Starting phenix.real_space_refine
on Fri Mar 14 02:16:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzr_41767/03_2025/8tzr_41767.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzr_41767/03_2025/8tzr_41767.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tzr_41767/03_2025/8tzr_41767.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzr_41767/03_2025/8tzr_41767.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzr_41767/03_2025/8tzr_41767.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzr_41767/03_2025/8tzr_41767.cif"
  }
  resolution = 3.5
  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=   0.006 sd=   0.060
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       1      5.49       5
     S      72      5.16       5
     C    5668      2.51       5
     N    1479      2.21       5
     O    1601      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8821
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2453
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 12, 'TRANS': 300}
    Chain: "B"
      Number of atoms: 4010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 4010
          Classifications: {'peptide': 493}
          Link IDs: {'PTRANS': 21, 'TRANS': 471}
    Chain: "C"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2218
          Classifications: {'peptide': 273}
          Link IDs: {'PTRANS': 11, 'TRANS': 261}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 83
          Unusual residues: {'BMA': 1, 'GLC': 1, 'MAN': 3, 'NAG': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'PAM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PAM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 40
          Unusual residues: {'POV': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 12
  Time building chain proxies: 5.83, per 1000 atoms: 0.66
  Number of scatterers: 8821
  At special positions: 0
  Unit cell: (97.11, 121.18, 135.29, 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      72     16.00
     P       1     15.00
     O    1601      8.00
     N    1479      7.00
     C    5668      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  42 " - pdb=" SG  CYS A  56 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS A  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 136 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 138 " - pdb=" SG  CYS A 155 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 205 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 281 " - pdb=" SG  CYS A 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 297 " - pdb=" SG  CYS A 307 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 311 " - pdb=" SG  CYS A 351 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 327 " - pdb=" SG  CYS A 342 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 329 " - pdb=" SG  CYS A 339 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 334 " - pdb=" SG  CYS A 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  71 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 162 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 105 " - pdb=" SG  CYS C 137 " 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=1, symmetry=0
  Links applied
    ALPHA1-2
      " MAN D   4 " - " MAN D   5 "
      " MAN D   5 " - " MAN D   6 "
    ALPHA1-3
      " BMA D   3 " - " MAN D   4 "
      " MAN D   6 " - " GLC D   7 "
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
    NAG-ASN
      " NAG D   1 " - " ASN A 298 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.60
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2000

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      43.4% alpha, 22.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 49 through 59
    Processing helix  chain 'A' and resid 61 through 81
      removed outlier: 4.595A  pdb=" N   SER A  65 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   PHE A  81 " --> pdb=" O   CYS A  77 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 104
      removed outlier: 3.742A  pdb=" N   LEU A 102 " --> pdb=" O   GLY A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 130
    Processing helix  chain 'A' and resid 149 through 154
    Processing helix  chain 'A' and resid 156 through 159
      removed outlier: 3.903A  pdb=" N   ILE A 159 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 156 through 159'
    Processing helix  chain 'A' and resid 160 through 171
    Processing helix  chain 'A' and resid 172 through 175
      removed outlier: 3.612A  pdb=" N   ASN A 175 " --> pdb=" O   ALA A 172 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 172 through 175'
    Processing helix  chain 'A' and resid 178 through 198
    Processing helix  chain 'A' and resid 223 through 237
      removed outlier: 3.533A  pdb=" N   ILE A 227 " --> pdb=" O   ASP A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 311
    Processing helix  chain 'B' and resid 4 through 9
      removed outlier: 3.782A  pdb=" N   ASN B   8 " --> pdb=" O   ALA B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 10 through 35
      removed outlier: 4.031A  pdb=" N   GLY B  32 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 81
    Processing helix  chain 'B' and resid 121 through 125
      removed outlier: 4.256A  pdb=" N   GLN B 125 " --> pdb=" O   LEU B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 173
      removed outlier: 3.591A  pdb=" N   GLU B 173 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 258
      removed outlier: 3.811A  pdb=" N   LYS B 232 " --> pdb=" O   GLY B 228 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   PHE B 240 " --> pdb=" O   ALA B 236 " (cutoff:3.500A)
      Proline residue:  B 243  - end of helix
    Processing helix  chain 'B' and resid 264 through 282
    Processing helix  chain 'B' and resid 283 through 288
    Processing helix  chain 'B' and resid 295 through 321
      removed outlier: 3.683A  pdb=" N   PHE B 307 " --> pdb=" O   ARG B 303 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   SER B 313 " --> pdb=" O   ALA B 309 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ILE B 316 " --> pdb=" O   LEU B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 334
      removed outlier: 3.599A  pdb=" N   GLY B 334 " --> pdb=" O   HIS B 331 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 331 through 334'
    Processing helix  chain 'B' and resid 335 through 358
      Proline residue:  B 341  - end of helix
    Processing helix  chain 'B' and resid 359 through 362
    Processing helix  chain 'B' and resid 367 through 370
    Processing helix  chain 'B' and resid 371 through 412
    Processing helix  chain 'B' and resid 413 through 417
      removed outlier: 3.769A  pdb=" N   MET B 417 " --> pdb=" O   LEU B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 456
    Processing helix  chain 'B' and resid 469 through 492
    Processing helix  chain 'C' and resid 32 through 36
    Processing helix  chain 'C' and resid 196 through 200
    Processing helix  chain 'C' and resid 302 through 307
      removed outlier: 3.722A  pdb=" N   ILE C 305 " --> pdb=" O   ASP C 302 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   TYR C 306 " --> pdb=" O   PRO C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 335 through 377
      removed outlier: 4.587A  pdb=" N   VAL C 349 " --> pdb=" O   GLU C 345 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   THR C 350 " --> pdb=" O   THR C 346 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ALA C 352 " --> pdb=" O   GLY C 348 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ALA C 353 " --> pdb=" O   VAL C 349 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LYS C 377 " --> pdb=" O   ASP C 373 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 206
    Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 258
      removed outlier: 3.661A  pdb=" N   TYR A 273 " --> pdb=" O   SER A 239 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 319 through 326
    Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 46
      removed outlier: 3.615A  pdb=" N   HIS B 225 " --> pdb=" O   THR B  41 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU B 215 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 6.984A  pdb=" N   ASP B 117 " --> pdb=" O   LYS B 217 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   ILE B 219 " --> pdb=" O   GLN B 115 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   GLN B 115 " --> pdb=" O   ILE B 219 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   LEU B 221 " --> pdb=" O   ILE B 113 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ILE B 113 " --> pdb=" O   LEU B 221 " (cutoff:3.500A)
      removed outlier: 4.365A  pdb=" N   GLY B 223 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   LEU B 111 " --> pdb=" O   GLY B 223 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   MET B 110 " --> pdb=" O   GLU B 186 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   GLU B 186 " --> pdb=" O   MET B 110 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   PHE B 112 " --> pdb=" O   PHE B 184 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 73 through 74
      removed outlier: 4.165A  pdb=" N   LYS B  49 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   ARG B 200 " --> pdb=" O   ASP B 135 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   VAL B 132 " --> pdb=" O   PRO B 157 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   MET B 134 " --> pdb=" O   ARG B 155 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ARG B 155 " --> pdb=" O   MET B 134 " (cutoff:3.500A)
      removed outlier: 6.872A  pdb=" N   VAL B 136 " --> pdb=" O   HIS B 153 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   HIS B 153 " --> pdb=" O   VAL B 136 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   LEU B 138 " --> pdb=" O   MET B 151 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 459 through 462
    Processing sheet with id=AA7, first strand: chain 'C' and resid 21 through 25
    Processing sheet with id=AA8, first strand: chain 'C' and resid 21 through 25
      removed outlier: 4.272A  pdb=" N   PHE C 330 " --> pdb=" O   GLN C  94 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   GLN C  94 " --> pdb=" O   PHE C 330 " (cutoff:3.500A)
      removed outlier: 4.460A  pdb=" N   ILE C 332 " --> pdb=" O   VAL C  92 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL C  92 " --> pdb=" O   ILE C 332 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   THR C 181 " --> pdb=" O   ARG C 177 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   TYR C 182 " --> pdb=" O   SER C 193 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   SER C 193 " --> pdb=" O   TYR C 182 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   VAL C 184 " --> pdb=" O   VAL C 191 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 39
      removed outlier: 5.147A  pdb=" N   GLY C 312 " --> pdb=" O   PHE C  81 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   TRP C 319 " --> pdb=" O   GLY C 107 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 37 through 39
      removed outlier: 5.147A  pdb=" N   GLY C 312 " --> pdb=" O   PHE C  81 " (cutoff:3.500A)

    459 hydrogen bonds defined for protein.
    1275 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: 2.72

  Time building geometry restraints manager: 3.02 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1414
        1.31 -     1.43: 2568
        1.43 -     1.56: 4962
        1.56 -     1.69: 6
        1.69 -     1.81: 105
  Bond restraints: 9055
  Sorted by residual:
  bond pdb=" C21 POV B 601 "
       pdb=" O21 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.330  1.419 -0.089 2.00e-02 2.50e+03 2.00e+01
  bond pdb=" C31 POV B 601 "
       pdb=" O31 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.327  1.415 -0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb="C210 POV B 601 "
       pdb="C211 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.497  1.557 -0.060 2.00e-02 2.50e+03 9.10e+00
  bond pdb=" C4  BMA D   3 "
       pdb=" C5  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.528  1.586 -0.058 2.00e-02 2.50e+03 8.47e+00
  bond pdb=" N   POV B 601 "
       pdb=" C14 POV B 601 "
    ideal  model  delta    sigma   weight residual
    1.490  1.433  0.057 2.00e-02 2.50e+03 8.13e+00
  ... (remaining 9050 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 11997
        2.66 -     5.33: 198
        5.33 -     7.99: 23
        7.99 -    10.65: 7
       10.65 -    13.31: 3
  Bond angle restraints: 12228
  Sorted by residual:
  angle pdb=" CA  PRO B  82 "
        pdb=" N   PRO B  82 "
        pdb=" CD  PRO B  82 "
      ideal   model   delta    sigma   weight residual
     112.00  105.50    6.50 1.40e+00 5.10e-01 2.16e+01
  angle pdb=" N   PHE A 331 "
        pdb=" CA  PHE A 331 "
        pdb=" C   PHE A 331 "
      ideal   model   delta    sigma   weight residual
     110.91  115.92   -5.01 1.17e+00 7.31e-01 1.83e+01
  angle pdb=" CG  ARG B 141 "
        pdb=" CD  ARG B 141 "
        pdb=" NE  ARG B 141 "
      ideal   model   delta    sigma   weight residual
     112.00  120.80   -8.80 2.20e+00 2.07e-01 1.60e+01
  angle pdb=" O13 POV B 601 "
        pdb=" P   POV B 601 "
        pdb=" O14 POV B 601 "
      ideal   model   delta    sigma   weight residual
     121.11  109.51   11.60 3.00e+00 1.11e-01 1.50e+01
  angle pdb=" CA  LEU C 367 "
        pdb=" CB  LEU C 367 "
        pdb=" CG  LEU C 367 "
      ideal   model   delta    sigma   weight residual
     116.30  129.61  -13.31 3.50e+00 8.16e-02 1.45e+01
  ... (remaining 12223 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.66: 5027
       23.66 -    47.33: 341
       47.33 -    70.99: 68
       70.99 -    94.65: 23
       94.65 -   118.31: 4
  Dihedral angle restraints: 5463
    sinusoidal: 2354
      harmonic: 3109
  Sorted by residual:
  dihedral pdb=" CB  CYS A 327 "
           pdb=" SG  CYS A 327 "
           pdb=" SG  CYS A 342 "
           pdb=" CB  CYS A 342 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.31  -59.31     1      1.00e+01 1.00e-02 4.70e+01
  dihedral pdb=" CB  CYS A 128 "
           pdb=" SG  CYS A 128 "
           pdb=" SG  CYS A 136 "
           pdb=" CB  CYS A 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -144.59   58.59     1      1.00e+01 1.00e-02 4.60e+01
  dihedral pdb=" CB  CYS A 297 "
           pdb=" SG  CYS A 297 "
           pdb=" SG  CYS A 307 "
           pdb=" CB  CYS A 307 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.62  -53.62     1      1.00e+01 1.00e-02 3.91e+01
  ... (remaining 5460 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 922
       0.044 -    0.087: 283
       0.087 -    0.131: 83
       0.131 -    0.175: 9
       0.175 -    0.219: 5
  Chirality restraints: 1302
  Sorted by residual:
  chirality pdb=" CA  PRO B  82 "
            pdb=" N   PRO B  82 "
            pdb=" C   PRO B  82 "
            pdb=" CB  PRO B  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.48    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" C2  NAG D   1 "
            pdb=" C1  NAG D   1 "
            pdb=" C3  NAG D   1 "
            pdb=" N2  NAG D   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.29   -0.20 2.00e-01 2.50e+01 9.74e-01
  ... (remaining 1299 not shown)

  Planarity restraints: 1551
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B  81 "    0.062 5.00e-02 4.00e+02   9.10e-02 1.32e+01
        pdb=" N   PRO B  82 "   -0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO B  82 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO B  82 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B  36 "   -0.042 5.00e-02 4.00e+02   6.50e-02 6.75e+00
        pdb=" N   PRO B  37 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO B  37 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B  37 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 252 "    0.008 2.00e-02 2.50e+03   1.46e-02 5.30e+00
        pdb=" CG  TRP A 252 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 252 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 252 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 252 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 252 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 252 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 252 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 252 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 252 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1548 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1537
        2.76 -     3.30: 8693
        3.30 -     3.83: 14697
        3.83 -     4.37: 16452
        4.37 -     4.90: 29010
  Nonbonded interactions: 70389
  Sorted by model distance:
  nonbonded pdb=" NE1 TRP C 319 "
            pdb=" O4  BMA D   3 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" N   SER B 133 "
            pdb=" OD1 ASN B 210 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" NE2 HIS A 332 "
            pdb=" OE2 GLU B 205 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" NZ  LYS B  49 "
            pdb=" OD1 ASP B 218 "
     model   vdw
     2.326 3.120
  nonbonded pdb=" O   GLN C  70 "
            pdb=" OH  TYR C  75 "
     model   vdw
     2.329 3.040
  ... (remaining 70384 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:             4.410
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.530
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
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      :  0.006   0.089   9055  Z= 0.360
  Angle     :  0.839  13.314  12228  Z= 0.425
  Chirality :  0.047   0.219   1302
  Planarity :  0.005   0.091   1550
  Dihedral  : 16.976 118.313   3418
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 13.13 %
    Favored  : 86.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.25), residues: 1071
  helix:  1.16 (0.25), residues: 392
  sheet: -0.55 (0.36), residues: 205
  loop : -0.96 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 252 
 HIS   0.006   0.001   HIS A 113 
 PHE   0.026   0.002   PHE C 148 
 TYR   0.018   0.002   TYR B 140 
 ARG   0.009   0.001   ARG B 431 

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8496 (mm-30)
  outliers start: 5
  outliers final: 2
  residues processed: 115
  average time/residue: 0.2193
  time to fit residues: 35.1512
Evaluate side-chains
  106 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  264 VAL
Chi-restraints excluded: chain B residue  438 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    0.3980
   chunk 27 optimal weight:    0.4980
   chunk 54 optimal weight:    0.0770
   chunk 43 optimal weight:    5.9990
   chunk 83 optimal weight:   20.0000
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 62 optimal weight:    0.7980
   chunk 97 optimal weight:   30.0000
   overall best weight:    0.5540

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

Flipped N/Q/H residues before XYZ refinement:
C  99 HIS
C 329 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.198607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.116959 restraints weight = 11728.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.115219 restraints weight = 6357.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.117521 restraints weight = 4654.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.1054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9055  Z= 0.174
  Angle     :  0.645   9.978  12228  Z= 0.324
  Chirality :  0.044   0.269   1302
  Planarity :  0.004   0.040   1550
  Dihedral  : 12.033 103.777   1348
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 13.34 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.04 (0.25), residues: 1071
  helix:  1.34 (0.25), residues: 409
  sheet: -0.41 (0.37), residues: 184
  loop : -1.06 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 200 
 HIS   0.004   0.001   HIS A 332 
 PHE   0.022   0.001   PHE C 113 
 TYR   0.011   0.001   TYR B 492 
 ARG   0.008   0.001   ARG B 141 

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 111
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 CYS cc_start: 0.5039 (OUTLIER) cc_final: 0.4830 (m)
REVERT: A  324 ARG cc_start: 0.7862 (ttp80) cc_final: 0.7662 (ttp80)
REVERT: B  128 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8508 (mm-30)
REVERT: B  379 MET cc_start: 0.8171 (tpp) cc_final: 0.7929 (tpt)
  outliers start: 18
  outliers final: 9
  residues processed: 122
  average time/residue: 0.2974
  time to fit residues: 51.3899
Evaluate side-chains
  105 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  146 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 10 optimal weight:   20.0000
   chunk 49 optimal weight:    0.0010
   chunk 15 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.5392

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  56 ASN
C  99 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.194724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.110631 restraints weight = 11623.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.115131 restraints weight = 5198.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.118025 restraints weight = 3400.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9055  Z= 0.254
  Angle     :  0.628  12.743  12228  Z= 0.318
  Chirality :  0.043   0.261   1302
  Planarity :  0.004   0.042   1550
  Dihedral  : 11.461 101.516   1345
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 14.30 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.11 (0.25), residues: 1071
  helix:  1.39 (0.25), residues: 406
  sheet: -0.63 (0.35), residues: 207
  loop : -1.11 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 200 
 HIS   0.007   0.001   HIS C  99 
 PHE   0.026   0.001   PHE C  46 
 TYR   0.013   0.001   TYR B 484 
 ARG   0.008   0.000   ARG B 141 

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 1.062 
Fit side-chains
REVERT: B  140 TYR cc_start: 0.8457 (p90) cc_final: 0.8178 (p90)
REVERT: B  379 MET cc_start: 0.8291 (tpp) cc_final: 0.8061 (tpt)
  outliers start: 23
  outliers final: 17
  residues processed: 127
  average time/residue: 0.2342
  time to fit residues: 42.9982
Evaluate side-chains
  123 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue  265 VAL
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 53 optimal weight:    0.8980
   chunk 99 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 22 optimal weight:   10.0000
   chunk 94 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 88 optimal weight:   40.0000
   chunk 102 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A 221 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.196484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.112447 restraints weight = 11505.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.117025 restraints weight = 5136.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.119947 restraints weight = 3354.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9055  Z= 0.184
  Angle     :  0.593  13.889  12228  Z= 0.297
  Chirality :  0.042   0.242   1302
  Planarity :  0.004   0.035   1550
  Dihedral  : 10.812  97.502   1345
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 14.83 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.09 (0.25), residues: 1071
  helix:  1.55 (0.25), residues: 410
  sheet: -0.50 (0.36), residues: 204
  loop : -1.04 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP C 200 
 HIS   0.005   0.001   HIS C  99 
 PHE   0.018   0.001   PHE C 113 
 TYR   0.009   0.001   TYR B 484 
 ARG   0.007   0.000   ARG B 141 

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 109
  time to evaluate  : 1.093 
Fit side-chains
REVERT: A  199 MET cc_start: 0.9030 (mtm) cc_final: 0.8748 (mtm)
REVERT: A  241 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7617 (ptm)
REVERT: A  319 ARG cc_start: 0.7384 (mpt180) cc_final: 0.7122 (mpt-90)
REVERT: B  140 TYR cc_start: 0.8419 (p90) cc_final: 0.8083 (p90)
REVERT: B  489 MET cc_start: 0.7036 (mtt) cc_final: 0.6716 (mtt)
  outliers start: 26
  outliers final: 16
  residues processed: 126
  average time/residue: 0.2013
  time to fit residues: 36.8701
Evaluate side-chains
  120 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 38 optimal weight:    0.3980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 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 = 0.4363 r_free = 0.4363 target = 0.196502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.112313 restraints weight = 11472.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.116903 restraints weight = 5119.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.119804 restraints weight = 3335.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9055  Z= 0.184
  Angle     :  0.584  14.287  12228  Z= 0.290
  Chirality :  0.042   0.232   1302
  Planarity :  0.004   0.033   1550
  Dihedral  : 10.301  92.666   1345
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 14.62 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.25), residues: 1071
  helix:  1.64 (0.25), residues: 410
  sheet: -0.47 (0.36), residues: 204
  loop : -1.06 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP C 200 
 HIS   0.004   0.001   HIS C 170 
 PHE   0.017   0.001   PHE C 113 
 TYR   0.009   0.001   TYR B 484 
 ARG   0.005   0.000   ARG B 141 

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 106
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7440 (ppp)
REVERT: A  319 ARG cc_start: 0.7408 (mpt180) cc_final: 0.7157 (mpt-90)
REVERT: A  331 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.8095 (m-10)
REVERT: B  140 TYR cc_start: 0.8489 (p90) cc_final: 0.8077 (p90)
REVERT: B  154 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6561 (mt-10)
REVERT: B  445 MET cc_start: 0.6397 (ttm) cc_final: 0.6184 (ttp)
REVERT: B  489 MET cc_start: 0.7089 (mtt) cc_final: 0.6806 (mtt)
REVERT: C   77 LEU cc_start: 0.3146 (OUTLIER) cc_final: 0.2756 (mm)
  outliers start: 31
  outliers final: 21
  residues processed: 126
  average time/residue: 0.2445
  time to fit residues: 44.1665
Evaluate side-chains
  124 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   56 PHE
Chi-restraints excluded: chain C residue   77 LEU
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 92 optimal weight:    8.9990
   chunk 3 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 99 optimal weight:   30.0000
   chunk 55 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0370
   chunk 52 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 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 = 0.4384 r_free = 0.4384 target = 0.198710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.118483 restraints weight = 11845.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.117862 restraints weight = 6004.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.119603 restraints weight = 4292.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9055  Z= 0.163
  Angle     :  0.574  12.521  12228  Z= 0.284
  Chirality :  0.042   0.236   1302
  Planarity :  0.004   0.034   1550
  Dihedral  :  9.743  86.999   1345
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.69 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.27 (0.26), residues: 1071
  helix:  1.77 (0.25), residues: 411
  sheet: -0.36 (0.36), residues: 206
  loop : -1.04 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C 200 
 HIS   0.004   0.001   HIS C 170 
 PHE   0.020   0.001   PHE A 169 
 TYR   0.012   0.001   TYR A 346 
 ARG   0.004   0.000   ARG B 141 

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 108
  time to evaluate  : 1.064 
Fit side-chains
REVERT: A  241 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7287 (ppp)
REVERT: A  268 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6770 (pm20)
REVERT: A  319 ARG cc_start: 0.7400 (mpt180) cc_final: 0.7157 (mpt-90)
REVERT: A  331 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.8097 (m-10)
REVERT: B  140 TYR cc_start: 0.8482 (p90) cc_final: 0.8037 (p90)
REVERT: B  141 ARG cc_start: 0.7814 (ttp-170) cc_final: 0.7412 (ttp-170)
REVERT: B  154 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6486 (mt-10)
REVERT: B  426 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8132 (tm-30)
REVERT: B  445 MET cc_start: 0.6381 (ttm) cc_final: 0.6105 (ttp)
REVERT: B  489 MET cc_start: 0.7151 (mtt) cc_final: 0.6854 (mtt)
REVERT: C   77 LEU cc_start: 0.3069 (OUTLIER) cc_final: 0.2663 (mm)
  outliers start: 30
  outliers final: 19
  residues processed: 127
  average time/residue: 0.1945
  time to fit residues: 35.4378
Evaluate side-chains
  127 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   77 LEU
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 101 optimal weight:    8.9990
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 97 optimal weight:    7.9990
   chunk 104 optimal weight:   20.0000
   chunk 83 optimal weight:    6.9990
   chunk 99 optimal weight:    0.6980
   chunk 96 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0030
   overall best weight:    2.1394

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

Flipped N/Q/H residues before XYZ refinement:
A 340 GLN
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.194082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.112289 restraints weight = 12021.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.111647 restraints weight = 6098.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.113059 restraints weight = 4527.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9055  Z= 0.327
  Angle     :  0.649  15.115  12228  Z= 0.322
  Chirality :  0.044   0.245   1302
  Planarity :  0.004   0.035   1550
  Dihedral  :  9.565  81.108   1345
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 16.01 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.03 (0.25), residues: 1071
  helix:  1.43 (0.25), residues: 411
  sheet: -0.44 (0.36), residues: 207
  loop : -1.15 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 336 
 HIS   0.005   0.001   HIS C 170 
 PHE   0.027   0.002   PHE B 318 
 TYR   0.016   0.001   TYR B 484 
 ARG   0.004   0.000   ARG B 141 

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 2.364 
Fit side-chains
REVERT: A  241 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7270 (ppp)
REVERT: A  268 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6569 (pp20)
REVERT: A  319 ARG cc_start: 0.7426 (mpt180) cc_final: 0.7196 (mpt-90)
REVERT: A  331 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.8171 (m-10)
REVERT: B  140 TYR cc_start: 0.8617 (p90) cc_final: 0.8112 (p90)
REVERT: B  141 ARG cc_start: 0.8021 (ttp-170) cc_final: 0.7516 (ttp-170)
REVERT: C   77 LEU cc_start: 0.3263 (OUTLIER) cc_final: 0.2840 (mm)
  outliers start: 35
  outliers final: 24
  residues processed: 127
  average time/residue: 0.2135
  time to fit residues: 39.8061
Evaluate side-chains
  134 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  289 ILE
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   56 PHE
Chi-restraints excluded: chain C residue   77 LEU
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 49 optimal weight:    0.3980
   chunk 96 optimal weight:   40.0000
   chunk 72 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 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 = 0.4379 r_free = 0.4379 target = 0.197935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.117399 restraints weight = 12073.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.116726 restraints weight = 6010.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.118231 restraints weight = 4384.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3498
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9055  Z= 0.166
  Angle     :  0.588  14.478  12228  Z= 0.288
  Chirality :  0.042   0.243   1302
  Planarity :  0.004   0.036   1550
  Dihedral  :  9.034  75.709   1345
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.44 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.40 (0.26), residues: 1071
  helix:  2.00 (0.25), residues: 396
  sheet: -0.30 (0.37), residues: 206
  loop : -0.98 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 200 
 HIS   0.005   0.001   HIS C 170 
 PHE   0.030   0.001   PHE B 318 
 TYR   0.011   0.001   TYR B 492 
 ARG   0.006   0.000   ARG C 177 

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 1.102 
Fit side-chains
REVERT: A  241 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7243 (ppp)
REVERT: A  268 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6814 (pm20)
REVERT: A  302 HIS cc_start: 0.5740 (t70) cc_final: 0.5510 (t70)
REVERT: A  331 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8175 (m-10)
REVERT: B   25 GLN cc_start: 0.7408 (tp40) cc_final: 0.7094 (tp40)
REVERT: B  140 TYR cc_start: 0.8567 (p90) cc_final: 0.7970 (p90)
REVERT: B  141 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7392 (ttp-170)
REVERT: B  154 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6452 (mt-10)
REVERT: B  436 MET cc_start: 0.6745 (mmt) cc_final: 0.6532 (mmt)
REVERT: C   77 LEU cc_start: 0.3212 (OUTLIER) cc_final: 0.2770 (mm)
  outliers start: 32
  outliers final: 24
  residues processed: 129
  average time/residue: 0.2002
  time to fit residues: 36.6616
Evaluate side-chains
  131 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   56 PHE
Chi-restraints excluded: chain C residue   77 LEU
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  311 PHE
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 5 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 105 optimal weight:   20.0000
   chunk 74 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 71 optimal weight:    0.4980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** C 115 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 = 0.4373 r_free = 0.4373 target = 0.197334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.116667 restraints weight = 12064.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.115978 restraints weight = 6048.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.117524 restraints weight = 4418.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7160
moved from start:          0.2460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9055  Z= 0.198
  Angle     :  0.600  14.250  12228  Z= 0.293
  Chirality :  0.042   0.241   1302
  Planarity :  0.004   0.037   1550
  Dihedral  :  8.761  71.150   1345
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.97 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.43 (0.26), residues: 1071
  helix:  2.01 (0.25), residues: 396
  sheet: -0.33 (0.37), residues: 207
  loop : -0.94 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 336 
 HIS   0.005   0.001   HIS C 170 
 PHE   0.032   0.001   PHE B 318 
 TYR   0.011   0.001   TYR B 478 
 ARG   0.013   0.000   ARG C 177 

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.7581 (OUTLIER) cc_final: 0.7208 (ppp)
REVERT: A  302 HIS cc_start: 0.5731 (t70) cc_final: 0.5519 (t70)
REVERT: A  325 GLU cc_start: 0.8445 (pt0) cc_final: 0.8244 (pm20)
REVERT: A  331 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.8159 (m-10)
REVERT: B  140 TYR cc_start: 0.8547 (p90) cc_final: 0.7976 (p90)
REVERT: B  141 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7367 (ttp-170)
REVERT: B  154 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6470 (mt-10)
REVERT: B  436 MET cc_start: 0.6784 (mmt) cc_final: 0.6578 (mmt)
REVERT: C   77 LEU cc_start: 0.3246 (OUTLIER) cc_final: 0.2825 (mm)
  outliers start: 27
  outliers final: 22
  residues processed: 125
  average time/residue: 0.2083
  time to fit residues: 36.6550
Evaluate side-chains
  132 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   56 PHE
Chi-restraints excluded: chain C residue   77 LEU
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 92 optimal weight:    6.9990
   chunk 86 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 62 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 89 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 76 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C  99 HIS
** C 115 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 = 0.4381 r_free = 0.4381 target = 0.198222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.117954 restraints weight = 12013.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.117273 restraints weight = 6035.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.118728 restraints weight = 4402.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9055  Z= 0.188
  Angle     :  0.606  13.887  12228  Z= 0.296
  Chirality :  0.042   0.233   1302
  Planarity :  0.004   0.059   1550
  Dihedral  :  8.368  64.285   1345
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.29 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.46 (0.26), residues: 1071
  helix:  2.07 (0.25), residues: 395
  sheet: -0.27 (0.37), residues: 204
  loop : -0.97 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 336 
 HIS   0.005   0.001   HIS C 170 
 PHE   0.032   0.001   PHE B 318 
 TYR   0.014   0.001   TYR A 346 
 ARG   0.008   0.000   ARG C 177 

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 110
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7203 (ppp)
REVERT: A  325 GLU cc_start: 0.8443 (pt0) cc_final: 0.8236 (pm20)
REVERT: A  331 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8148 (m-10)
REVERT: B  140 TYR cc_start: 0.8544 (p90) cc_final: 0.7912 (p90)
REVERT: B  141 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7345 (ttp-170)
REVERT: B  154 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6403 (mt-10)
REVERT: B  436 MET cc_start: 0.6814 (mmt) cc_final: 0.6593 (mmt)
REVERT: C   77 LEU cc_start: 0.3222 (OUTLIER) cc_final: 0.2793 (mm)
  outliers start: 29
  outliers final: 24
  residues processed: 128
  average time/residue: 0.2141
  time to fit residues: 38.2470
Evaluate side-chains
  135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 108
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  163 THR
Chi-restraints excluded: chain B residue  169 THR
Chi-restraints excluded: chain B residue  171 GLU
Chi-restraints excluded: chain B residue  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue   56 PHE
Chi-restraints excluded: chain C residue   77 LEU
Chi-restraints excluded: chain C residue   99 HIS
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain C residue  311 PHE
Chi-restraints excluded: chain C residue  318 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 67 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 98 optimal weight:    7.9990
   chunk 13 optimal weight:    5.9990
   chunk 86 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
C  99 HIS
** C 115 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 = 0.4383 r_free = 0.4383 target = 0.198345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.117582 restraints weight = 11974.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.118064 restraints weight = 5966.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.119295 restraints weight = 4210.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9055  Z= 0.186
  Angle     :  0.599  13.888  12228  Z= 0.293
  Chirality :  0.042   0.225   1302
  Planarity :  0.004   0.045   1550
  Dihedral  :  8.179  60.518   1345
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.40 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.49 (0.26), residues: 1071
  helix:  2.09 (0.25), residues: 395
  sheet: -0.23 (0.37), residues: 204
  loop : -0.96 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 336 
 HIS   0.006   0.001   HIS C 170 
 PHE   0.031   0.001   PHE B 318 
 TYR   0.010   0.001   TYR B 478 
 ARG   0.008   0.000   ARG B 127 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3628.16 seconds
wall clock time: 65 minutes 33.76 seconds (3933.76 seconds total)