_2026/8djm_27461.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8djm_27461/07_2026/8djm_27461.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8djm_27461/07_2026/8djm_27461.cif"
  }
  resolution = 3.23
  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=   0.002 sd=   0.081
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    4601      2.51       5
     N    1114      2.21       5
     O    1281      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7032
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1871
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 7, 'TRANS': 229}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2152
          Classifications: {'peptide': 281}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 266}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 944
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 4, 'TRANS': 115}
    Chain: "L"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 808
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 930
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 930
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "A"
      Number of atoms: 214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 214
          Unusual residues: {'AJP': 1, 'Y01': 4}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 113
          Unusual residues: {'AJP': 1, 'Y01': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 19
  Time building chain proxies: 1.50, per 1000 atoms: 0.21
  Number of scatterers: 7032
  At special positions: 0
  Unit cell: (113.67, 101.04, 106.934, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1281      8.00
     N    1114      7.00
     C    4601      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  42 " - pdb=" SG  CYS L 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 255.0 milliseconds
  

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1606

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      67.6% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 0 through 16
    Processing helix  chain 'A' and resid 16 through 33
      removed outlier: 3.689A  pdb=" N   VAL A  20 " --> pdb=" O   HIS A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 85
      removed outlier: 3.734A  pdb=" N   ILE A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A  74 " --> pdb=" O   CYS A  70 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLN A  85 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 113
      removed outlier: 4.281A  pdb=" N   LEU A  92 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE A 101 " --> pdb=" O   LEU A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 132
      removed outlier: 3.700A  pdb=" N   LEU A 130 " --> pdb=" O   PRO A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 146
      removed outlier: 3.712A  pdb=" N   ALA A 137 " --> pdb=" O   ASP A 133 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA A 141 " --> pdb=" O   ALA A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 181
      removed outlier: 4.468A  pdb=" N   ARG A 154 " --> pdb=" O   GLN A 150 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   GLU A 155 " --> pdb=" O   ASP A 151 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE A 163 " --> pdb=" O   ARG A 159 " (cutoff:3.500A)
      Proline residue:  A 166  - end of helix
      removed outlier: 3.568A  pdb=" N   ASP A 171 " --> pdb=" O   THR A 167 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   CYS A 176 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 185
    Processing helix  chain 'A' and resid 187 through 223
      removed outlier: 3.572A  pdb=" N   CYS A 195 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE A 208 " --> pdb=" O   ASN A 204 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      Proline residue:  A 213  - end of helix
    Processing helix  chain 'A' and resid 235 through 247
      removed outlier: 4.716A  pdb=" N   VAL A 241 " --> pdb=" O   HIS A 237 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU A 242 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   GLU A 244 " --> pdb=" O   ARG A 240 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   GLU A 245 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 273
      removed outlier: 3.759A  pdb=" N   MET A 258 " --> pdb=" O   GLN A 254 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU A 266 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 47
    Processing helix  chain 'B' and resid 48 through 53
      removed outlier: 3.979A  pdb=" N   ALA B  52 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 77
      removed outlier: 4.615A  pdb=" N   THR B  63 " --> pdb=" O   SER B  59 " (cutoff:3.500A)
      Proline residue:  B  64  - end of helix
    Processing helix  chain 'B' and resid 80 through 106
      removed outlier: 3.720A  pdb=" N   LEU B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL B  85 " --> pdb=" O   PRO B  81 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL B  94 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL B 101 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   SER B 102 " --> pdb=" O   GLY B  98 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   TYR B 105 " --> pdb=" O   VAL B 101 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ASP B 106 " --> pdb=" O   SER B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 153
      removed outlier: 4.021A  pdb=" N   VAL B 131 " --> pdb=" O   GLU B 127 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   VAL B 132 " --> pdb=" O   PRO B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 165
    Processing helix  chain 'B' and resid 170 through 175
      removed outlier: 4.300A  pdb=" N   TYR B 174 " --> pdb=" O   GLY B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 182 through 208
      removed outlier: 3.852A  pdb=" N   LEU B 188 " --> pdb=" O   ALA B 184 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   ILE B 189 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ILE B 190 " --> pdb=" O   GLY B 186 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   THR B 193 " --> pdb=" O   ILE B 189 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLY B 195 " --> pdb=" O   LEU B 191 " (cutoff:3.500A)
      Proline residue:  B 196  - end of helix
    Processing helix  chain 'B' and resid 212 through 218
      removed outlier: 4.016A  pdb=" N   VAL B 216 " --> pdb=" O   ILE B 212 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA B 218 " --> pdb=" O   PRO B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 218 through 236
      removed outlier: 3.539A  pdb=" N   GLU B 226 " --> pdb=" O   ALA B 222 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ILE B 228 " --> pdb=" O   SER B 224 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ARG B 235 " --> pdb=" O   SER B 231 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASP B 236 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 236 through 244
    Processing helix  chain 'B' and resid 247 through 253
    Processing helix  chain 'B' and resid 253 through 279
      Proline residue:  B 268  - end of helix
      removed outlier: 3.527A  pdb=" N   THR B 277 " --> pdb=" O   SER B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 288
      Proline residue:  B 286  - end of helix
    Processing helix  chain 'B' and resid 289 through 299
    Processing helix  chain 'B' and resid 310 through 330
    Processing helix  chain 'C' and resid 265 through 286
    Processing helix  chain 'C' and resid 288 through 309
      removed outlier: 4.255A  pdb=" N   VAL C 292 " --> pdb=" O   ASN C 288 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   THR C 297 " --> pdb=" O   LYS C 293 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LYS C 308 " --> pdb=" O   LEU C 304 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA C 309 " --> pdb=" O   ASP C 305 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 311 through 315
      removed outlier: 3.713A  pdb=" N   GLU C 315 " --> pdb=" O   PRO C 312 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 321 through 346
    Processing helix  chain 'C' and resid 350 through 367
    Processing helix  chain 'C' and resid 367 through 383
      removed outlier: 4.023A  pdb=" N   SER C 377 " --> pdb=" O   GLU C 373 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LYS C 381 " --> pdb=" O   SER C 377 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLU C 382 " --> pdb=" O   THR C 378 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL C 383 " --> pdb=" O   LEU C 379 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 102
      removed outlier: 4.094A  pdb=" N   ILE L 102 " --> pdb=" O   SER L  99 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 81 through 84
      removed outlier: 3.863A  pdb=" N   LYS H  84 " --> pdb=" O   GLN H  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 81 through 84'
    Processing helix  chain 'H' and resid 106 through 109
    Processing sheet with id=AA1, first strand: chain 'L' and resid 23 through 25
    Processing sheet with id=AA2, first strand: chain 'L' and resid 38 through 39
    Processing sheet with id=AA3, first strand: chain 'L' and resid 72 through 73
      removed outlier: 6.803A  pdb=" N   TRP L  54 " --> pdb=" O   VAL L  66 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 22 through 25
    Processing sheet with id=AA5, first strand: chain 'H' and resid 29 through 30
      removed outlier: 6.493A  pdb=" N   GLU H  29 " --> pdb=" O   THR H 136 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'H' and resid 77 through 79
      removed outlier: 3.940A  pdb=" N   SER H  63 " --> pdb=" O   SER H  59 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   SER H  59 " --> pdb=" O   SER H  63 " (cutoff:3.500A)
      removed outlier: 6.730A  pdb=" N   TRP H  55 " --> pdb=" O   ILE H  67 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   TYR H 128 " --> pdb=" O   ARG H 117 " (cutoff:3.500A)

    418 hydrogen bonds defined for protein.
    1188 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: 1.19

  Time building geometry restraints manager: 0.61 seconds

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

  Histogram of bond lengths:
        1.00 -     1.20: 12
        1.20 -     1.40: 2776
        1.40 -     1.60: 4287
        1.60 -     1.81: 110
        1.81 -     2.01: 21
  Bond restraints: 7206
  Sorted by residual:
  bond pdb=" C07 AJP B 402 "
       pdb=" C08 AJP B 402 "
    ideal  model  delta    sigma   weight residual
    1.550  2.008 -0.458 2.00e-02 2.50e+03 5.25e+02
  bond pdb=" C07 AJP A 405 "
       pdb=" C08 AJP A 405 "
    ideal  model  delta    sigma   weight residual
    1.550  2.003 -0.453 2.00e-02 2.50e+03 5.13e+02
  bond pdb=" C01 AJP B 402 "
       pdb=" C02 AJP B 402 "
    ideal  model  delta    sigma   weight residual
    1.521  1.959 -0.438 2.00e-02 2.50e+03 4.79e+02
  bond pdb=" C01 AJP A 405 "
       pdb=" C02 AJP A 405 "
    ideal  model  delta    sigma   weight residual
    1.521  1.954 -0.433 2.00e-02 2.50e+03 4.69e+02
  bond pdb=" C02 AJP A 405 "
       pdb=" C03 AJP A 405 "
    ideal  model  delta    sigma   weight residual
    1.525  1.103  0.422 2.00e-02 2.50e+03 4.44e+02
  ... (remaining 7201 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.64: 9687
        4.64 -     9.27: 128
        9.27 -    13.91: 11
       13.91 -    18.54: 3
       18.54 -    23.18: 3
  Bond angle restraints: 9832
  Sorted by residual:
  angle pdb=" C   TRP L 113 "
        pdb=" CA  TRP L 113 "
        pdb=" CB  TRP L 113 "
      ideal   model   delta    sigma   weight residual
     108.68   85.50   23.18 1.39e+00 5.18e-01 2.78e+02
  angle pdb=" C   SER L  26 "
        pdb=" N   PRO L  27 "
        pdb=" CA  PRO L  27 "
      ideal   model   delta    sigma   weight residual
     120.51  104.02   16.49 1.26e+00 6.30e-01 1.71e+02
  angle pdb=" N   SER L  26 "
        pdb=" CA  SER L  26 "
        pdb=" C   SER L  26 "
      ideal   model   delta    sigma   weight residual
     109.81  128.99  -19.18 2.21e+00 2.05e-01 7.53e+01
  angle pdb=" N   PRO L  27 "
        pdb=" CA  PRO L  27 "
        pdb=" C   PRO L  27 "
      ideal   model   delta    sigma   weight residual
     112.01  100.76   11.25 1.84e+00 2.95e-01 3.74e+01
  angle pdb=" N   ILE C 368 "
        pdb=" CA  ILE C 368 "
        pdb=" C   ILE C 368 "
      ideal   model   delta    sigma   weight residual
     110.23  116.10   -5.87 1.04e+00 9.25e-01 3.18e+01
  ... (remaining 9827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.44: 3864
       22.44 -    44.87: 222
       44.87 -    67.31: 49
       67.31 -    89.74: 5
       89.74 -   112.18: 10
  Dihedral angle restraints: 4150
    sinusoidal: 1657
      harmonic: 2493
  Sorted by residual:
  dihedral pdb=" C   TRP L 113 "
           pdb=" N   TRP L 113 "
           pdb=" CA  TRP L 113 "
           pdb=" CB  TRP L 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -95.39  -27.21     0      2.50e+00 1.60e-01 1.18e+02
  dihedral pdb=" N   SER L  26 "
           pdb=" C   SER L  26 "
           pdb=" CA  SER L  26 "
           pdb=" CB  SER L  26 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.69  -15.89     0      2.50e+00 1.60e-01 4.04e+01
  dihedral pdb=" C   SER L  26 "
           pdb=" N   SER L  26 "
           pdb=" CA  SER L  26 "
           pdb=" CB  SER L  26 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.67   15.07     0      2.50e+00 1.60e-01 3.63e+01
  ... (remaining 4147 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.148: 1124
       1.148 -    2.295: 0
       2.295 -    3.443: 0
       3.443 -    4.590: 5
       4.590 -    5.738: 46
  Chirality restraints: 1175
  Sorted by residual:
  chirality pdb=" C20 AJP A 405 "
            pdb=" C15 AJP A 405 "
            pdb=" C19 AJP A 405 "
            pdb=" C21 AJP A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.96   -2.78    5.74 2.00e-01 2.50e+01 8.23e+02
  chirality pdb=" C20 AJP B 402 "
            pdb=" C15 AJP B 402 "
            pdb=" C19 AJP B 402 "
            pdb=" C21 AJP B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.96   -2.76    5.72 2.00e-01 2.50e+01 8.18e+02
  chirality pdb=" C16 AJP A 405 "
            pdb=" C11 AJP A 405 "
            pdb=" C15 AJP A 405 "
            pdb=" C17 AJP A 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.70    2.87   -5.57 2.00e-01 2.50e+01 7.75e+02
  ... (remaining 1172 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP L 113 "   -0.013 2.00e-02 2.50e+03   2.56e-02 6.54e+00
        pdb=" C   TRP L 113 "    0.044 2.00e-02 2.50e+03
        pdb=" O   TRP L 113 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   PRO L 114 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 367 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.91e+00
        pdb=" C   TYR C 367 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   TYR C 367 "    0.016 2.00e-02 2.50e+03
        pdb=" N   ILE C 368 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO L  27 "    0.008 2.00e-02 2.50e+03   1.62e-02 2.61e+00
        pdb=" C   PRO L  27 "   -0.028 2.00e-02 2.50e+03
        pdb=" O   PRO L  27 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ALA L  28 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 8
        2.45 -     3.07: 3841
        3.07 -     3.68: 10424
        3.68 -     4.29: 14629
        4.29 -     4.90: 25443
  Nonbonded interactions: 54345
  Sorted by model distance:
  nonbonded pdb=" N   PRO B 309 "
            pdb=" O   VAL C 383 "
     model   vdw
     1.844 3.120
  nonbonded pdb=" CA  PRO B 309 "
            pdb=" O   VAL C 383 "
     model   vdw
     2.320 3.470
  nonbonded pdb=" C04 AJP A 405 "
            pdb=" C85 AJP A 405 "
     model   vdw
     2.408 3.072
  nonbonded pdb=" C04 AJP B 402 "
            pdb=" C85 AJP B 402 "
     model   vdw
     2.416 3.072
  nonbonded pdb=" C03 AJP B 402 "
            pdb=" O84 AJP B 402 "
     model   vdw
     2.440 2.752
  ... (remaining 54340 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:             1.980
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.440
  Find NCS groups from input model:        0.050
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
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      :  0.029   0.458   7208  Z= 1.509
  Angle     :  1.526  23.179   9836  Z= 0.875
  Chirality :  1.041   5.738   1175
  Planarity :  0.004   0.038   1172
  Dihedral  : 15.984 112.177   2538
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  3.70 %
    Favored  : 95.47 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -2.26 (0.25), residues: 842
  helix: -0.85 (0.19), residues: 501
  sheet: -3.36 (0.36), residues: 110
  loop : -1.49 (0.40), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A   7 
 TYR   0.014   0.002   TYR B 150 
 PHE   0.014   0.002   PHE B 256 
 TRP   0.010   0.001   TRP H  66 
 HIS   0.004   0.001   HIS B  95 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.02898 /  1.51 ( 7206)
  covalent geometry    : angle       1.52598 /  0.87 ( 9832)
  SS BOND              : bond        0.00327 /  0.17 (    2)
  SS BOND              : angle       0.81940 /  0.44 (    4)
  hydrogen bonds       : bond        0.21774 / 14.85 (  418)
  hydrogen bonds       : angle       7.56211 /  5.31 ( 1188)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.7902 (mmm) cc_final: 0.7561 (tpp)
REVERT: B  325 PHE cc_start: 0.7150 (m-10) cc_final: 0.6947 (m-10)
REVERT: C  342 LEU cc_start: 0.8466 (tt) cc_final: 0.8212 (pp)
REVERT: L   43 ARG cc_start: 0.7443 (ttp-170) cc_final: 0.6648 (ttm-80)
REVERT: H   42 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7633 (tttp)
REVERT: H   51 TYR cc_start: 0.8871 (m-80) cc_final: 0.8591 (m-80)
REVERT: H   86 LYS cc_start: 0.7613 (ptpt) cc_final: 0.7295 (ptpt)
REVERT: H   88 THR cc_start: 0.7242 (p) cc_final: 0.6880 (p)
REVERT: H  101 GLU cc_start: 0.7664 (tt0) cc_final: 0.7253 (tt0)
  outliers start: 6
  outliers final: 4
  residues processed: 99
  average time/residue: 0.0867
  time to fit residues: 11.1181
Evaluate side-chains
  82 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain L residue   52 ILE
Chi-restraints excluded: chain H residue  121 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  79 GLN
B  95 HIS
B 316 ASN
C 272 ASN
C 277 ASN
C 279 ASN
C 337 GLN
C 380 GLN
L  25 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.194419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.126715 restraints weight = 7862.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 2.54
r_work: 0.3421 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7208  Z= 0.164
  Angle     :  1.392  34.455   9836  Z= 0.511
  Chirality :  0.141   2.061   1175
  Planarity :  0.004   0.036   1172
  Dihedral  :  9.702 105.180   1021
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  7.96 %
    Favored  : 90.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.29), residues: 842
  helix:  1.27 (0.23), residues: 504
  sheet: -2.16 (0.40), residues: 124
  loop : -1.10 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 118 
 TYR   0.014   0.001   TYR B 174 
 PHE   0.012   0.001   PHE B 107 
 TRP   0.014   0.001   TRP C 273 
 HIS   0.002   0.001   HIS B 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.16 ( 7206)
  covalent geometry    : angle       1.39203 /  0.51 ( 9832)
  SS BOND              : bond        0.00366 /  0.17 (    2)
  SS BOND              : angle       0.72347 /  0.52 (    4)
  hydrogen bonds       : bond        0.04258 /  2.86 (  418)
  hydrogen bonds       : angle       4.46101 /  3.14 ( 1188)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7908 (mp)
REVERT: A  152 GLU cc_start: 0.6755 (tp30) cc_final: 0.6352 (tp30)
REVERT: A  218 LEU cc_start: 0.8314 (tp) cc_final: 0.8066 (mp)
REVERT: C  342 LEU cc_start: 0.8362 (tt) cc_final: 0.8125 (pp)
REVERT: L   43 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7040 (ttm-80)
REVERT: H   42 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7719 (tttm)
REVERT: H   86 LYS cc_start: 0.8263 (ptpt) cc_final: 0.7993 (ptpt)
  outliers start: 10
  outliers final: 9
  residues processed: 94
  average time/residue: 0.0716
  time to fit residues: 9.1461
Evaluate side-chains
  90 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain L residue   32 VAL
Chi-restraints excluded: chain L residue   52 ILE
Chi-restraints excluded: chain L residue  112 SER
Chi-restraints excluded: chain L residue  116 THR
Chi-restraints excluded: chain H residue  116 VAL
Chi-restraints excluded: chain H residue  121 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 56 optimal weight:    7.9990
   chunk 25 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 77 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0870
   chunk 3 optimal weight:   20.0000
   chunk 54 optimal weight:    6.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.5758

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  95 HIS
B  99 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.195771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.140241 restraints weight = 7789.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 2.65
r_work: 0.3245 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7208  Z= 0.124
  Angle     :  1.327  32.570   9836  Z= 0.478
  Chirality :  0.141   2.040   1175
  Planarity :  0.004   0.034   1172
  Dihedral  :  9.251 111.017   1019
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  8.78 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.30), residues: 842
  helix:  1.84 (0.23), residues: 505
  sheet: -1.50 (0.46), residues: 122
  loop : -1.02 (0.43), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.014   0.001   TYR H  79 
 PHE   0.012   0.001   PHE B 213 
 TRP   0.024   0.001   TRP C 273 
 HIS   0.002   0.000   HIS B 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 ( 7206)
  covalent geometry    : angle       1.32697 /  0.48 ( 9832)
  SS BOND              : bond        0.00211 /  0.10 (    2)
  SS BOND              : angle       0.48271 /  0.36 (    4)
  hydrogen bonds       : bond        0.03419 /  2.31 (  418)
  hydrogen bonds       : angle       3.95297 /  2.81 ( 1188)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7976 (mp)
REVERT: A  152 GLU cc_start: 0.6673 (tp30) cc_final: 0.6298 (tp30)
REVERT: C  342 LEU cc_start: 0.8330 (tt) cc_final: 0.8094 (pp)
REVERT: L   43 ARG cc_start: 0.7646 (ttp-170) cc_final: 0.7061 (ttm-80)
REVERT: H   86 LYS cc_start: 0.8342 (ptpt) cc_final: 0.8059 (ptpt)
  outliers start: 11
  outliers final: 8
  residues processed: 99
  average time/residue: 0.0742
  time to fit residues: 10.0610
Evaluate side-chains
  93 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain L residue   32 VAL
Chi-restraints excluded: chain L residue   52 ILE
Chi-restraints excluded: chain L residue  112 SER
Chi-restraints excluded: chain H residue  121 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 55 optimal weight:    0.0000
   chunk 0 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    0.9190

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  95 HIS
B  99 ASN
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.193181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.138061 restraints weight = 7934.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 2.71
r_work: 0.3225 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8317
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7208  Z= 0.148
  Angle     :  1.336  33.091   9836  Z= 0.484
  Chirality :  0.141   2.022   1175
  Planarity :  0.004   0.035   1172
  Dihedral  :  9.183 109.580   1019
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.60 %
    Favored  : 88.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.30), residues: 842
  helix:  1.84 (0.23), residues: 504
  sheet: -1.26 (0.46), residues: 121
  loop : -0.98 (0.43), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.017   0.001   TYR H  79 
 PHE   0.012   0.001   PHE B 213 
 TRP   0.017   0.001   TRP C 273 
 HIS   0.002   0.001   HIS B 230 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00359 /  0.15 ( 7206)
  covalent geometry    : angle       1.33623 /  0.48 ( 9832)
  SS BOND              : bond        0.00266 /  0.13 (    2)
  SS BOND              : angle       0.55619 /  0.46 (    4)
  hydrogen bonds       : bond        0.03630 /  2.45 (  418)
  hydrogen bonds       : angle       3.94353 /  2.82 ( 1188)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A  100 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7958 (mp)
REVERT: A  152 GLU cc_start: 0.6714 (tp30) cc_final: 0.6349 (tp30)
REVERT: C  304 LEU cc_start: 0.8000 (tp) cc_final: 0.7647 (mm)
REVERT: C  342 LEU cc_start: 0.8258 (tt) cc_final: 0.8032 (pp)
REVERT: L   43 ARG cc_start: 0.7649 (ttp-170) cc_final: 0.7022 (ttm-80)
  outliers start: 15
  outliers final: 13
  residues processed: 99
  average time/residue: 0.0820
  time to fit residues: 11.1715
Evaluate side-chains
  102 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  242 GLU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain L residue   32 VAL
Chi-restraints excluded: chain L residue   52 ILE
Chi-restraints excluded: chain L residue  112 SER
Chi-restraints excluded: chain H residue  116 VAL
Chi-restraints excluded: chain H residue  121 ASP
Chi-restraints excluded: chain H residue  137 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    0.0870
   chunk 47 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0020
   chunk 64 optimal weight:    5.9990
   chunk 13 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.5366

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 277 ASN
** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 354 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.195506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.139202 restraints weight = 7865.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.77
r_work: 0.3215 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7208  Z= 0.114
  Angle     :  1.313  32.469   9836  Z= 0.471
  Chirality :  0.141   2.013   1175
  Planarity :  0.004   0.037   1172
  Dihedral  :  9.005 110.734   1019
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  :  9.88 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.30), residues: 842
  helix:  1.90 (0.23), residues: 514
  sheet: -1.16 (0.47), residues: 122
  loop : -0.83 (0.44), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.018   0.001   TYR H  79 
 PHE   0.010   0.001   PHE B 213 
 TRP   0.032   0.001   TRP C 273 
 HIS   0.001   0.000   HIS B 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.11 ( 7206)
  covalent geometry    : angle       1.31320 /  0.47 ( 9832)
  SS BOND              : bond        0.00224 /  0.11 (    2)
  SS BOND              : angle       0.40725 /  0.31 (    4)
  hydrogen bonds       : bond        0.03100 /  2.11 (  418)
  hydrogen bonds       : angle       3.75378 /  2.68 ( 1188)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  100 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7996 (mp)
REVERT: A  152 GLU cc_start: 0.6689 (tp30) cc_final: 0.6330 (tp30)
REVERT: C  273 TRP cc_start: 0.5769 (t-100) cc_final: 0.5536 (t-100)
REVERT: C  304 LEU cc_start: 0.8030 (tp) cc_final: 0.7693 (mm)
REVERT: C  342 LEU cc_start: 0.8234 (tt) cc_final: 0.8016 (pp)
REVERT: C  370 LYS cc_start: 0.5434 (pptt) cc_final: 0.4744 (ptpt)
REVERT: L   43 ARG cc_start: 0.7601 (ttp-170) cc_final: 0.7018 (ttm-80)
  outliers start: 15
  outliers final: 9
  residues processed: 101
  average time/residue: 0.0872
  time to fit residues: 12.0237
Evaluate side-chains
  96 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain L residue   32 VAL
Chi-restraints excluded: chain L residue   52 ILE
Chi-restraints excluded: chain L residue  112 SER
Chi-restraints excluded: chain L residue  116 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:   20.0000
   chunk 47 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0050
   chunk 3 optimal weight:    0.0670
   chunk 64 optimal weight:    5.9990
   chunk 56 optimal weight:   20.0000
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.6734

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 277 ASN
** C 279 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 = 0.4181 r_free = 0.4181 target = 0.193804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.138223 restraints weight = 7951.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.57
r_work: 0.3224 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7208  Z= 0.124
  Angle     :  1.317  32.758   9836  Z= 0.473
  Chirality :  0.141   2.010   1175
  Planarity :  0.004   0.040   1172
  Dihedral  :  8.800 110.354   1017
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 11.11 %
    Favored  : 87.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.30), residues: 842
  helix:  1.96 (0.23), residues: 513
  sheet: -1.00 (0.48), residues: 122
  loop : -0.81 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.018   0.001   TYR H  79 
 PHE   0.011   0.001   PHE B 213 
 TRP   0.020   0.001   TRP C 273 
 HIS   0.002   0.001   HIS H  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.12 ( 7206)
  covalent geometry    : angle       1.31712 /  0.47 ( 9832)
  SS BOND              : bond        0.00244 /  0.12 (    2)
  SS BOND              : angle       0.53288 /  0.45 (    4)
  hydrogen bonds       : bond        0.03234 /  2.20 (  418)
  hydrogen bonds       : angle       3.75122 /  2.67 ( 1188)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8129 (mp)
REVERT: A  152 GLU cc_start: 0.6644 (tp30) cc_final: 0.6333 (tp30)
REVERT: B   50 VAL cc_start: 0.8178 (OUTLIER) cc_final: 0.7939 (t)
REVERT: L   43 ARG cc_start: 0.7566 (ttp-170) cc_final: 0.6997 (ttm-80)
  outliers start: 13
  outliers final: 8
  residues processed: 93
  average time/residue: 0.0933
  time to fit residues: 11.6750
Evaluate side-chains
  91 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain L residue   32 VAL
Chi-restraints excluded: chain L residue   52 ILE
Chi-restraints excluded: chain L residue  112 SER
Chi-restraints excluded: chain L residue  116 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 72 optimal weight:    0.1980
   chunk 26 optimal weight:    0.0000
   chunk 32 optimal weight:    1.9990
   chunk 57 optimal weight:   20.0000
   chunk 66 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 75 optimal weight:    0.3980
   chunk 34 optimal weight:    0.5980
   chunk 48 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 279 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 = 0.4200 r_free = 0.4200 target = 0.195959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.139724 restraints weight = 7846.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.49
r_work: 0.3264 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   7208  Z= 0.103
  Angle     :  1.308  32.297   9836  Z= 0.467
  Chirality :  0.141   2.008   1175
  Planarity :  0.004   0.040   1172
  Dihedral  :  8.684 111.692   1017
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.80 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.30), residues: 842
  helix:  2.14 (0.23), residues: 512
  sheet: -0.90 (0.48), residues: 122
  loop : -0.74 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.017   0.001   TYR H  79 
 PHE   0.009   0.001   PHE B 213 
 TRP   0.020   0.001   TRP C 273 
 HIS   0.001   0.000   HIS H  99 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00228 /  0.10 ( 7206)
  covalent geometry    : angle       1.30801 /  0.47 ( 9832)
  SS BOND              : bond        0.00218 /  0.10 (    2)
  SS BOND              : angle       0.38072 /  0.31 (    4)
  hydrogen bonds       : bond        0.02868 /  1.95 (  418)
  hydrogen bonds       : angle       3.64263 /  2.59 ( 1188)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 GLU cc_start: 0.6515 (tp30) cc_final: 0.6269 (tp30)
REVERT: B   50 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7901 (t)
REVERT: B  290 ILE cc_start: 0.7780 (OUTLIER) cc_final: 0.7427 (mt)
REVERT: C  370 LYS cc_start: 0.5278 (pptt) cc_final: 0.4665 (ptpt)
REVERT: L   29 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.9000 (mt)
REVERT: L   43 ARG cc_start: 0.7529 (ttp-170) cc_final: 0.6981 (ttm-80)
  outliers start: 11
  outliers final: 6
  residues processed: 95
  average time/residue: 0.0929
  time to fit residues: 12.0348
Evaluate side-chains
  91 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   32 VAL
Chi-restraints excluded: chain L residue   52 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0370
   chunk 43 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.8660

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 247 ASN
** C 279 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 = 0.4179 r_free = 0.4179 target = 0.193523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.133581 restraints weight = 7958.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 2.54
r_work: 0.3244 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7208  Z= 0.142
  Angle     :  1.331  32.965   9836  Z= 0.480
  Chirality :  0.141   2.005   1175
  Planarity :  0.004   0.040   1172
  Dihedral  :  8.709 110.718   1017
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.93 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.35 (0.30), residues: 842
  helix:  2.04 (0.23), residues: 512
  sheet: -1.06 (0.47), residues: 124
  loop : -0.71 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.017   0.001   TYR H  79 
 PHE   0.012   0.001   PHE B 213 
 TRP   0.020   0.001   TRP C 273 
 HIS   0.002   0.001   HIS B 230 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.14 ( 7206)
  covalent geometry    : angle       1.33154 /  0.48 ( 9832)
  SS BOND              : bond        0.00287 /  0.14 (    2)
  SS BOND              : angle       0.54721 /  0.46 (    4)
  hydrogen bonds       : bond        0.03382 /  2.29 (  418)
  hydrogen bonds       : angle       3.81867 /  2.73 ( 1188)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A  152 GLU cc_start: 0.6613 (tp30) cc_final: 0.6312 (tp30)
REVERT: B   50 VAL cc_start: 0.8186 (OUTLIER) cc_final: 0.7941 (t)
REVERT: C  370 LYS cc_start: 0.5301 (pptt) cc_final: 0.4703 (ptpt)
REVERT: L   29 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8994 (mt)
REVERT: L   43 ARG cc_start: 0.7546 (ttp-170) cc_final: 0.7017 (ttm-80)
REVERT: L   80 ARG cc_start: 0.8166 (ptp-170) cc_final: 0.7823 (ptp-170)
  outliers start: 11
  outliers final: 9
  residues processed: 91
  average time/residue: 0.0909
  time to fit residues: 11.2161
Evaluate side-chains
  94 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   32 VAL
Chi-restraints excluded: chain L residue   52 ILE
Chi-restraints excluded: chain L residue  101 ASP
Chi-restraints excluded: chain L residue  116 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 82 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0060
   chunk 79 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    0.4980
   overall best weight:    0.5796

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 279 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 = 0.4190 r_free = 0.4190 target = 0.195002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.137446 restraints weight = 7888.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.64
r_work: 0.3228 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7208  Z= 0.118
  Angle     :  1.320  32.493   9836  Z= 0.474
  Chirality :  0.141   2.001   1175
  Planarity :  0.004   0.040   1172
  Dihedral  :  8.687 112.257   1017
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 12.07 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.30), residues: 842
  helix:  2.07 (0.23), residues: 512
  sheet: -0.94 (0.47), residues: 122
  loop : -0.63 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  96 
 TYR   0.016   0.001   TYR H  79 
 PHE   0.011   0.001   PHE B 213 
 TRP   0.019   0.001   TRP C 273 
 HIS   0.002   0.001   HIS B 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 ( 7206)
  covalent geometry    : angle       1.32009 /  0.47 ( 9832)
  SS BOND              : bond        0.00262 /  0.13 (    2)
  SS BOND              : angle       0.48424 /  0.40 (    4)
  hydrogen bonds       : bond        0.03068 /  2.08 (  418)
  hydrogen bonds       : angle       3.76571 /  2.70 ( 1188)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  152 GLU cc_start: 0.6643 (tp30) cc_final: 0.6354 (tp30)
REVERT: B   50 VAL cc_start: 0.8164 (OUTLIER) cc_final: 0.7927 (t)
REVERT: C  299 MET cc_start: 0.7099 (mmp) cc_final: 0.6795 (mtp)
REVERT: C  370 LYS cc_start: 0.5251 (pptt) cc_final: 0.4639 (ptpt)
REVERT: L   29 ILE cc_start: 0.9266 (OUTLIER) cc_final: 0.9008 (mt)
REVERT: L   43 ARG cc_start: 0.7491 (ttp-170) cc_final: 0.6923 (ttm-80)
  outliers start: 10
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0850
  time to fit residues: 10.3661
Evaluate side-chains
  90 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 CYS
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   32 VAL
Chi-restraints excluded: chain L residue   52 ILE
Chi-restraints excluded: chain L residue  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 69 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0010
   chunk 65 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   chunk 48 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.6186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 279 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 = 0.4185 r_free = 0.4185 target = 0.194830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.137800 restraints weight = 7865.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3552 rms_B_bonded: 2.61
r_work: 0.3227 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7208  Z= 0.122
  Angle     :  1.321  32.644   9836  Z= 0.475
  Chirality :  0.141   2.004   1175
  Planarity :  0.004   0.039   1172
  Dihedral  :  8.673 112.106   1017
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.80 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.30), residues: 842
  helix:  2.07 (0.23), residues: 512
  sheet: -1.02 (0.47), residues: 124
  loop : -0.57 (0.46), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.017   0.001   TYR H  79 
 PHE   0.011   0.001   PHE B 213 
 TRP   0.018   0.001   TRP C 273 
 HIS   0.002   0.001   HIS B 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.12 ( 7206)
  covalent geometry    : angle       1.32169 /  0.48 ( 9832)
  SS BOND              : bond        0.00237 /  0.12 (    2)
  SS BOND              : angle       0.45532 /  0.38 (    4)
  hydrogen bonds       : bond        0.03140 /  2.13 (  418)
  hydrogen bonds       : angle       3.75938 /  2.69 ( 1188)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  152 GLU cc_start: 0.6619 (tp30) cc_final: 0.6365 (tp30)
REVERT: B   50 VAL cc_start: 0.8190 (OUTLIER) cc_final: 0.7956 (t)
REVERT: C  299 MET cc_start: 0.7082 (mmp) cc_final: 0.6846 (mtp)
REVERT: C  370 LYS cc_start: 0.5175 (pptt) cc_final: 0.4559 (ptpt)
REVERT: L   29 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9007 (mt)
REVERT: L   43 ARG cc_start: 0.7481 (ttp-170) cc_final: 0.6909 (ttm-80)
  outliers start: 12
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0761
  time to fit residues: 9.3204
Evaluate side-chains
  93 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  231 SER
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  290 ILE
Chi-restraints excluded: chain L residue   29 ILE
Chi-restraints excluded: chain L residue   32 VAL
Chi-restraints excluded: chain L residue   52 ILE
Chi-restraints excluded: chain L residue  101 ASP
Chi-restraints excluded: chain L residue  112 SER
Chi-restraints excluded: chain L residue  116 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 71 optimal weight:    0.6980
   chunk 70 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0070
   chunk 15 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.5998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 279 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 = 0.4193 r_free = 0.4193 target = 0.195620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.137725 restraints weight = 7835.346|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.52
r_work: 0.3252 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7208  Z= 0.119
  Angle     :  1.318  32.551   9836  Z= 0.474
  Chirality :  0.141   2.001   1175
  Planarity :  0.004   0.040   1172
  Dihedral  :  8.666 112.682   1017
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.07 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.30), residues: 842
  helix:  2.11 (0.23), residues: 512
  sheet: -1.00 (0.47), residues: 124
  loop : -0.56 (0.46), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  96 
 TYR   0.012   0.001   TYR B 139 
 PHE   0.011   0.001   PHE B 213 
 TRP   0.018   0.001   TRP C 273 
 HIS   0.002   0.000   HIS B 278 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 7206)
  covalent geometry    : angle       1.31796 /  0.47 ( 9832)
  SS BOND              : bond        0.00260 /  0.13 (    2)
  SS BOND              : angle       0.45466 /  0.37 (    4)
  hydrogen bonds       : bond        0.03086 /  2.09 (  418)
  hydrogen bonds       : angle       3.73694 /  2.68 ( 1188)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1784.59 seconds
wall clock time: 31 minutes 19.02 seconds (1879.02 seconds total)