Starting phenix.real_space_refine
on Sun Jun  8 00:34:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tqd_26066/06_2025/7tqd_26066.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tqd_26066/06_2025/7tqd_26066.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tqd_26066/06_2025/7tqd_26066.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tqd_26066/06_2025/7tqd_26066.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tqd_26066/06_2025/7tqd_26066.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tqd_26066/06_2025/7tqd_26066.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      28      5.16       5
     C    5503      2.51       5
     N    1511      2.21       5
     O    1640      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8690
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1730
          Classifications: {'peptide': 226}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215}
    Chain: "B"
      Number of atoms: 3999
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 3999
          Classifications: {'peptide': 513}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 484}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "C"
      Number of atoms: 2878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2878
          Classifications: {'peptide': 357}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 335}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 83
          Unusual residues: {' MG': 2, 'ADP': 1, 'AMP%rna2p': 1, 'ATP': 1}
          Classifications: {'RNA_mixed': 1, 'undetermined': 4}
          Modifications used: {'rna2p': 1}
          Link IDs: {None: 4}
  Time building chain proxies: 6.27, per 1000 atoms: 0.72
  Number of scatterers: 8690
  At special positions: 0
  Unit cell: (72.24, 100.8, 136.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      28     16.00
     P       6     15.00
     Mg      2     11.99
     O    1640      8.00
     N    1511      7.00
     C    5503      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.20
  Conformation dependent library (CDL) restraints added in 973.9 milliseconds
  

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2066

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 7 sheets defined
      41.8% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 387 through 401
      removed outlier: 3.567A  pdb=" N   SER A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   MET A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 421
      removed outlier: 4.079A  pdb=" N   HIS A 421 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 428
    Processing helix  chain 'A' and resid 431 through 442
    Processing helix  chain 'A' and resid 460 through 468
    Processing helix  chain 'A' and resid 479 through 489
      removed outlier: 3.539A  pdb=" N   LEU A 483 " --> pdb=" O   ASP A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 506
      No H-bonds generated for 'chain 'A' and resid 504 through 506'
    Processing helix  chain 'A' and resid 520 through 531
      removed outlier: 3.838A  pdb=" N   ALA A 524 " --> pdb=" O   PRO A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 577
    Processing helix  chain 'B' and resid 9 through 22
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 128 through 150
    Processing helix  chain 'B' and resid 178 through 180
      No H-bonds generated for 'chain 'B' and resid 178 through 180'
    Processing helix  chain 'B' and resid 181 through 187
      removed outlier: 3.512A  pdb=" N   TRP B 185 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   SER B 187 " --> pdb=" O   PRO B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 231
      removed outlier: 3.707A  pdb=" N   LYS B 231 " --> pdb=" O   PRO B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 269
    Processing helix  chain 'B' and resid 271 through 286
    Processing helix  chain 'B' and resid 362 through 366
    Processing helix  chain 'B' and resid 373 through 378
    Processing helix  chain 'B' and resid 387 through 401
      removed outlier: 3.662A  pdb=" N   SER B 391 " --> pdb=" O   GLY B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 442
    Processing helix  chain 'B' and resid 460 through 469
    Processing helix  chain 'B' and resid 479 through 489
      removed outlier: 3.584A  pdb=" N   LEU B 483 " --> pdb=" O   ASP B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 506
      No H-bonds generated for 'chain 'B' and resid 504 through 506'
    Processing helix  chain 'B' and resid 520 through 530
      removed outlier: 3.839A  pdb=" N   ALA B 524 " --> pdb=" O   PRO B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 577
    Processing helix  chain 'C' and resid 3 through 14
    Processing helix  chain 'C' and resid 17 through 38
    Processing helix  chain 'C' and resid 52 through 56
    Processing helix  chain 'C' and resid 84 through 91
    Processing helix  chain 'C' and resid 92 through 100
    Processing helix  chain 'C' and resid 131 through 142
    Processing helix  chain 'C' and resid 206 through 221
      removed outlier: 3.948A  pdb=" N   GLN C 210 " --> pdb=" O   HIS C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 239
    Processing helix  chain 'C' and resid 249 through 260
    Processing helix  chain 'C' and resid 266 through 282
    Processing helix  chain 'C' and resid 282 through 288
    Processing helix  chain 'C' and resid 303 through 307
      removed outlier: 3.604A  pdb=" N   ALA C 306 " --> pdb=" O   ASP C 303 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ARG C 307 " --> pdb=" O   VAL C 304 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 303 through 307'
    Processing helix  chain 'C' and resid 309 through 333
      removed outlier: 3.589A  pdb=" N   ALA C 332 " --> pdb=" O   ARG C 328 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER C 333 " --> pdb=" O   ASN C 329 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 335 through 348
      removed outlier: 3.919A  pdb=" N   LEU C 346 " --> pdb=" O   LEU C 342 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 448 through 452
      removed outlier: 6.624A  pdb=" N   GLN A 405 " --> pdb=" O   ARG A 450 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   PHE A 452 " --> pdb=" O   GLN A 405 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ILE A 407 " --> pdb=" O   PHE A 452 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   LEU A 382 " --> pdb=" O   ILE A 474 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 26
    Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 26
    Processing sheet with id=AA4, first strand: chain 'B' and resid 221 through 222
      removed outlier: 3.624A  pdb=" N   ARG B 221 " --> pdb=" O   PHE B 212 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   SER B 196 " --> pdb=" O   ARG B 210 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   PHE B 212 " --> pdb=" O   PHE B 194 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   PHE B 194 " --> pdb=" O   PHE B 212 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   SER B 197 " --> pdb=" O   THR B 236 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   THR B 236 " --> pdb=" O   SER B 197 " (cutoff:3.500A)
      removed outlier: 9.363A  pdb=" N   LEU B 294 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   ASN B 237 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   LEU B 296 " --> pdb=" O   ASN B 237 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   VAL B 239 " --> pdb=" O   LEU B 296 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   GLY B 298 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   SER B 241 " --> pdb=" O   GLY B 298 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ARG B 311 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 11.311A  pdb=" N   ILE B 312 " --> pdb=" O   ASN B 360 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   ASN B 360 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   TRP B 314 " --> pdb=" O   THR B 358 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   THR B 358 " --> pdb=" O   TRP B 314 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ALA B 316 " --> pdb=" O   VAL B 356 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   ARG B 354 " --> pdb=" O   ARG B 318 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   TRP B 355 " --> pdb=" O   GLN B 167 " (cutoff:3.500A)
      removed outlier: 8.586A  pdb=" N   ARG B 357 " --> pdb=" O   PRO B 169 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   THR B 171 " --> pdb=" O   ARG B 357 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   GLN B 359 " --> pdb=" O   THR B 171 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ILE B 173 " --> pdb=" O   GLN B 359 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   LEU B 207 " --> pdb=" O   PHE B 170 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   VAL B 172 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   LEU B 209 " --> pdb=" O   VAL B 172 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   GLY B 174 " --> pdb=" O   LEU B 209 " (cutoff:3.500A)
      removed outlier: 8.710A  pdb=" N   GLU B 211 " --> pdb=" O   GLY B 174 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 448 through 452
      removed outlier: 6.607A  pdb=" N   VAL B 381 " --> pdb=" O   GLY B 406 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   LEU B 408 " --> pdb=" O   VAL B 381 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   ILE B 383 " --> pdb=" O   LEU B 408 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 51
      removed outlier: 6.728A  pdb=" N   VAL C  75 " --> pdb=" O   VAL C  46 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   THR C  48 " --> pdb=" O   VAL C  73 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   VAL C  73 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   LEU C  50 " --> pdb=" O   ASP C  71 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   ASP C  71 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 192 through 195

    400 hydrogen bonds defined for protein.
    1149 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.48

  Time building geometry restraints manager: 2.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2843
        1.34 -     1.46: 1677
        1.46 -     1.58: 4328
        1.58 -     1.69: 8
        1.69 -     1.81: 46
  Bond restraints: 8902
  Sorted by residual:
  bond pdb=" C4' AMP C 401 "
       pdb=" O4' AMP C 401 "
    ideal  model  delta    sigma   weight residual
    1.426  1.453 -0.027 2.00e-02 2.50e+03 1.82e+00
  bond pdb=" CA  ILE C  93 "
       pdb=" CB  ILE C  93 "
    ideal  model  delta    sigma   weight residual
    1.539  1.532  0.007 5.40e-03 3.43e+04 1.66e+00
  bond pdb=" C4  ADP C 405 "
       pdb=" C5  ADP C 405 "
    ideal  model  delta    sigma   weight residual
    1.490  1.466  0.024 2.00e-02 2.50e+03 1.47e+00
  bond pdb=" C4  AMP C 401 "
       pdb=" C5  AMP C 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.468  0.022 2.00e-02 2.50e+03 1.17e+00
  bond pdb=" CG  PRO B 251 "
       pdb=" CD  PRO B 251 "
    ideal  model  delta    sigma   weight residual
    1.512  1.484  0.028 2.70e-02 1.37e+03 1.10e+00
  ... (remaining 8897 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 11951
        1.91 -     3.82: 129
        3.82 -     5.73: 29
        5.73 -     7.64: 3
        7.64 -     9.55: 2
  Bond angle restraints: 12114
  Sorted by residual:
  angle pdb=" C1' AMP C 401 "
        pdb=" C2' AMP C 401 "
        pdb=" C3' AMP C 401 "
      ideal   model   delta    sigma   weight residual
     111.00  101.45    9.55 3.00e+00 1.11e-01 1.01e+01
  angle pdb=" CA  TRP C  24 "
        pdb=" CB  TRP C  24 "
        pdb=" CG  TRP C  24 "
      ideal   model   delta    sigma   weight residual
     113.60  119.01   -5.41 1.90e+00 2.77e-01 8.12e+00
  angle pdb=" C2' AMP C 401 "
        pdb=" C3' AMP C 401 "
        pdb=" C4' AMP C 401 "
      ideal   model   delta    sigma   weight residual
     111.00  102.84    8.16 3.00e+00 1.11e-01 7.39e+00
  angle pdb=" CA  ALA B 291 "
        pdb=" C   ALA B 291 "
        pdb=" O   ALA B 291 "
      ideal   model   delta    sigma   weight residual
     119.13  121.16   -2.03 1.00e+00 1.00e+00 4.11e+00
  angle pdb=" CA  ALA B 291 "
        pdb=" C   ALA B 291 "
        pdb=" N   PRO B 292 "
      ideal   model   delta    sigma   weight residual
     118.95  116.36    2.59 1.29e+00 6.01e-01 4.04e+00
  ... (remaining 12109 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.65: 5243
       34.65 -    69.30: 67
       69.30 -   103.95: 1
      103.95 -   138.60: 1
      138.60 -   173.25: 2
  Dihedral angle restraints: 5314
    sinusoidal: 2143
      harmonic: 3171
  Sorted by residual:
  dihedral pdb=" O2A ADP C 405 "
           pdb=" O3A ADP C 405 "
           pdb=" PA  ADP C 405 "
           pdb=" PB  ADP C 405 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  126.75  173.25     1      2.00e+01 2.50e-03 4.78e+01
  dihedral pdb=" C5' AMP C 401 "
           pdb=" O5' AMP C 401 "
           pdb=" P   AMP C 401 "
           pdb=" O3P AMP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  150.14  149.87     1      2.00e+01 2.50e-03 4.48e+01
  dihedral pdb=" O1B ADP C 405 "
           pdb=" O3A ADP C 405 "
           pdb=" PB  ADP C 405 "
           pdb=" PA  ADP C 405 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   59.27 -119.27     1      2.00e+01 2.50e-03 3.57e+01
  ... (remaining 5311 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1092
       0.048 -    0.095: 179
       0.095 -    0.143: 58
       0.143 -    0.190: 0
       0.190 -    0.238: 1
  Chirality restraints: 1330
  Sorted by residual:
  chirality pdb=" C3' AMP C 401 "
            pdb=" C2' AMP C 401 "
            pdb=" C4' AMP C 401 "
            pdb=" O3' AMP C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.75    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" C2' ADP C 405 "
            pdb=" C1' ADP C 405 "
            pdb=" C3' ADP C 405 "
            pdb=" O2' ADP C 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.65    0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CA  ILE C 127 "
            pdb=" N   ILE C 127 "
            pdb=" C   ILE C 127 "
            pdb=" CB  ILE C 127 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.61e-01
  ... (remaining 1327 not shown)

  Planarity restraints: 1551
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 291 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.96e+00
        pdb=" C   ALA B 291 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ALA B 291 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   PRO B 292 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 290 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.84e+00
        pdb=" C   ARG B 290 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ARG B 290 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA B 291 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  49 "    0.032 5.00e-02 4.00e+02   4.87e-02 3.79e+00
        pdb=" N   PRO B  50 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO B  50 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  50 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1548 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 20
        2.55 -     3.14: 6196
        3.14 -     3.72: 12740
        3.72 -     4.31: 18284
        4.31 -     4.90: 31305
  Nonbonded interactions: 68545
  Sorted by model distance:
  nonbonded pdb="MG    MG C 403 "
            pdb=" O2B ATP C 404 "
     model   vdw
     1.960 2.170
  nonbonded pdb=" OD2 ASP C  69 "
            pdb="MG    MG C 402 "
     model   vdw
     1.995 2.170
  nonbonded pdb=" OD2 ASP C  71 "
            pdb="MG    MG C 403 "
     model   vdw
     2.254 2.170
  nonbonded pdb=" O   ARG B 468 "
            pdb=" NZ  LYS B 495 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" OD1 ASN B 374 "
            pdb=" NH2 ARG B 377 "
     model   vdw
     2.314 3.120
  ... (remaining 68540 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.070
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
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      :  0.004   0.211   8903  Z= 0.265
  Angle     :  0.540   9.548  12114  Z= 0.267
  Chirality :  0.039   0.238   1330
  Planarity :  0.004   0.049   1551
  Dihedral  : 12.123 173.252   3248
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1078
  helix:  2.65 (0.26), residues: 402
  sheet:  0.52 (0.34), residues: 232
  loop : -1.28 (0.26), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.009   0.001   PHE C  49 
 TYR   0.007   0.001   TYR C 225 
 ARG   0.007   0.000   ARG A 420 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16953 (  398)
  hydrogen bonds       : angle       5.98035 ( 1149)
  covalent geometry    : bond        0.00307 ( 8902)
  covalent geometry    : angle       0.54042 (12114)
  Misc. bond           : bond        0.21139 (    1)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.924 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7872 (mtm-85)
REVERT: A  479 ASP cc_start: 0.7808 (t0) cc_final: 0.7472 (t0)
REVERT: B   11 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8218 (tp30)
REVERT: B   37 LYS cc_start: 0.9298 (mttt) cc_final: 0.8972 (mmmt)
REVERT: B   73 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7397 (mmm160)
REVERT: B  102 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7811 (tp30)
REVERT: B  216 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8924 (mptt)
REVERT: B  231 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8117 (pptt)
REVERT: B  276 PHE cc_start: 0.7312 (m-80) cc_final: 0.7054 (m-80)
REVERT: B  388 SER cc_start: 0.8518 (m) cc_final: 0.8267 (p)
REVERT: B  507 GLU cc_start: 0.8605 (tt0) cc_final: 0.8027 (pt0)
REVERT: B  527 ARG cc_start: 0.7413 (mmp80) cc_final: 0.5999 (mmm-85)
REVERT: C  342 LEU cc_start: 0.8196 (mt) cc_final: 0.7914 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 1.6473
  time to fit residues: 271.5918
Evaluate side-chains
  69 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.0370
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.5858

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

Flipped N/Q/H residues before XYZ refinement:
B  94 ASN
B 178 GLN
C   8 ASN
C 210 GLN
C 254 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.102871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.081750 restraints weight = 16161.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 3.09
r_work: 0.3139 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3143
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8903  Z= 0.131
  Angle     :  0.589   8.041  12114  Z= 0.284
  Chirality :  0.040   0.170   1330
  Planarity :  0.004   0.046   1551
  Dihedral  :  9.552 160.734   1224
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.09 %
    Favored  : 87.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.26), residues: 1078
  helix:  2.61 (0.26), residues: 408
  sheet:  0.57 (0.33), residues: 228
  loop : -1.22 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C  24 
 HIS   0.005   0.001   HIS C 206 
 PHE   0.011   0.001   PHE B 510 
 TYR   0.007   0.001   TYR C 250 
 ARG   0.008   0.000   ARG B 450 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04758 (  398)
  hydrogen bonds       : angle       4.49155 ( 1149)
  covalent geometry    : bond        0.00299 ( 8902)
  covalent geometry    : angle       0.58909 (12114)
  Misc. bond           : bond        0.00061 (    1)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8269 (mtm180) cc_final: 0.7809 (mtm-85)
REVERT: A  479 ASP cc_start: 0.7898 (t0) cc_final: 0.7620 (t0)
REVERT: A  539 ASP cc_start: 0.8079 (m-30) cc_final: 0.7873 (m-30)
REVERT: A  595 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7925 (tttp)
REVERT: B   11 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8154 (tp30)
REVERT: B   37 LYS cc_start: 0.9229 (mttt) cc_final: 0.9004 (mmmt)
REVERT: B  102 GLU cc_start: 0.8669 (mt-10) cc_final: 0.7862 (tp30)
REVERT: B  150 GLU cc_start: 0.7262 (tp30) cc_final: 0.6592 (tt0)
REVERT: B  216 LYS cc_start: 0.9221 (mmtt) cc_final: 0.8899 (mptt)
REVERT: B  231 LYS cc_start: 0.8634 (mtmt) cc_final: 0.8046 (pptt)
REVERT: B  259 GLN cc_start: 0.8141 (tp40) cc_final: 0.7900 (tp40)
REVERT: B  507 GLU cc_start: 0.8825 (tt0) cc_final: 0.8137 (pt0)
REVERT: B  527 ARG cc_start: 0.7483 (mmp80) cc_final: 0.6109 (mmm-85)
REVERT: C  325 GLU cc_start: 0.8602 (tt0) cc_final: 0.8296 (tp30)
  outliers start: 15
  outliers final: 2
  residues processed: 81
  average time/residue: 1.6540
  time to fit residues: 141.5369
Evaluate side-chains
  61 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 1.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  179 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0060
   chunk 88 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0870
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
A 561 GLN
B  58 ASN
B 561 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.101509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.080402 restraints weight = 16430.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 3.12
r_work: 0.3105 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8903  Z= 0.119
  Angle     :  0.553  10.234  12114  Z= 0.262
  Chirality :  0.040   0.149   1330
  Planarity :  0.004   0.040   1551
  Dihedral  :  8.631 169.651   1224
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.29 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.26), residues: 1078
  helix:  2.71 (0.26), residues: 408
  sheet:  0.40 (0.33), residues: 236
  loop : -1.18 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C  24 
 HIS   0.005   0.001   HIS C 206 
 PHE   0.011   0.001   PHE A 510 
 TYR   0.009   0.001   TYR C 250 
 ARG   0.009   0.000   ARG B 450 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04193 (  398)
  hydrogen bonds       : angle       4.13655 ( 1149)
  covalent geometry    : bond        0.00267 ( 8902)
  covalent geometry    : angle       0.55300 (12114)
  Misc. bond           : bond        0.00024 (    1)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8220 (mtm180) cc_final: 0.7907 (ttp-110)
REVERT: A  479 ASP cc_start: 0.7916 (t0) cc_final: 0.7641 (t0)
REVERT: A  539 ASP cc_start: 0.7987 (m-30) cc_final: 0.7747 (m-30)
REVERT: B   11 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8019 (tp30)
REVERT: B   37 LYS cc_start: 0.9241 (mttt) cc_final: 0.8982 (mmmt)
REVERT: B  102 GLU cc_start: 0.8664 (mt-10) cc_final: 0.7859 (tp30)
REVERT: B  216 LYS cc_start: 0.9219 (mmtt) cc_final: 0.8916 (mptt)
REVERT: B  231 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8052 (pptt)
REVERT: B  259 GLN cc_start: 0.8204 (tp40) cc_final: 0.7706 (tm-30)
REVERT: B  267 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7446 (mp10)
REVERT: B  507 GLU cc_start: 0.8815 (tt0) cc_final: 0.8126 (pt0)
REVERT: B  527 ARG cc_start: 0.7620 (mmp80) cc_final: 0.6291 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7871 (tp30)
  outliers start: 12
  outliers final: 6
  residues processed: 75
  average time/residue: 1.5072
  time to fit residues: 119.9193
Evaluate side-chains
  67 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  179 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 35 optimal weight:    0.5980
   chunk 50 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
C 227 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.100488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.079392 restraints weight = 16789.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 3.09
r_work: 0.3123 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3136
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3136
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8903  Z= 0.141
  Angle     :  0.578  11.825  12114  Z= 0.273
  Chirality :  0.041   0.164   1330
  Planarity :  0.004   0.040   1551
  Dihedral  :  7.289 114.532   1224
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.73 %
    Favored  : 85.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.26), residues: 1078
  helix:  2.69 (0.26), residues: 408
  sheet:  0.40 (0.32), residues: 237
  loop : -1.27 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  24 
 HIS   0.005   0.001   HIS C 206 
 PHE   0.013   0.001   PHE A 510 
 TYR   0.010   0.001   TYR C 250 
 ARG   0.005   0.000   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04437 (  398)
  hydrogen bonds       : angle       4.15764 ( 1149)
  covalent geometry    : bond        0.00333 ( 8902)
  covalent geometry    : angle       0.57797 (12114)
  Misc. bond           : bond        0.00065 (    1)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8184 (mtm180) cc_final: 0.7848 (ttp-110)
REVERT: A  539 ASP cc_start: 0.8000 (m-30) cc_final: 0.7767 (m-30)
REVERT: A  595 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8174 (tttp)
REVERT: B   11 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8075 (tp30)
REVERT: B   37 LYS cc_start: 0.9235 (mttt) cc_final: 0.9030 (mmmt)
REVERT: B  216 LYS cc_start: 0.9249 (mmtt) cc_final: 0.8953 (mptt)
REVERT: B  218 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.7195 (ttpp)
REVERT: B  231 LYS cc_start: 0.8752 (mtmt) cc_final: 0.8410 (ptpp)
REVERT: B  259 GLN cc_start: 0.8188 (tp40) cc_final: 0.7659 (tm-30)
REVERT: B  267 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7430 (mp10)
REVERT: B  507 GLU cc_start: 0.8814 (tt0) cc_final: 0.8129 (pt0)
REVERT: B  527 ARG cc_start: 0.7855 (mmp80) cc_final: 0.6475 (mmm-85)
REVERT: B  561 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7672 (mp10)
REVERT: B  594 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7766 (mm-30)
  outliers start: 19
  outliers final: 6
  residues processed: 73
  average time/residue: 1.6772
  time to fit residues: 129.6220
Evaluate side-chains
  66 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 1.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  561 GLN
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  179 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 63 optimal weight:    0.3980
   chunk 72 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 60 optimal weight:    0.0470
   chunk 5 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A 561 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.100441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.079458 restraints weight = 16749.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 3.06
r_work: 0.3123 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.57   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8903  Z= 0.119
  Angle     :  0.556  11.784  12114  Z= 0.260
  Chirality :  0.040   0.157   1330
  Planarity :  0.004   0.038   1551
  Dihedral  :  6.602  88.750   1224
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.17 %
    Favored  : 84.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.26), residues: 1078
  helix:  2.76 (0.26), residues: 408
  sheet:  0.42 (0.32), residues: 237
  loop : -1.16 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.013   0.001   PHE A 510 
 TYR   0.009   0.001   TYR C 250 
 ARG   0.005   0.000   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03992 (  398)
  hydrogen bonds       : angle       4.00930 ( 1149)
  covalent geometry    : bond        0.00276 ( 8902)
  covalent geometry    : angle       0.55591 (12114)
  Misc. bond           : bond        0.00047 (    1)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8208 (mtm180) cc_final: 0.7845 (ttp-110)
REVERT: A  516 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6702 (mm-30)
REVERT: A  539 ASP cc_start: 0.7971 (m-30) cc_final: 0.7734 (m-30)
REVERT: A  595 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8241 (tttp)
REVERT: B   11 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8030 (tp30)
REVERT: B  216 LYS cc_start: 0.9251 (mmtt) cc_final: 0.8982 (mptt)
REVERT: B  218 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7288 (ttpp)
REVERT: B  231 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8436 (ptpp)
REVERT: B  259 GLN cc_start: 0.8141 (tp40) cc_final: 0.7624 (tm-30)
REVERT: B  267 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7587 (mp10)
REVERT: B  507 GLU cc_start: 0.8794 (tt0) cc_final: 0.8133 (pt0)
REVERT: B  527 ARG cc_start: 0.7997 (mmp80) cc_final: 0.6642 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7790 (mm-30)
REVERT: C  194 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7699 (pt)
  outliers start: 20
  outliers final: 7
  residues processed: 72
  average time/residue: 1.4605
  time to fit residues: 111.7646
Evaluate side-chains
  65 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 52
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue   83 MET
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  194 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 52 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 94 optimal weight:    2.9990
   chunk 18 optimal weight:    0.2980
   chunk 102 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0030
   chunk 38 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.8194

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

Flipped N/Q/H residues before XYZ refinement:
A 561 GLN
B 178 GLN
C 227 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.098873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.077900 restraints weight = 16869.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 3.07
r_work: 0.3099 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3096
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3096 r_free = 0.3096    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8903  Z= 0.144
  Angle     :  0.578  11.946  12114  Z= 0.273
  Chirality :  0.041   0.152   1330
  Planarity :  0.004   0.036   1551
  Dihedral  :  6.611  85.852   1224
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.28 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.26), residues: 1078
  helix:  2.71 (0.26), residues: 407
  sheet:  0.32 (0.32), residues: 238
  loop : -1.16 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.014   0.002   PHE A 510 
 TYR   0.010   0.001   TYR C 250 
 ARG   0.004   0.000   ARG C  82 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04450 (  398)
  hydrogen bonds       : angle       4.09109 ( 1149)
  covalent geometry    : bond        0.00345 ( 8902)
  covalent geometry    : angle       0.57754 (12114)
  Misc. bond           : bond        0.00010 (    1)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.922 
Fit side-chains
REVERT: A  377 ARG cc_start: 0.8161 (mtm180) cc_final: 0.7836 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8205 (mtmt)
REVERT: A  516 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6793 (mm-30)
REVERT: A  539 ASP cc_start: 0.7989 (m-30) cc_final: 0.7748 (m-30)
REVERT: A  595 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8230 (tttp)
REVERT: B   11 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8023 (tp30)
REVERT: B  216 LYS cc_start: 0.9232 (mmtt) cc_final: 0.8935 (mptt)
REVERT: B  231 LYS cc_start: 0.8880 (mtmt) cc_final: 0.8535 (ptpp)
REVERT: B  259 GLN cc_start: 0.8098 (tp40) cc_final: 0.7587 (tm-30)
REVERT: B  267 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7628 (mt0)
REVERT: B  507 GLU cc_start: 0.8751 (tt0) cc_final: 0.8025 (pt0)
REVERT: B  527 ARG cc_start: 0.7940 (mmp80) cc_final: 0.6585 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7824 (mm-30)
  outliers start: 21
  outliers final: 6
  residues processed: 71
  average time/residue: 1.5568
  time to fit residues: 117.1621
Evaluate side-chains
  62 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 51
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  179 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 79 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 102 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 561 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.099427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.078557 restraints weight = 17050.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 3.08
r_work: 0.3071 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3092
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.69   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.3374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8903  Z= 0.130
  Angle     :  0.565  12.002  12114  Z= 0.266
  Chirality :  0.040   0.150   1330
  Planarity :  0.004   0.036   1551
  Dihedral  :  6.552  86.488   1224
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 13.83 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.26), residues: 1078
  helix:  2.72 (0.26), residues: 407
  sheet:  0.38 (0.32), residues: 237
  loop : -1.10 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.013   0.001   PHE A 510 
 TYR   0.009   0.001   TYR C 250 
 ARG   0.005   0.000   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04127 (  398)
  hydrogen bonds       : angle       4.06575 ( 1149)
  covalent geometry    : bond        0.00307 ( 8902)
  covalent geometry    : angle       0.56530 (12114)
  Misc. bond           : bond        0.00007 (    1)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 1.095 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8128 (mtm180) cc_final: 0.7770 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8151 (mtmt)
REVERT: A  516 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6767 (mm-30)
REVERT: A  539 ASP cc_start: 0.7952 (m-30) cc_final: 0.7710 (m-30)
REVERT: A  595 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8212 (tttp)
REVERT: B   11 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8100 (tp30)
REVERT: B   55 MET cc_start: 0.8137 (tpt) cc_final: 0.7765 (tpt)
REVERT: B  216 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8910 (mptt)
REVERT: B  267 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7591 (mp10)
REVERT: B  507 GLU cc_start: 0.8714 (tt0) cc_final: 0.7918 (pt0)
REVERT: B  527 ARG cc_start: 0.7858 (mmp80) cc_final: 0.6494 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7852 (mm-30)
  outliers start: 17
  outliers final: 8
  residues processed: 66
  average time/residue: 1.9614
  time to fit residues: 137.9596
Evaluate side-chains
  64 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 1.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LYS
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  179 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 101 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0050
   chunk 46 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
A 561 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.099642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.078310 restraints weight = 17241.810|
|-----------------------------------------------------------------------------|
r_work (start): 0.3204 rms_B_bonded: 3.16
r_work: 0.3071 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3079 r_free = 0.3079    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8903  Z= 0.120
  Angle     :  0.563  12.335  12114  Z= 0.265
  Chirality :  0.040   0.149   1330
  Planarity :  0.004   0.035   1551
  Dihedral  :  6.504  87.830   1224
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.27 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.26), residues: 1078
  helix:  2.73 (0.26), residues: 408
  sheet:  0.38 (0.32), residues: 238
  loop : -1.07 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.013   0.001   PHE A 510 
 TYR   0.010   0.001   TYR B 582 
 ARG   0.004   0.000   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03975 (  398)
  hydrogen bonds       : angle       4.00220 ( 1149)
  covalent geometry    : bond        0.00284 ( 8902)
  covalent geometry    : angle       0.56276 (12114)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 2.294 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8134 (mtm180) cc_final: 0.7779 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8136 (mtmt)
REVERT: A  516 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6792 (mm-30)
REVERT: A  539 ASP cc_start: 0.7928 (m-30) cc_final: 0.7669 (m-30)
REVERT: B   11 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8087 (tp30)
REVERT: B  216 LYS cc_start: 0.9186 (mmtt) cc_final: 0.8905 (mptt)
REVERT: B  267 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7612 (mt0)
REVERT: B  507 GLU cc_start: 0.8705 (tt0) cc_final: 0.7891 (pt0)
REVERT: B  527 ARG cc_start: 0.7818 (mmp80) cc_final: 0.6454 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7862 (mm-30)
REVERT: C  194 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7586 (pt)
  outliers start: 17
  outliers final: 7
  residues processed: 65
  average time/residue: 1.7520
  time to fit residues: 122.0027
Evaluate side-chains
  63 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LYS
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  194 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 36 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 44 optimal weight:    0.0040
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
A 561 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.099419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.078118 restraints weight = 17119.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 3.15
r_work: 0.3068 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.3559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8903  Z= 0.127
  Angle     :  0.573  12.311  12114  Z= 0.270
  Chirality :  0.040   0.148   1330
  Planarity :  0.004   0.035   1551
  Dihedral  :  6.508  87.840   1224
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.49 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.26), residues: 1078
  helix:  2.73 (0.26), residues: 407
  sheet:  0.38 (0.32), residues: 237
  loop : -1.00 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.013   0.001   PHE A 510 
 TYR   0.011   0.001   TYR B 582 
 ARG   0.004   0.000   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04054 (  398)
  hydrogen bonds       : angle       4.00856 ( 1149)
  covalent geometry    : bond        0.00302 ( 8902)
  covalent geometry    : angle       0.57256 (12114)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8131 (mtm180) cc_final: 0.7810 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8135 (mtmt)
REVERT: A  516 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6747 (mm-30)
REVERT: A  539 ASP cc_start: 0.7934 (m-30) cc_final: 0.7680 (m-30)
REVERT: B   11 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8027 (tp30)
REVERT: B  216 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8902 (mptt)
REVERT: B  507 GLU cc_start: 0.8694 (tt0) cc_final: 0.7866 (pt0)
REVERT: B  527 ARG cc_start: 0.7771 (mmp80) cc_final: 0.6407 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7857 (mm-30)
REVERT: C  194 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7584 (pt)
  outliers start: 15
  outliers final: 7
  residues processed: 63
  average time/residue: 1.4229
  time to fit residues: 95.6064
Evaluate side-chains
  61 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LYS
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  194 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 82 optimal weight:    0.4980
   chunk 35 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0570
   chunk 40 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0980
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
A 561 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.100461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.079830 restraints weight = 17107.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 3.09
r_work: 0.3093 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3116
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.70   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3116
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8903  Z= 0.107
  Angle     :  0.545  12.526  12114  Z= 0.258
  Chirality :  0.039   0.147   1330
  Planarity :  0.004   0.034   1551
  Dihedral  :  6.415  88.556   1224
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 14.71 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.26), residues: 1078
  helix:  2.77 (0.26), residues: 408
  sheet:  0.35 (0.32), residues: 239
  loop : -0.92 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.012   0.001   PHE A 510 
 TYR   0.012   0.001   TYR B 582 
 ARG   0.004   0.000   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03681 (  398)
  hydrogen bonds       : angle       3.91037 ( 1149)
  covalent geometry    : bond        0.00246 ( 8902)
  covalent geometry    : angle       0.54531 (12114)
  Misc. bond           : bond        0.00017 (    1)

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7803 (ttp-110)
REVERT: A  444 LEU cc_start: 0.8274 (pp) cc_final: 0.8072 (pp)
REVERT: A  516 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6646 (mm-30)
REVERT: A  539 ASP cc_start: 0.7932 (m-30) cc_final: 0.7666 (m-30)
REVERT: B   11 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8027 (tp30)
REVERT: B  216 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8894 (mptt)
REVERT: B  527 ARG cc_start: 0.7741 (mmp80) cc_final: 0.6365 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7892 (mm-30)
REVERT: C  194 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7541 (pt)
  outliers start: 10
  outliers final: 5
  residues processed: 58
  average time/residue: 1.4128
  time to fit residues: 87.5424
Evaluate side-chains
  56 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  194 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 28 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0020
   chunk 47 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0670
   chunk 25 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 106 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0370
   overall best weight:    0.3004

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

Flipped N/Q/H residues before XYZ refinement:
A 561 GLN
C 107 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.101111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.080270 restraints weight = 17052.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 3.10
r_work: 0.3109 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.72   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049   8903  Z= 0.097
  Angle     :  0.552  15.954  12114  Z= 0.257
  Chirality :  0.039   0.150   1330
  Planarity :  0.003   0.033   1551
  Dihedral  :  6.280  84.654   1224
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 14.93 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.26), residues: 1078
  helix:  2.82 (0.26), residues: 408
  sheet:  0.39 (0.33), residues: 239
  loop : -0.88 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C  24 
 HIS   0.003   0.001   HIS C 206 
 PHE   0.012   0.001   PHE A 510 
 TYR   0.013   0.001   TYR B 582 
 ARG   0.004   0.000   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03397 (  398)
  hydrogen bonds       : angle       3.82911 ( 1149)
  covalent geometry    : bond        0.00221 ( 8902)
  covalent geometry    : angle       0.55188 (12114)
  Misc. bond           : bond        0.00018 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5642.01 seconds
wall clock time: 100 minutes 33.23 seconds (6033.23 seconds total)