Starting phenix.real_space_refine
on Tue Mar  3 22:54:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tqd_26066/03_2026/7tqd_26066.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tqd_26066/03_2026/7tqd_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_26066/03_2026/7tqd_26066.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tqd_26066/03_2026/7tqd_26066.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tqd_26066/03_2026/7tqd_26066.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tqd_26066/03_2026/7tqd_26066.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1, 'GLN:plan1': 1, 'GLU: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: 1.89, per 1000 atoms: 0.22
  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: 0.61
  Conformation dependent library (CDL) restraints added in 265.0 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: 0.28
  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: 1.32

  Time building geometry restraints manager: 0.79 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:             7.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.770
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.510
-------------------------------------------------------------------------------
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 : 3.15
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (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
 ARG   0.007   0.000   ARG A 420 
 TYR   0.007   0.001   TYR C 225 
 PHE   0.009   0.001   PHE C  49 
 TRP   0.030   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8902)
  covalent geometry    : angle       0.54042 (12114)
  hydrogen bonds       : bond        0.16953 (  398)
  hydrogen bonds       : angle       5.98035 ( 1149)
  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  : 0.251 
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: 0.7536
  time to fit residues: 123.6700
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  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B   7 GLN
B  94 ASN
C   8 ASN
C 210 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.101524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.080371 restraints weight = 16371.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 3.11
r_work: 0.3115 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3116 r_free = 0.3116    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3116
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8903  Z= 0.152
  Angle     :  0.605   7.921  12114  Z= 0.294
  Chirality :  0.041   0.163   1330
  Planarity :  0.004   0.046   1551
  Dihedral  :  9.509 163.367   1224
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 10.65 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.26), residues: 1078
  helix:  2.55 (0.26), residues: 408
  sheet:  0.42 (0.32), residues: 236
  loop : -1.27 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 505 
 TYR   0.007   0.001   TYR C 250 
 PHE   0.011   0.002   PHE A 510 
 TRP   0.024   0.001   TRP C  24 
 HIS   0.006   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 8902)
  covalent geometry    : angle       0.60461 (12114)
  hydrogen bonds       : bond        0.04948 (  398)
  hydrogen bonds       : angle       4.53344 ( 1149)
  Misc. bond           : bond        0.00007 (    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: 17
    poor density    : 69
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8276 (mtm180) cc_final: 0.7796 (mtm-85)
REVERT: A  479 ASP cc_start: 0.7936 (t0) cc_final: 0.7658 (t0)
REVERT: A  539 ASP cc_start: 0.8104 (m-30) cc_final: 0.7899 (m-30)
REVERT: A  595 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7950 (tttp)
REVERT: B   11 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8114 (tp30)
REVERT: B   37 LYS cc_start: 0.9224 (mttt) cc_final: 0.8996 (mmmt)
REVERT: B  102 GLU cc_start: 0.8676 (mt-10) cc_final: 0.7857 (tp30)
REVERT: B  150 GLU cc_start: 0.7286 (tp30) cc_final: 0.6632 (tt0)
REVERT: B  216 LYS cc_start: 0.9225 (mmtt) cc_final: 0.8904 (mptt)
REVERT: B  231 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8056 (pptt)
REVERT: B  259 GLN cc_start: 0.8156 (tp40) cc_final: 0.7644 (tm-30)
REVERT: B  507 GLU cc_start: 0.8800 (tt0) cc_final: 0.8118 (pt0)
REVERT: B  527 ARG cc_start: 0.7545 (mmp80) cc_final: 0.6126 (mmm-85)
REVERT: C  325 GLU cc_start: 0.8594 (tt0) cc_final: 0.8296 (tp30)
  outliers start: 17
  outliers final: 3
  residues processed: 81
  average time/residue: 0.6958
  time to fit residues: 59.4146
Evaluate side-chains
  62 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain B residue  375 ASP
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 24 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 71 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0040
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
A 417 ASN
A 561 GLN
B  58 ASN
B 561 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.101852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.080672 restraints weight = 16678.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 3.10
r_work: 0.3140 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    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 = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3158
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8903  Z= 0.127
  Angle     :  0.557   9.129  12114  Z= 0.267
  Chirality :  0.040   0.166   1330
  Planarity :  0.004   0.040   1551
  Dihedral  :  8.470 164.408   1224
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 2.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 11.86 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.26), residues: 1078
  helix:  2.67 (0.26), residues: 408
  sheet:  0.43 (0.32), residues: 234
  loop : -1.26 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 450 
 TYR   0.009   0.001   TYR C 250 
 PHE   0.012   0.001   PHE A 510 
 TRP   0.022   0.001   TRP C  24 
 HIS   0.005   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 8902)
  covalent geometry    : angle       0.55656 (12114)
  hydrogen bonds       : bond        0.04391 (  398)
  hydrogen bonds       : angle       4.20378 ( 1149)
  Misc. bond           : bond        0.00014 (    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
  82 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8244 (mtm180) cc_final: 0.7948 (ttp-110)
REVERT: A  539 ASP cc_start: 0.8001 (m-30) cc_final: 0.7776 (m-30)
REVERT: A  595 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8153 (tttp)
REVERT: B   11 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8027 (tp30)
REVERT: B   37 LYS cc_start: 0.9230 (mttt) cc_final: 0.9007 (mmmt)
REVERT: B  102 GLU cc_start: 0.8656 (mt-10) cc_final: 0.7868 (tp30)
REVERT: B  216 LYS cc_start: 0.9238 (mmtt) cc_final: 0.8931 (mptt)
REVERT: B  218 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7146 (ttpp)
REVERT: B  231 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8094 (pptt)
REVERT: B  259 GLN cc_start: 0.8186 (tp40) cc_final: 0.7692 (tm-30)
REVERT: B  267 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7518 (mp10)
REVERT: B  507 GLU cc_start: 0.8846 (tt0) cc_final: 0.8204 (pt0)
REVERT: B  527 ARG cc_start: 0.7752 (mmp80) cc_final: 0.6336 (mmm-85)
REVERT: C  194 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7594 (pt)
  outliers start: 16
  outliers final: 5
  residues processed: 76
  average time/residue: 0.7023
  time to fit residues: 56.4033
Evaluate side-chains
  65 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain B residue  218 LYS
Chi-restraints excluded: chain B residue  267 GLN
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 = 0.3522 r_free = 0.3522 target = 0.096919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.075876 restraints weight = 17382.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3180 rms_B_bonded: 3.10
r_work: 0.3052 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   8903  Z= 0.225
  Angle     :  0.654  10.816  12114  Z= 0.318
  Chirality :  0.044   0.165   1330
  Planarity :  0.005   0.043   1551
  Dihedral  :  7.367 102.960   1224
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 12.62 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.25), residues: 1078
  helix:  2.36 (0.26), residues: 413
  sheet:  0.25 (0.32), residues: 239
  loop : -1.48 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 450 
 TYR   0.012   0.002   TYR C 250 
 PHE   0.018   0.002   PHE C  10 
 TRP   0.023   0.001   TRP C  24 
 HIS   0.006   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 8902)
  covalent geometry    : angle       0.65397 (12114)
  hydrogen bonds       : bond        0.05717 (  398)
  hydrogen bonds       : angle       4.50935 ( 1149)
  Misc. bond           : bond        0.00010 (    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
  87 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 61
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8209 (mtm180) cc_final: 0.7865 (ttp-110)
REVERT: A  539 ASP cc_start: 0.8022 (m-30) cc_final: 0.7801 (m-30)
REVERT: A  595 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8231 (tttp)
REVERT: B   11 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8074 (tp30)
REVERT: B   37 LYS cc_start: 0.9295 (mttt) cc_final: 0.9058 (mmmt)
REVERT: B  216 LYS cc_start: 0.9204 (mmtt) cc_final: 0.8943 (mptt)
REVERT: B  231 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8541 (ptpp)
REVERT: B  259 GLN cc_start: 0.8130 (tp40) cc_final: 0.7631 (tm-30)
REVERT: B  267 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7532 (mp10)
REVERT: B  507 GLU cc_start: 0.8839 (tt0) cc_final: 0.8155 (pt0)
REVERT: B  527 ARG cc_start: 0.7931 (mmp80) cc_final: 0.6450 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7898 (mm-30)
  outliers start: 26
  outliers final: 8
  residues processed: 83
  average time/residue: 0.6932
  time to fit residues: 60.7930
Evaluate side-chains
  65 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  595 LYS
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  493 SER
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue   58 THR
Chi-restraints excluded: chain C residue   83 MET
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 43 optimal weight:    1.9990
   chunk 100 optimal weight:    0.5980
   chunk 71 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 11 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 60 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 149 GLN
C 227 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.099082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.077660 restraints weight = 17038.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 3.14
r_work: 0.3057 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.3209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8903  Z= 0.132
  Angle     :  0.576  10.861  12114  Z= 0.273
  Chirality :  0.041   0.152   1330
  Planarity :  0.004   0.040   1551
  Dihedral  :  6.771  78.212   1224
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.94 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.26), residues: 1078
  helix:  2.62 (0.26), residues: 407
  sheet:  0.27 (0.32), residues: 237
  loop : -1.32 (0.28), residues: 434

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8902)
  covalent geometry    : angle       0.57610 (12114)
  hydrogen bonds       : bond        0.04411 (  398)
  hydrogen bonds       : angle       4.20741 ( 1149)
  Misc. bond           : bond        0.00004 (    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
  71 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8134 (mtm180) cc_final: 0.7775 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8149 (mtmt)
REVERT: A  444 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8353 (pp)
REVERT: A  539 ASP cc_start: 0.7930 (m-30) cc_final: 0.7697 (m-30)
REVERT: A  595 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8182 (tttp)
REVERT: B   11 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8045 (tp30)
REVERT: B   37 LYS cc_start: 0.9299 (mttt) cc_final: 0.9089 (mmmt)
REVERT: B   55 MET cc_start: 0.8084 (tpt) cc_final: 0.7814 (tpt)
REVERT: B  216 LYS cc_start: 0.9199 (mmtt) cc_final: 0.8941 (mptt)
REVERT: B  231 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8472 (ptpp)
REVERT: B  259 GLN cc_start: 0.8069 (tp40) cc_final: 0.7588 (tm-30)
REVERT: B  267 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7550 (mt0)
REVERT: B  507 GLU cc_start: 0.8781 (tt0) cc_final: 0.8049 (pt0)
REVERT: B  527 ARG cc_start: 0.7909 (mmp80) cc_final: 0.6484 (mmm-85)
  outliers start: 16
  outliers final: 6
  residues processed: 66
  average time/residue: 0.6943
  time to fit residues: 48.3403
Evaluate side-chains
  66 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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  444 LEU
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  179 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0770
   chunk 75 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.6338

-------------------------------------------------------------------------------
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 = 0.3557 r_free = 0.3557 target = 0.099569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.078605 restraints weight = 16964.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 3.07
r_work: 0.3066 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3097
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3097 r_free = 0.3097    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3097
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.3382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8903  Z= 0.123
  Angle     :  0.554  11.825  12114  Z= 0.261
  Chirality :  0.040   0.151   1330
  Planarity :  0.004   0.037   1551
  Dihedral  :  6.561  82.384   1224
  Min Nonbonded Distance : 1.982

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.83 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.26), residues: 1078
  helix:  2.71 (0.26), residues: 408
  sheet:  0.33 (0.32), residues: 237
  loop : -1.21 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 450 
 TYR   0.009   0.001   TYR C 250 
 PHE   0.014   0.001   PHE A 510 
 TRP   0.020   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8902)
  covalent geometry    : angle       0.55362 (12114)
  hydrogen bonds       : bond        0.04093 (  398)
  hydrogen bonds       : angle       4.04240 ( 1149)
  Misc. bond           : bond        0.00011 (    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
  76 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 56
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8167 (mtm180) cc_final: 0.7836 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8166 (mtmt)
REVERT: A  444 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8164 (pp)
REVERT: A  516 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6858 (mm-30)
REVERT: A  539 ASP cc_start: 0.7945 (m-30) cc_final: 0.7712 (m-30)
REVERT: A  595 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8224 (tttp)
REVERT: B   11 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8086 (tp30)
REVERT: B   37 LYS cc_start: 0.9322 (mttt) cc_final: 0.9105 (mmmt)
REVERT: B   55 MET cc_start: 0.8110 (tpt) cc_final: 0.7882 (tpt)
REVERT: B  216 LYS cc_start: 0.9189 (mmtt) cc_final: 0.8923 (mptt)
REVERT: B  259 GLN cc_start: 0.8065 (tp40) cc_final: 0.7595 (tm-30)
REVERT: B  267 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7599 (mt0)
REVERT: B  507 GLU cc_start: 0.8716 (tt0) cc_final: 0.7923 (pt0)
REVERT: B  527 ARG cc_start: 0.7832 (mmp80) cc_final: 0.6340 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7895 (mm-30)
  outliers start: 20
  outliers final: 6
  residues processed: 71
  average time/residue: 0.6999
  time to fit residues: 52.3562
Evaluate side-chains
  64 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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  444 LEU
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  179 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0970
   chunk 76 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 102 optimal weight:    0.0060
   chunk 18 optimal weight:    0.1980
   chunk 94 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0870
   overall best weight:    0.2372

-------------------------------------------------------------------------------
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
C 227 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.101824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.080959 restraints weight = 17092.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 3.11
r_work: 0.3118 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3166
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8903  Z= 0.093
  Angle     :  0.535  12.393  12114  Z= 0.250
  Chirality :  0.039   0.156   1330
  Planarity :  0.004   0.035   1551
  Dihedral  :  6.383  89.761   1224
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.60 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.26), residues: 1078
  helix:  2.92 (0.26), residues: 408
  sheet:  0.38 (0.32), residues: 239
  loop : -1.01 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 281 
 TYR   0.011   0.001   TYR B 582 
 PHE   0.012   0.001   PHE A 510 
 TRP   0.022   0.001   TRP C  24 
 HIS   0.003   0.000   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 8902)
  covalent geometry    : angle       0.53493 (12114)
  hydrogen bonds       : bond        0.03263 (  398)
  hydrogen bonds       : angle       3.78480 ( 1149)
  Misc. bond           : bond        0.00019 (    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
  67 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8126 (mtm180) cc_final: 0.7801 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8126 (mtmt)
REVERT: A  539 ASP cc_start: 0.7916 (m-30) cc_final: 0.7687 (m-30)
REVERT: B   11 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7997 (tp30)
REVERT: B   37 LYS cc_start: 0.9315 (mttt) cc_final: 0.9110 (mmmt)
REVERT: B  150 GLU cc_start: 0.7226 (tp30) cc_final: 0.6373 (tt0)
REVERT: B  216 LYS cc_start: 0.9185 (mmtt) cc_final: 0.8900 (mptt)
REVERT: B  267 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7575 (mt0)
REVERT: B  484 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7260 (mttt)
REVERT: B  507 GLU cc_start: 0.8680 (tt0) cc_final: 0.7908 (pt0)
REVERT: B  527 ARG cc_start: 0.7782 (mmp80) cc_final: 0.6311 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7932 (mm-30)
  outliers start: 13
  outliers final: 4
  residues processed: 63
  average time/residue: 0.7169
  time to fit residues: 47.6004
Evaluate side-chains
  57 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LYS
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  484 LYS
Chi-restraints excluded: chain B residue  594 GLU
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 42 optimal weight:    0.6980
   chunk 86 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 31 optimal weight:    0.1980
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3560 r_free = 0.3560 target = 0.099798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.078566 restraints weight = 16942.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 3.12
r_work: 0.3073 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3090
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.82   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3090 r_free = 0.3090    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3090
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8903  Z= 0.126
  Angle     :  0.564  12.122  12114  Z= 0.265
  Chirality :  0.040   0.147   1330
  Planarity :  0.004   0.035   1551
  Dihedral  :  6.434  87.986   1224
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.60 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.26), residues: 1078
  helix:  2.84 (0.26), residues: 408
  sheet:  0.39 (0.32), residues: 237
  loop : -1.03 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 281 
 TYR   0.009   0.001   TYR C 250 
 PHE   0.013   0.001   PHE A 510 
 TRP   0.021   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8902)
  covalent geometry    : angle       0.56367 (12114)
  hydrogen bonds       : bond        0.04008 (  398)
  hydrogen bonds       : angle       3.90222 ( 1149)
  Misc. bond           : bond        0.00009 (    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
  66 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8156 (mtm180) cc_final: 0.7817 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8148 (mtmt)
REVERT: A  516 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6828 (mm-30)
REVERT: A  539 ASP cc_start: 0.7938 (m-30) cc_final: 0.7684 (m-30)
REVERT: B   11 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8014 (tp30)
REVERT: B   37 LYS cc_start: 0.9329 (mttt) cc_final: 0.9091 (mmmt)
REVERT: B  216 LYS cc_start: 0.9172 (mmtt) cc_final: 0.8889 (mptt)
REVERT: B  507 GLU cc_start: 0.8688 (tt0) cc_final: 0.7862 (pt0)
REVERT: B  527 ARG cc_start: 0.7763 (mmp80) cc_final: 0.6392 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7961 (mm-30)
  outliers start: 15
  outliers final: 7
  residues processed: 64
  average time/residue: 0.7106
  time to fit residues: 48.1015
Evaluate side-chains
  61 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
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  127 GLU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 86 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3529 r_free = 0.3529 target = 0.096587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.076145 restraints weight = 16788.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.95
r_work: 0.3064 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3072
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3072 r_free = 0.3072    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.74   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3072 r_free = 0.3072    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3072
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8903  Z= 0.150
  Angle     :  0.575  12.163  12114  Z= 0.274
  Chirality :  0.041   0.154   1330
  Planarity :  0.004   0.036   1551
  Dihedral  :  6.522  84.428   1224
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.82 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.26), residues: 1078
  helix:  2.70 (0.26), residues: 407
  sheet:  0.33 (0.32), residues: 238
  loop : -1.08 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 281 
 TYR   0.009   0.001   TYR B 582 
 PHE   0.014   0.002   PHE C  10 
 TRP   0.024   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8902)
  covalent geometry    : angle       0.57535 (12114)
  hydrogen bonds       : bond        0.04406 (  398)
  hydrogen bonds       : angle       4.05055 ( 1149)
  Misc. bond           : bond        0.00007 (    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
  65 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7857 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8196 (mtmt)
REVERT: A  516 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6877 (mm-30)
REVERT: A  539 ASP cc_start: 0.7948 (m-30) cc_final: 0.7694 (m-30)
REVERT: B   11 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7977 (tp30)
REVERT: B   37 LYS cc_start: 0.9355 (mttt) cc_final: 0.9120 (mmmt)
REVERT: B  216 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8875 (mptt)
REVERT: B  507 GLU cc_start: 0.8682 (tt0) cc_final: 0.7887 (pt0)
REVERT: B  586 LYS cc_start: 0.8599 (tttt) cc_final: 0.8392 (ptmm)
REVERT: B  594 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7926 (mm-30)
  outliers start: 14
  outliers final: 7
  residues processed: 63
  average time/residue: 0.7222
  time to fit residues: 48.1529
Evaluate side-chains
  58 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
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 B residue  127 GLU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0970
   chunk 78 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 106 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 103 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.6378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.097561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.077134 restraints weight = 16810.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.96
r_work: 0.3077 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3098
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.65   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3098 r_free = 0.3098    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3098
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8903  Z= 0.123
  Angle     :  0.560  12.390  12114  Z= 0.265
  Chirality :  0.040   0.146   1330
  Planarity :  0.004   0.035   1551
  Dihedral  :  6.490  86.192   1224
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 15.15 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.26), residues: 1078
  helix:  2.75 (0.26), residues: 407
  sheet:  0.37 (0.32), residues: 237
  loop : -1.00 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 281 
 TYR   0.012   0.001   TYR B 582 
 PHE   0.012   0.001   PHE A 510 
 TRP   0.028   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8902)
  covalent geometry    : angle       0.56033 (12114)
  hydrogen bonds       : bond        0.04009 (  398)
  hydrogen bonds       : angle       3.96727 ( 1149)
  Misc. bond           : bond        0.00013 (    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
  57 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8189 (mtm180) cc_final: 0.7854 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8184 (mtmt)
REVERT: B   11 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7970 (tp30)
REVERT: B   37 LYS cc_start: 0.9343 (mttt) cc_final: 0.9110 (mmmt)
REVERT: B  216 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8870 (mptt)
REVERT: B  594 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7927 (mm-30)
  outliers start: 10
  outliers final: 6
  residues processed: 56
  average time/residue: 0.6740
  time to fit residues: 40.2240
Evaluate side-chains
  54 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LYS
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue  127 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 82 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0070
   chunk 105 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.5800

-------------------------------------------------------------------------------
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 = 0.099743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.078697 restraints weight = 16968.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 3.09
r_work: 0.3073 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3093
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.67   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.3748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8903  Z= 0.119
  Angle     :  0.563  15.918  12114  Z= 0.264
  Chirality :  0.040   0.146   1330
  Planarity :  0.004   0.035   1551
  Dihedral  :  6.470  87.744   1224
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.82 %
    Favored  : 83.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.26), residues: 1078
  helix:  2.69 (0.26), residues: 408
  sheet:  0.39 (0.33), residues: 237
  loop : -1.01 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 281 
 TYR   0.012   0.001   TYR B 582 
 PHE   0.012   0.001   PHE A 510 
 TRP   0.027   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8902)
  covalent geometry    : angle       0.56273 (12114)
  hydrogen bonds       : bond        0.03929 (  398)
  hydrogen bonds       : angle       3.95965 ( 1149)
  Misc. bond           : bond        0.00014 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2367.15 seconds
wall clock time: 41 minutes 10.37 seconds (2470.37 seconds total)