Starting phenix.real_space_refine
on Thu Feb 13 22:35:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzr_41767/02_2025/8tzr_41767.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzr_41767/02_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_41767/02_2025/8tzr_41767.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzr_41767/02_2025/8tzr_41767.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzr_41767/02_2025/8tzr_41767.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzr_41767/02_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-5592/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: 6.14, per 1000 atoms: 0.70
  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: 2.33
  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: 1.01
  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: 3.15

  Time building geometry restraints manager: 2.69 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:             2.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.040
  Process input model:                     24.000
  Find NCS groups from input model:        0.130
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.950
-------------------------------------------------------------------------------
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  : 0.989 
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: 0.2208
  time to fit residues: 35.3428
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  : 0.905 
-------------------------------------------------------------------------------
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 = 0.116963 restraints weight = 11728.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.115213 restraints weight = 6355.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.117408 restraints weight = 4651.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
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  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 CYS cc_start: 0.5014 (OUTLIER) cc_final: 0.4807 (m)
REVERT: A  324 ARG cc_start: 0.7866 (ttp80) cc_final: 0.7664 (ttp80)
REVERT: B  128 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8526 (mm-30)
REVERT: B  379 MET cc_start: 0.8133 (tpp) cc_final: 0.7895 (tpt)
  outliers start: 18
  outliers final: 9
  residues processed: 122
  average time/residue: 0.2242
  time to fit residues: 38.7128
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  : 1.478 
-------------------------------------------------------------------------------
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:    0.2980
   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:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0770
   chunk 15 optimal weight:    0.9990
   chunk 46 optimal weight:    7.9990
   overall best weight:    1.0142

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
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 = 0.4359 r_free = 0.4359 target = 0.196356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.112339 restraints weight = 11573.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.116886 restraints weight = 5213.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.119804 restraints weight = 3418.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9055  Z= 0.200
  Angle     :  0.609  12.611  12228  Z= 0.307
  Chirality :  0.043   0.260   1302
  Planarity :  0.004   0.040   1550
  Dihedral  : 11.373 101.270   1345
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.73 %
    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: -0.02 (0.25), residues: 1071
  helix:  1.48 (0.25), residues: 406
  sheet: -0.56 (0.35), residues: 206
  loop : -1.09 (0.27), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 200 
 HIS   0.005   0.001   HIS A 332 
 PHE   0.020   0.001   PHE C  46 
 TYR   0.011   0.001   TYR B 335 
 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
  131 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 1.051 
Fit side-chains
REVERT: B  140 TYR cc_start: 0.8410 (p90) cc_final: 0.8132 (p90)
REVERT: B  379 MET cc_start: 0.8274 (tpp) cc_final: 0.8060 (tpt)
  outliers start: 19
  outliers final: 13
  residues processed: 123
  average time/residue: 0.2021
  time to fit residues: 35.4789
Evaluate side-chains
  119 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
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  239 THR
Chi-restraints excluded: chain B residue  246 PHE
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:    0.9980
   chunk 99 optimal weight:   40.0000
   chunk 83 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 88 optimal weight:   20.0000
   chunk 102 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    1.7984

-------------------------------------------------------------------------------
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 = 0.4347 r_free = 0.4347 target = 0.194699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.107160 restraints weight = 12051.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.111899 restraints weight = 5465.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.114809 restraints weight = 3612.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.1667

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= 0.285
  Angle     :  0.633  13.964  12228  Z= 0.319
  Chirality :  0.044   0.239   1302
  Planarity :  0.004   0.040   1550
  Dihedral  : 10.927  97.574   1345
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 14.09 %
    Favored  : 82.50 %
  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: -0.08 (0.25), residues: 1071
  helix:  1.36 (0.25), residues: 409
  sheet: -0.57 (0.36), residues: 204
  loop : -1.08 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP C 200 
 HIS   0.005   0.001   HIS C  99 
 PHE   0.018   0.002   PHE A 169 
 TYR   0.015   0.001   TYR B 484 
 ARG   0.007   0.001   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
  142 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 110
  time to evaluate  : 1.077 
Fit side-chains
REVERT: A  319 ARG cc_start: 0.7395 (mpt180) cc_final: 0.7162 (mpt-90)
REVERT: B  140 TYR cc_start: 0.8525 (p90) cc_final: 0.8125 (p90)
REVERT: B  161 LYS cc_start: 0.7406 (tptp) cc_final: 0.7167 (tptt)
REVERT: B  205 GLU cc_start: 0.7942 (mp0) cc_final: 0.7690 (mp0)
  outliers start: 32
  outliers final: 22
  residues processed: 130
  average time/residue: 0.1939
  time to fit residues: 36.9695
Evaluate side-chains
  125 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
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  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  284 VAL
Chi-restraints excluded: chain B residue  289 ILE
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:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 85 optimal weight:    9.9990
   chunk 54 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0020
   chunk 67 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 10 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7388

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

Flipped N/Q/H residues before XYZ refinement:
** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.4374 r_free = 0.4374 target = 0.197548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.117003 restraints weight = 11941.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.116343 restraints weight = 5962.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.117684 restraints weight = 4477.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7103
moved from start:          0.1904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9055  Z= 0.167
  Angle     :  0.588  14.519  12228  Z= 0.292
  Chirality :  0.042   0.233   1302
  Planarity :  0.004   0.034   1550
  Dihedral  : 10.403  93.723   1345
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.90 %
    Favored  : 81.43 %
  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:  0.13 (0.25), residues: 1071
  helix:  1.65 (0.25), residues: 410
  sheet: -0.47 (0.36), residues: 204
  loop : -1.09 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   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 492 
 ARG   0.006   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
  136 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8735 (mtp)
REVERT: A  241 MET cc_start: 0.7374 (ptm) cc_final: 0.6913 (ppp)
REVERT: A  319 ARG cc_start: 0.7434 (mpt180) cc_final: 0.7174 (mpt-90)
REVERT: A  331 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8142 (m-10)
REVERT: B  128 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8475 (mm-30)
REVERT: B  140 TYR cc_start: 0.8498 (p90) cc_final: 0.8060 (p90)
REVERT: B  489 MET cc_start: 0.7181 (mtt) cc_final: 0.6933 (mtt)
REVERT: C   77 LEU cc_start: 0.3122 (OUTLIER) cc_final: 0.2728 (mm)
  outliers start: 25
  outliers final: 18
  residues processed: 127
  average time/residue: 0.1953
  time to fit residues: 35.6639
Evaluate side-chains
  124 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
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  199 MET
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  246 PHE
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:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 60 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0370
   chunk 52 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 115 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.199301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.119510 restraints weight = 11837.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.118926 restraints weight = 6025.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.120484 restraints weight = 4316.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9055  Z= 0.150
  Angle     :  0.572  12.559  12228  Z= 0.284
  Chirality :  0.042   0.234   1302
  Planarity :  0.004   0.034   1550
  Dihedral  :  9.783  87.813   1345
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.22 %
    Favored  : 80.90 %
  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:  0.25 (0.26), residues: 1071
  helix:  1.80 (0.25), residues: 410
  sheet: -0.39 (0.36), residues: 206
  loop : -1.07 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   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   0.005   0.000   ARG C 177 

*********************** 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
  140 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.887 
Fit side-chains
REVERT: A  199 MET cc_start: 0.9060 (mtp) cc_final: 0.8728 (mtp)
REVERT: A  241 MET cc_start: 0.7409 (ptm) cc_final: 0.7159 (ppp)
REVERT: A  268 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6694 (pm20)
REVERT: A  319 ARG cc_start: 0.7405 (mpt180) cc_final: 0.7157 (mpt-90)
REVERT: A  331 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8095 (m-10)
REVERT: B  140 TYR cc_start: 0.8477 (p90) cc_final: 0.8040 (p90)
REVERT: B  141 ARG cc_start: 0.7774 (ttp-170) cc_final: 0.7276 (ttp-170)
REVERT: B  426 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8153 (tm-30)
REVERT: B  489 MET cc_start: 0.7165 (mtt) cc_final: 0.6883 (mtt)
REVERT: C   77 LEU cc_start: 0.3041 (OUTLIER) cc_final: 0.2632 (mm)
  outliers start: 27
  outliers final: 17
  residues processed: 132
  average time/residue: 0.2012
  time to fit residues: 37.7653
Evaluate side-chains
  126 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
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  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  246 PHE
Chi-restraints excluded: chain B residue  280 ILE
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 101 optimal weight:   20.0000
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 97 optimal weight:    5.9990
   chunk 104 optimal weight:   20.0000
   chunk 83 optimal weight:   20.0000
   chunk 99 optimal weight:    0.3980
   chunk 96 optimal weight:   10.0000
   chunk 55 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0870
   overall best weight:    1.6362

-------------------------------------------------------------------------------
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 = 0.4350 r_free = 0.4350 target = 0.194877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.110376 restraints weight = 11554.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.114816 restraints weight = 5191.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.117637 restraints weight = 3416.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7190
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9055  Z= 0.265
  Angle     :  0.621  15.489  12228  Z= 0.306
  Chirality :  0.043   0.244   1302
  Planarity :  0.004   0.033   1550
  Dihedral  :  9.500  82.167   1345
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 16.33 %
    Favored  : 79.94 %
  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:  1.57 (0.25), residues: 411
  sheet: -0.40 (0.37), residues: 207
  loop : -1.12 (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   0.028   0.002   PHE B 318 
 TYR   0.014   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
  149 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 0.958 
Fit side-chains
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.7679 (ptm) cc_final: 0.7392 (ppp)
REVERT: A  319 ARG cc_start: 0.7410 (mpt180) cc_final: 0.7162 (mpt-90)
REVERT: A  325 GLU cc_start: 0.8566 (pt0) cc_final: 0.8364 (pm20)
REVERT: A  331 PHE cc_start: 0.8402 (OUTLIER) cc_final: 0.8120 (m-10)
REVERT: B  140 TYR cc_start: 0.8530 (p90) cc_final: 0.8041 (p90)
REVERT: B  141 ARG cc_start: 0.7935 (ttp-170) cc_final: 0.7408 (ttp-170)
REVERT: B  154 GLU cc_start: 0.7233 (mt-10) cc_final: 0.6532 (mt-10)
REVERT: B  330 ASN cc_start: 0.6088 (p0) cc_final: 0.5747 (p0)
REVERT: B  480 MET cc_start: 0.7876 (ttm) cc_final: 0.7610 (tpp)
REVERT: C   77 LEU cc_start: 0.3268 (OUTLIER) cc_final: 0.2855 (mm)
  outliers start: 35
  outliers final: 21
  residues processed: 135
  average time/residue: 0.1996
  time to fit residues: 38.1646
Evaluate side-chains
  135 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
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  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  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  284 VAL
Chi-restraints excluded: chain B residue  289 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:    3.9990
   chunk 11 optimal weight:    0.0870
   chunk 49 optimal weight:    0.0010
   chunk 96 optimal weight:   30.0000
   chunk 72 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0370
   chunk 92 optimal weight:    0.0370
   overall best weight:    0.1520

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.201163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.121878 restraints weight = 12002.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.120466 restraints weight = 5975.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.122221 restraints weight = 4332.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9055  Z= 0.136
  Angle     :  0.572  14.740  12228  Z= 0.279
  Chirality :  0.041   0.243   1302
  Planarity :  0.003   0.037   1550
  Dihedral  :  8.804  75.076   1345
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 17.08 %
    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:  0.58 (0.26), residues: 1071
  helix:  2.29 (0.25), residues: 389
  sheet: -0.30 (0.37), residues: 206
  loop : -0.93 (0.28), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C 200 
 HIS   0.004   0.001   HIS C 170 
 PHE   0.026   0.001   PHE B 318 
 TYR   0.014   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
  146 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.7476 (ptm) cc_final: 0.7154 (ppp)
REVERT: A  331 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7949 (m-10)
REVERT: B  140 TYR cc_start: 0.8416 (p90) cc_final: 0.7883 (p90)
REVERT: B  141 ARG cc_start: 0.7792 (ttp-170) cc_final: 0.7284 (ttp-170)
REVERT: B  154 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6379 (mt-10)
REVERT: B  480 MET cc_start: 0.7503 (ttm) cc_final: 0.7275 (tpp)
REVERT: C   77 LEU cc_start: 0.3224 (OUTLIER) cc_final: 0.2796 (mm)
  outliers start: 25
  outliers final: 16
  residues processed: 137
  average time/residue: 0.2042
  time to fit residues: 39.1322
Evaluate side-chains
  126 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 1.063 
-------------------------------------------------------------------------------
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  331 PHE
Chi-restraints excluded: chain B residue   64 VAL
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  246 PHE
Chi-restraints excluded: chain B residue  280 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  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:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 83 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 105 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 91 optimal weight:   20.0000
   chunk 71 optimal weight:    0.1980
   overall best weight:    1.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.197732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.117864 restraints weight = 12061.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.115002 restraints weight = 6581.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.118488 restraints weight = 4585.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.2596

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= 0.215
  Angle     :  0.614  15.155  12228  Z= 0.300
  Chirality :  0.043   0.237   1302
  Planarity :  0.004   0.035   1550
  Dihedral  :  8.529  68.695   1345
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.50 %
    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:  0.37 (0.25), residues: 1071
  helix:  1.94 (0.25), residues: 397
  sheet: -0.22 (0.37), residues: 204
  loop : -1.03 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 336 
 HIS   0.005   0.001   HIS C 170 
 PHE   0.032   0.001   PHE B 318 
 TYR   0.010   0.001   TYR B 484 
 ARG   0.016   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
  136 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 109
  time to evaluate  : 1.108 
Fit side-chains
REVERT: A  241 MET cc_start: 0.7500 (ptm) cc_final: 0.6118 (ppp)
REVERT: A  268 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6753 (pm20)
REVERT: A  331 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7986 (m-10)
REVERT: B  140 TYR cc_start: 0.8526 (p90) cc_final: 0.7999 (p90)
REVERT: B  141 ARG cc_start: 0.7927 (ttp-170) cc_final: 0.7380 (ttp-170)
REVERT: B  154 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6444 (mt-10)
REVERT: C   77 LEU cc_start: 0.3356 (OUTLIER) cc_final: 0.2949 (mm)
  outliers start: 27
  outliers final: 20
  residues processed: 125
  average time/residue: 0.2009
  time to fit residues: 35.8665
Evaluate side-chains
  130 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
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   63 MET
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  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  289 ILE
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  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 61 optimal weight:    0.6980
   chunk 92 optimal weight:   20.0000
   chunk 86 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 5 optimal weight:   10.0000
   chunk 62 optimal weight:    0.6980
   chunk 24 optimal weight:    9.9990
   chunk 89 optimal weight:    5.9990
   chunk 46 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 ASN
C  99 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.195542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.107991 restraints weight = 12049.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.112686 restraints weight = 5472.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.115635 restraints weight = 3625.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9055  Z= 0.288
  Angle     :  0.662  18.572  12228  Z= 0.320
  Chirality :  0.044   0.223   1302
  Planarity :  0.004   0.036   1550
  Dihedral  :  8.341  63.127   1345
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 17.82 %
    Favored  : 78.98 %
  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:  0.10 (0.25), residues: 1071
  helix:  1.52 (0.25), residues: 411
  sheet: -0.33 (0.37), residues: 205
  loop : -1.07 (0.28), residues: 455

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   0.034   0.002   PHE B 318 
 TYR   0.011   0.001   TYR B 478 
 ARG   0.007   0.000   ARG B 422 

********************** 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
  140 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 110
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 PHE cc_start: 0.8268 (OUTLIER) cc_final: 0.8032 (m-10)
REVERT: B  140 TYR cc_start: 0.8583 (p90) cc_final: 0.7974 (p90)
REVERT: B  154 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6505 (mt-10)
REVERT: B  249 MET cc_start: 0.7693 (mmt) cc_final: 0.7429 (mmp)
REVERT: B  330 ASN cc_start: 0.6463 (p0) cc_final: 0.6114 (p0)
REVERT: B  489 MET cc_start: 0.7613 (mtt) cc_final: 0.7335 (mtt)
REVERT: C   77 LEU cc_start: 0.3454 (OUTLIER) cc_final: 0.3064 (mm)
  outliers start: 30
  outliers final: 22
  residues processed: 129
  average time/residue: 0.1877
  time to fit residues: 34.6579
Evaluate side-chains
  129 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
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  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  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  246 PHE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  284 VAL
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:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 30 optimal weight:   20.0000
   chunk 40 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0270
   chunk 13 optimal weight:    7.9990
   chunk 86 optimal weight:    8.9990
   chunk 100 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    1.3644

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

Flipped N/Q/H residues before XYZ refinement:
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 ASN
C  99 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.196313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.114577 restraints weight = 12025.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.114410 restraints weight = 6001.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.115878 restraints weight = 4374.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9055  Z= 0.240
  Angle     :  0.639  14.577  12228  Z= 0.310
  Chirality :  0.043   0.224   1302
  Planarity :  0.004   0.044   1550
  Dihedral  :  8.174  61.331   1345
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 18.78 %
    Favored  : 78.55 %
  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:  0.25 (0.25), residues: 1071
  helix:  1.81 (0.25), residues: 395
  sheet: -0.44 (0.37), residues: 211
  loop : -0.96 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 336 
 HIS   0.006   0.001   HIS C  99 
 PHE   0.035   0.001   PHE B 318 
 TYR   0.010   0.001   TYR B 484 
 ARG   0.008   0.000   ARG B 261 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3410.44 seconds
wall clock time: 61 minutes 42.38 seconds (3702.38 seconds total)