Starting phenix.real_space_refine
on Sat Aug 23 03:36:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tzr_41767/08_2025/8tzr_41767.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tzr_41767/08_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_41767/08_2025/8tzr_41767.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tzr_41767/08_2025/8tzr_41767.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tzr_41767/08_2025/8tzr_41767.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tzr_41767/08_2025/8tzr_41767.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.006 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.09, per 1000 atoms: 0.24
  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: 0.91
  Conformation dependent library (CDL) restraints added in 351.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.32
  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: 1.49

  Time building geometry restraints manager: 1.17 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:             2.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.630
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.240
-------------------------------------------------------------------------------
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   9078  Z= 0.254
  Angle     :  0.846  13.314  12279  Z= 0.427
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.009   0.001   ARG B 431 
 TYR   0.018   0.002   TYR B 140 
 PHE   0.026   0.002   PHE C 148 
 TRP   0.037   0.002   TRP A 252 
 HIS   0.006   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00561 ( 9055)
  covalent geometry    : angle       0.83857 (12228)
  SS BOND              : bond        0.00306 (   15)
  SS BOND              : angle       0.93532 (   30)
  hydrogen bonds       : bond        0.15344 (  436)
  hydrogen bonds       : angle       7.28379 ( 1275)
  Misc. bond           : bond        0.00166 (    1)
  link_ALPHA1-2        : bond        0.00521 (    2)
  link_ALPHA1-2        : angle       1.65276 (    6)
  link_ALPHA1-3        : bond        0.00083 (    2)
  link_ALPHA1-3        : angle       2.22397 (    6)
  link_BETA1-4         : bond        0.01150 (    2)
  link_BETA1-4         : angle       2.63475 (    6)
  link_NAG-ASN         : bond        0.00064 (    1)
  link_NAG-ASN         : angle       4.66901 (    3)

*********************** 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  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  268 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6093 (pp20)
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: 0.0938
  time to fit residues: 15.1650
Evaluate side-chains
  107 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
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 49 optimal weight:    4.9990
   chunk 97 optimal weight:   30.0000
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 172 HIS
C  99 HIS
C 329 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.198159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.116304 restraints weight = 11869.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.114311 restraints weight = 6524.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.115660 restraints weight = 4735.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.116881 restraints weight = 3968.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.116867 restraints weight = 3443.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6998
moved from start:          0.1000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9078  Z= 0.136
  Angle     :  0.662  10.504  12279  Z= 0.330
  Chirality :  0.044   0.258   1302
  Planarity :  0.004   0.041   1550
  Dihedral  : 12.199 104.444   1348
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.55 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.25), residues: 1071
  helix:  1.31 (0.25), residues: 406
  sheet: -0.44 (0.37), residues: 184
  loop : -1.08 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 141 
 TYR   0.011   0.001   TYR B 492 
 PHE   0.021   0.001   PHE C 113 
 TRP   0.029   0.002   TRP C 200 
 HIS   0.004   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 9055)
  covalent geometry    : angle       0.65232 (12228)
  SS BOND              : bond        0.00247 (   15)
  SS BOND              : angle       0.87884 (   30)
  hydrogen bonds       : bond        0.04290 (  436)
  hydrogen bonds       : angle       5.25712 ( 1275)
  Misc. bond           : bond        0.00101 (    1)
  link_ALPHA1-2        : bond        0.00835 (    2)
  link_ALPHA1-2        : angle       1.48557 (    6)
  link_ALPHA1-3        : bond        0.00413 (    2)
  link_ALPHA1-3        : angle       1.63915 (    6)
  link_BETA1-4         : bond        0.01111 (    2)
  link_BETA1-4         : angle       3.50619 (    6)
  link_NAG-ASN         : bond        0.00816 (    1)
  link_NAG-ASN         : angle       4.29893 (    3)

*********************** 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
  128 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 111
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   42 CYS cc_start: 0.5108 (OUTLIER) cc_final: 0.4899 (m)
REVERT: A  324 ARG cc_start: 0.7849 (ttp80) cc_final: 0.7649 (ttp80)
REVERT: B  128 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8526 (mm-30)
REVERT: B  379 MET cc_start: 0.8168 (tpp) cc_final: 0.7920 (tpt)
  outliers start: 17
  outliers final: 9
  residues processed: 121
  average time/residue: 0.0782
  time to fit residues: 13.5972
Evaluate side-chains
  109 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
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 51 optimal weight:    0.0060
   chunk 32 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0870
   chunk 83 optimal weight:   30.0000
   chunk 73 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 39 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 96 optimal weight:   30.0000
   chunk 79 optimal weight:    0.6980
   overall best weight:    0.4774

-------------------------------------------------------------------------------
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 = 0.4368 r_free = 0.4368 target = 0.199521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.118036 restraints weight = 11947.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.115685 restraints weight = 6741.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.119103 restraints weight = 4769.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.118716 restraints weight = 3538.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.119030 restraints weight = 3276.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9078  Z= 0.118
  Angle     :  0.610  12.645  12279  Z= 0.305
  Chirality :  0.043   0.262   1302
  Planarity :  0.004   0.038   1550
  Dihedral  : 11.373 101.582   1345
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.62 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.25), residues: 1071
  helix:  1.53 (0.25), residues: 406
  sheet: -0.58 (0.35), residues: 207
  loop : -1.04 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 141 
 TYR   0.010   0.001   TYR B 492 
 PHE   0.025   0.001   PHE C  46 
 TRP   0.024   0.001   TRP C 200 
 HIS   0.005   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9055)
  covalent geometry    : angle       0.60051 (12228)
  SS BOND              : bond        0.00224 (   15)
  SS BOND              : angle       0.74156 (   30)
  hydrogen bonds       : bond        0.03844 (  436)
  hydrogen bonds       : angle       4.90964 ( 1275)
  Misc. bond           : bond        0.00058 (    1)
  link_ALPHA1-2        : bond        0.00744 (    2)
  link_ALPHA1-2        : angle       1.55413 (    6)
  link_ALPHA1-3        : bond        0.00345 (    2)
  link_ALPHA1-3        : angle       1.47286 (    6)
  link_BETA1-4         : bond        0.01108 (    2)
  link_BETA1-4         : angle       3.64296 (    6)
  link_NAG-ASN         : bond        0.00310 (    1)
  link_NAG-ASN         : angle       3.09655 (    3)

*********************** 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  : 0.302 
Fit side-chains
REVERT: B  140 TYR cc_start: 0.8330 (p90) cc_final: 0.8110 (p90)
REVERT: B  154 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6521 (mt-10)
  outliers start: 19
  outliers final: 12
  residues processed: 125
  average time/residue: 0.0781
  time to fit residues: 14.2218
Evaluate side-chains
  116 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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 B residue  114 LEU
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  190 VAL
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 71 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 89 optimal weight:    7.9990
   chunk 28 optimal weight:   30.0000
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0980
   chunk 66 optimal weight:    0.8980
   chunk 36 optimal weight:   10.0000
   chunk 81 optimal weight:    9.9990
   chunk 53 optimal weight:    0.8980
   chunk 85 optimal weight:   20.0000
   overall best weight:    1.3784

-------------------------------------------------------------------------------
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
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.197261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.115136 restraints weight = 12053.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.112609 restraints weight = 6996.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.116229 restraints weight = 4920.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.115678 restraints weight = 3610.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.116050 restraints weight = 3397.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9078  Z= 0.159
  Angle     :  0.622  13.914  12279  Z= 0.309
  Chirality :  0.043   0.244   1302
  Planarity :  0.004   0.036   1550
  Dihedral  : 10.805  97.344   1345
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 14.51 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.25), residues: 1071
  helix:  1.52 (0.25), residues: 409
  sheet: -0.56 (0.35), residues: 207
  loop : -1.09 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 141 
 TYR   0.013   0.001   TYR B 484 
 PHE   0.018   0.001   PHE C 113 
 TRP   0.028   0.002   TRP C 200 
 HIS   0.005   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9055)
  covalent geometry    : angle       0.61406 (12228)
  SS BOND              : bond        0.00251 (   15)
  SS BOND              : angle       0.76955 (   30)
  hydrogen bonds       : bond        0.03756 (  436)
  hydrogen bonds       : angle       4.79772 ( 1275)
  Misc. bond           : bond        0.00105 (    1)
  link_ALPHA1-2        : bond        0.00687 (    2)
  link_ALPHA1-2        : angle       1.49908 (    6)
  link_ALPHA1-3        : bond        0.00312 (    2)
  link_ALPHA1-3        : angle       1.46150 (    6)
  link_BETA1-4         : bond        0.01216 (    2)
  link_BETA1-4         : angle       3.63521 (    6)
  link_NAG-ASN         : bond        0.00156 (    1)
  link_NAG-ASN         : angle       1.83785 (    3)

*********************** 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
  130 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A  184 ASN cc_start: 0.8689 (m110) cc_final: 0.8422 (m110)
REVERT: B  140 TYR cc_start: 0.8411 (p90) cc_final: 0.8034 (p90)
REVERT: B  445 MET cc_start: 0.6283 (ttm) cc_final: 0.6019 (ttp)
  outliers start: 25
  outliers final: 17
  residues processed: 119
  average time/residue: 0.0829
  time to fit residues: 14.5909
Evaluate side-chains
  120 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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 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  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain 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 95 optimal weight:   20.0000
   chunk 96 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 83 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 81 optimal weight:    6.9990
   chunk 72 optimal weight:    0.1980
   chunk 47 optimal weight:    0.0040
   chunk 24 optimal weight:   20.0000
   chunk 99 optimal weight:   20.0000
   chunk 49 optimal weight:    0.1980
   overall best weight:    1.6796

-------------------------------------------------------------------------------
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 = 0.4336 r_free = 0.4336 target = 0.195547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.108861 restraints weight = 11702.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.113400 restraints weight = 5331.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.116309 restraints weight = 3521.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.117875 restraints weight = 2822.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.118822 restraints weight = 2520.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9078  Z= 0.178
  Angle     :  0.626  14.410  12279  Z= 0.310
  Chirality :  0.043   0.231   1302
  Planarity :  0.004   0.035   1550
  Dihedral  : 10.449  93.402   1345
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 14.94 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.25), residues: 1071
  helix:  1.48 (0.25), residues: 409
  sheet: -0.55 (0.36), residues: 206
  loop : -1.07 (0.27), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 141 
 TYR   0.013   0.001   TYR B 335 
 PHE   0.017   0.001   PHE C 113 
 TRP   0.026   0.002   TRP C 200 
 HIS   0.004   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 9055)
  covalent geometry    : angle       0.61921 (12228)
  SS BOND              : bond        0.00295 (   15)
  SS BOND              : angle       0.78647 (   30)
  hydrogen bonds       : bond        0.03779 (  436)
  hydrogen bonds       : angle       4.75673 ( 1275)
  Misc. bond           : bond        0.00095 (    1)
  link_ALPHA1-2        : bond        0.00708 (    2)
  link_ALPHA1-2        : angle       1.47580 (    6)
  link_ALPHA1-3        : bond        0.00295 (    2)
  link_ALPHA1-3        : angle       1.47917 (    6)
  link_BETA1-4         : bond        0.01227 (    2)
  link_BETA1-4         : angle       3.57159 (    6)
  link_NAG-ASN         : bond        0.00113 (    1)
  link_NAG-ASN         : angle       1.49203 (    3)

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

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  241 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7074 (ppp)
REVERT: B  140 TYR cc_start: 0.8547 (p90) cc_final: 0.8164 (p90)
REVERT: B  154 GLU cc_start: 0.7222 (mt-10) cc_final: 0.6517 (mt-10)
REVERT: C  109 TYR cc_start: 0.6573 (OUTLIER) cc_final: 0.6199 (p90)
  outliers start: 30
  outliers final: 18
  residues processed: 126
  average time/residue: 0.0748
  time to fit residues: 13.9299
Evaluate side-chains
  122 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue   85 ILE
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  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 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  109 TYR
Chi-restraints excluded: chain C residue  122 MET
Chi-restraints excluded: chain C residue  146 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 99 optimal weight:   20.0000
   chunk 30 optimal weight:    3.9990
   chunk 95 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   chunk 18 optimal weight:    0.6980
   chunk 79 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 23 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0980
   overall best weight:    0.6180

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.198747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.110902 restraints weight = 12017.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.115794 restraints weight = 5443.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.118911 restraints weight = 3583.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.120527 restraints weight = 2873.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.121523 restraints weight = 2571.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7069
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9078  Z= 0.115
  Angle     :  0.596  15.004  12279  Z= 0.292
  Chirality :  0.042   0.230   1302
  Planarity :  0.004   0.035   1550
  Dihedral  :  9.890  88.800   1345
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.54 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.25), residues: 1071
  helix:  1.73 (0.25), residues: 410
  sheet: -0.38 (0.36), residues: 204
  loop : -1.04 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 141 
 TYR   0.010   0.001   TYR B 492 
 PHE   0.019   0.001   PHE A 169 
 TRP   0.026   0.002   TRP C 200 
 HIS   0.004   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 9055)
  covalent geometry    : angle       0.58899 (12228)
  SS BOND              : bond        0.00230 (   15)
  SS BOND              : angle       0.77638 (   30)
  hydrogen bonds       : bond        0.03392 (  436)
  hydrogen bonds       : angle       4.58408 ( 1275)
  Misc. bond           : bond        0.00064 (    1)
  link_ALPHA1-2        : bond        0.00637 (    2)
  link_ALPHA1-2        : angle       1.60818 (    6)
  link_ALPHA1-3        : bond        0.00290 (    2)
  link_ALPHA1-3        : angle       1.43867 (    6)
  link_BETA1-4         : bond        0.01292 (    2)
  link_BETA1-4         : angle       3.56364 (    6)
  link_NAG-ASN         : bond        0.00028 (    1)
  link_NAG-ASN         : angle       1.07175 (    3)

*********************** 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: 28
    poor density    : 112
  time to evaluate  : 0.236 
Fit side-chains
REVERT: A  241 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.6840 (ppp)
REVERT: A  331 PHE cc_start: 0.8389 (OUTLIER) cc_final: 0.8120 (m-10)
REVERT: B  140 TYR cc_start: 0.8447 (p90) cc_final: 0.7996 (p90)
REVERT: B  141 ARG cc_start: 0.7798 (ttp-170) cc_final: 0.7266 (ttp-170)
REVERT: B  154 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6420 (mt-10)
REVERT: B  426 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: B  445 MET cc_start: 0.6361 (ttm) cc_final: 0.6096 (ttp)
REVERT: B  489 MET cc_start: 0.6975 (mtt) cc_final: 0.6659 (mtt)
  outliers start: 28
  outliers final: 19
  residues processed: 128
  average time/residue: 0.0745
  time to fit residues: 14.1221
Evaluate side-chains
  127 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  256 LEU
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  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  394 LEU
Chi-restraints excluded: chain C residue  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 78 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   chunk 60 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 104 optimal weight:    8.9990
   chunk 37 optimal weight:    4.9990
   chunk 88 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   overall best weight:    1.6384

-------------------------------------------------------------------------------
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**
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.196043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.107366 restraints weight = 12131.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.112055 restraints weight = 5559.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.115007 restraints weight = 3689.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.116537 restraints weight = 2980.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.117640 restraints weight = 2676.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9078  Z= 0.179
  Angle     :  0.628  13.611  12279  Z= 0.309
  Chirality :  0.043   0.244   1302
  Planarity :  0.004   0.033   1550
  Dihedral  :  9.602  83.434   1345
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.01 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.25), residues: 1071
  helix:  1.53 (0.25), residues: 411
  sheet: -0.51 (0.36), residues: 210
  loop : -1.11 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 177 
 TYR   0.014   0.001   TYR B 484 
 PHE   0.027   0.002   PHE B 318 
 TRP   0.026   0.002   TRP C 200 
 HIS   0.005   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 9055)
  covalent geometry    : angle       0.62102 (12228)
  SS BOND              : bond        0.00278 (   15)
  SS BOND              : angle       0.77538 (   30)
  hydrogen bonds       : bond        0.03642 (  436)
  hydrogen bonds       : angle       4.61500 ( 1275)
  Misc. bond           : bond        0.00112 (    1)
  link_ALPHA1-2        : bond        0.00565 (    2)
  link_ALPHA1-2        : angle       1.56910 (    6)
  link_ALPHA1-3        : bond        0.00215 (    2)
  link_ALPHA1-3        : angle       1.42769 (    6)
  link_BETA1-4         : bond        0.01295 (    2)
  link_BETA1-4         : angle       3.49426 (    6)
  link_NAG-ASN         : bond        0.00057 (    1)
  link_NAG-ASN         : angle       1.24473 (    3)

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

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

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

  2142 Ramachandran restraints generated.
    1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 107
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  241 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.6123 (ppp)
REVERT: A  331 PHE cc_start: 0.8415 (OUTLIER) cc_final: 0.8153 (m-10)
REVERT: B  140 TYR cc_start: 0.8517 (p90) cc_final: 0.7974 (p90)
REVERT: B  141 ARG cc_start: 0.7868 (ttp-170) cc_final: 0.7282 (ttp-170)
REVERT: B  154 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6402 (mt-10)
REVERT: B  445 MET cc_start: 0.6395 (ttm) cc_final: 0.6149 (ttp)
REVERT: C   77 LEU cc_start: 0.3313 (OUTLIER) cc_final: 0.2904 (mm)
  outliers start: 34
  outliers final: 22
  residues processed: 128
  average time/residue: 0.0757
  time to fit residues: 14.1961
Evaluate side-chains
  126 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  164 MET
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  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  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  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 31 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   chunk 99 optimal weight:   20.0000
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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
B 424 HIS
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.197695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.111297 restraints weight = 11670.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.116005 restraints weight = 5225.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.119080 restraints weight = 3416.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.120757 restraints weight = 2721.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.121531 restraints weight = 2422.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7045
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9078  Z= 0.125
  Angle     :  0.594  12.677  12279  Z= 0.290
  Chirality :  0.042   0.244   1302
  Planarity :  0.004   0.035   1550
  Dihedral  :  9.110  77.866   1345
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 16.33 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.26), residues: 1071
  helix:  1.74 (0.25), residues: 410
  sheet: -0.36 (0.37), residues: 208
  loop : -1.12 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 177 
 TYR   0.011   0.001   TYR B 492 
 PHE   0.026   0.001   PHE B 318 
 TRP   0.026   0.002   TRP B 336 
 HIS   0.004   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9055)
  covalent geometry    : angle       0.58705 (12228)
  SS BOND              : bond        0.00237 (   15)
  SS BOND              : angle       0.73798 (   30)
  hydrogen bonds       : bond        0.03390 (  436)
  hydrogen bonds       : angle       4.49781 ( 1275)
  Misc. bond           : bond        0.00069 (    1)
  link_ALPHA1-2        : bond        0.00575 (    2)
  link_ALPHA1-2        : angle       1.60712 (    6)
  link_ALPHA1-3        : bond        0.00338 (    2)
  link_ALPHA1-3        : angle       1.38970 (    6)
  link_BETA1-4         : bond        0.01324 (    2)
  link_BETA1-4         : angle       3.61125 (    6)
  link_NAG-ASN         : bond        0.00050 (    1)
  link_NAG-ASN         : angle       1.01539 (    3)

*********************** 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
  138 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 104
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  241 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.7379 (ppp)
REVERT: A  302 HIS cc_start: 0.5576 (t70) cc_final: 0.5329 (t70)
REVERT: A  325 GLU cc_start: 0.8537 (pt0) cc_final: 0.8327 (pm20)
REVERT: A  331 PHE cc_start: 0.8395 (OUTLIER) cc_final: 0.8126 (m-10)
REVERT: B  140 TYR cc_start: 0.8469 (p90) cc_final: 0.7890 (p90)
REVERT: B  141 ARG cc_start: 0.7825 (ttp-170) cc_final: 0.7269 (ttp-170)
REVERT: B  154 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6301 (mt-10)
REVERT: B  426 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8070 (tm-30)
REVERT: B  436 MET cc_start: 0.6667 (mmt) cc_final: 0.6462 (mmt)
REVERT: C   77 LEU cc_start: 0.3348 (OUTLIER) cc_final: 0.2921 (mm)
  outliers start: 34
  outliers final: 21
  residues processed: 128
  average time/residue: 0.0865
  time to fit residues: 16.1231
Evaluate side-chains
  127 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   45 ILE
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  330 VAL
Chi-restraints excluded: chain A residue  331 PHE
Chi-restraints excluded: chain B residue   64 VAL
Chi-restraints excluded: chain B residue  111 LEU
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  123 ASN
Chi-restraints excluded: chain B residue  163 THR
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  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  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  318 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 83 optimal weight:    9.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
C  99 HIS
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 170 HIS ** 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 = 0.4345 r_free = 0.4345 target = 0.196485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.108254 restraints weight = 11952.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.112945 restraints weight = 5487.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.115891 restraints weight = 3645.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.117587 restraints weight = 2947.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.118274 restraints weight = 2635.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9078  Z= 0.156
  Angle     :  0.627  16.437  12279  Z= 0.304
  Chirality :  0.043   0.239   1302
  Planarity :  0.004   0.035   1550
  Dihedral  :  8.753  70.512   1345
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 16.86 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.26), residues: 1071
  helix:  1.79 (0.25), residues: 403
  sheet: -0.43 (0.37), residues: 209
  loop : -1.05 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 177 
 TYR   0.014   0.001   TYR A 346 
 PHE   0.027   0.001   PHE B 318 
 TRP   0.029   0.002   TRP B 336 
 HIS   0.005   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9055)
  covalent geometry    : angle       0.61932 (12228)
  SS BOND              : bond        0.00258 (   15)
  SS BOND              : angle       0.74559 (   30)
  hydrogen bonds       : bond        0.03551 (  436)
  hydrogen bonds       : angle       4.52738 ( 1275)
  Misc. bond           : bond        0.00102 (    1)
  link_ALPHA1-2        : bond        0.00485 (    2)
  link_ALPHA1-2        : angle       1.58221 (    6)
  link_ALPHA1-3        : bond        0.00313 (    2)
  link_ALPHA1-3        : angle       1.44613 (    6)
  link_BETA1-4         : bond        0.01368 (    2)
  link_BETA1-4         : angle       3.72932 (    6)
  link_NAG-ASN         : bond        0.00017 (    1)
  link_NAG-ASN         : angle       1.17177 (    3)

*********************** 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
  138 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.411 
Fit side-chains
REVERT: A  241 MET cc_start: 0.7563 (ptm) cc_final: 0.7101 (ppp)
REVERT: A  302 HIS cc_start: 0.5627 (t70) cc_final: 0.5402 (t70)
REVERT: A  325 GLU cc_start: 0.8494 (pt0) cc_final: 0.8272 (pm20)
REVERT: A  331 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.8140 (m-10)
REVERT: B  140 TYR cc_start: 0.8504 (p90) cc_final: 0.7944 (p90)
REVERT: B  154 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6347 (mt-10)
REVERT: B  330 ASN cc_start: 0.6452 (p0) cc_final: 0.6066 (p0)
REVERT: B  436 MET cc_start: 0.6724 (mmt) cc_final: 0.6494 (mmt)
REVERT: C   77 LEU cc_start: 0.3317 (OUTLIER) cc_final: 0.2879 (mm)
  outliers start: 32
  outliers final: 23
  residues processed: 127
  average time/residue: 0.0892
  time to fit residues: 16.3945
Evaluate side-chains
  130 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
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  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  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 84 optimal weight:   40.0000
   chunk 58 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 81 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   chunk 3 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 92 optimal weight:   20.0000
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
C  99 HIS
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 170 HIS ** 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 = 0.4364 r_free = 0.4364 target = 0.198474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.110320 restraints weight = 11992.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.115194 restraints weight = 5442.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.118255 restraints weight = 3596.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 62)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.119993 restraints weight = 2891.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.120804 restraints weight = 2588.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9078  Z= 0.125
  Angle     :  0.626  15.915  12279  Z= 0.301
  Chirality :  0.042   0.241   1302
  Planarity :  0.004   0.036   1550
  Dihedral  :  8.474  66.595   1345
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 18.14 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.26), residues: 1071
  helix:  1.97 (0.25), residues: 402
  sheet: -0.36 (0.37), residues: 208
  loop : -1.02 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C 177 
 TYR   0.010   0.001   TYR B 478 
 PHE   0.034   0.001   PHE B 318 
 TRP   0.029   0.002   TRP B 336 
 HIS   0.012   0.001   HIS C  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9055)
  covalent geometry    : angle       0.61884 (12228)
  SS BOND              : bond        0.00220 (   15)
  SS BOND              : angle       0.71861 (   30)
  hydrogen bonds       : bond        0.03418 (  436)
  hydrogen bonds       : angle       4.43263 ( 1275)
  Misc. bond           : bond        0.00079 (    1)
  link_ALPHA1-2        : bond        0.00496 (    2)
  link_ALPHA1-2        : angle       1.59581 (    6)
  link_ALPHA1-3        : bond        0.00391 (    2)
  link_ALPHA1-3        : angle       1.43159 (    6)
  link_BETA1-4         : bond        0.01450 (    2)
  link_BETA1-4         : angle       3.83404 (    6)
  link_NAG-ASN         : bond        0.00034 (    1)
  link_NAG-ASN         : angle       1.09800 (    3)

********************** 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
  129 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A  241 MET cc_start: 0.7504 (ptm) cc_final: 0.6654 (ppp)
REVERT: A  302 HIS cc_start: 0.5770 (t70) cc_final: 0.5550 (t70)
REVERT: A  325 GLU cc_start: 0.8500 (pt0) cc_final: 0.8291 (pm20)
REVERT: A  331 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8123 (m-10)
REVERT: B   46 MET cc_start: 0.8260 (tpp) cc_final: 0.8054 (tpp)
REVERT: B  140 TYR cc_start: 0.8465 (p90) cc_final: 0.7829 (p90)
REVERT: B  154 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6392 (mt-10)
REVERT: B  436 MET cc_start: 0.6713 (mmt) cc_final: 0.6491 (mmt)
REVERT: C   77 LEU cc_start: 0.3397 (OUTLIER) cc_final: 0.2976 (mm)
  outliers start: 25
  outliers final: 20
  residues processed: 120
  average time/residue: 0.0880
  time to fit residues: 15.3137
Evaluate side-chains
  122 residues out of total 937 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
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  182 LEU
Chi-restraints excluded: chain B residue  185 MET
Chi-restraints excluded: chain B residue  190 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  246 PHE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  319 CYS
Chi-restraints excluded: chain B residue  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  318 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 80 optimal weight:   20.0000
   chunk 104 optimal weight:    9.9990
   chunk 84 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.9384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.198498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.110693 restraints weight = 11843.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.115533 restraints weight = 5376.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.118492 restraints weight = 3553.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 69)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.120267 restraints weight = 2870.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.120938 restraints weight = 2560.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9078  Z= 0.131
  Angle     :  0.613  15.599  12279  Z= 0.295
  Chirality :  0.042   0.225   1302
  Planarity :  0.004   0.037   1550
  Dihedral  :  8.064  58.656   1345
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 17.18 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.26), residues: 1071
  helix:  2.10 (0.25), residues: 395
  sheet: -0.29 (0.37), residues: 204
  loop : -1.04 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 261 
 TYR   0.013   0.001   TYR A 346 
 PHE   0.034   0.001   PHE B 318 
 TRP   0.029   0.002   TRP B 336 
 HIS   0.005   0.001   HIS C 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 9055)
  covalent geometry    : angle       0.60458 (12228)
  SS BOND              : bond        0.00221 (   15)
  SS BOND              : angle       0.70447 (   30)
  hydrogen bonds       : bond        0.03414 (  436)
  hydrogen bonds       : angle       4.41184 ( 1275)
  Misc. bond           : bond        0.00080 (    1)
  link_ALPHA1-2        : bond        0.00461 (    2)
  link_ALPHA1-2        : angle       1.60928 (    6)
  link_ALPHA1-3        : bond        0.00391 (    2)
  link_ALPHA1-3        : angle       1.45036 (    6)
  link_BETA1-4         : bond        0.01500 (    2)
  link_BETA1-4         : angle       3.98686 (    6)
  link_NAG-ASN         : bond        0.00038 (    1)
  link_NAG-ASN         : angle       1.08069 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2007.94 seconds
wall clock time: 35 minutes 7.88 seconds (2107.88 seconds total)