Starting phenix.real_space_refine
on Thu Feb 13 15:34:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tqd_26066/02_2025/7tqd_26066.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tqd_26066/02_2025/7tqd_26066.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tqd_26066/02_2025/7tqd_26066.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tqd_26066/02_2025/7tqd_26066.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tqd_26066/02_2025/7tqd_26066.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tqd_26066/02_2025/7tqd_26066.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      28      5.16       5
     C    5503      2.51       5
     N    1511      2.21       5
     O    1640      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8690
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1730
          Classifications: {'peptide': 226}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 215}
    Chain: "B"
      Number of atoms: 3999
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 3999
          Classifications: {'peptide': 513}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 484}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 42
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "C"
      Number of atoms: 2878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2878
          Classifications: {'peptide': 357}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 335}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 83
          Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1}
          Classifications: {'RNA': 1, 'undetermined': 4}
          Modifications used: {'rna2p': 1}
          Link IDs: {None: 4}
  Time building chain proxies: 6.24, per 1000 atoms: 0.72
  Number of scatterers: 8690
  At special positions: 0
  Unit cell: (72.24, 100.8, 136.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      28     16.00
     P       6     15.00
     Mg      2     11.99
     O    1640      8.00
     N    1511      7.00
     C    5503      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.38
  Conformation dependent library (CDL) restraints added in 972.8 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: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 387 through 401
      removed outlier: 3.567A  pdb=" N   SER A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   MET A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 415 through 421
      removed outlier: 4.079A  pdb=" N   HIS A 421 " --> pdb=" O   LEU A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 428
    Processing helix  chain 'A' and resid 431 through 442
    Processing helix  chain 'A' and resid 460 through 468
    Processing helix  chain 'A' and resid 479 through 489
      removed outlier: 3.539A  pdb=" N   LEU A 483 " --> pdb=" O   ASP A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 506
      No H-bonds generated for 'chain 'A' and resid 504 through 506'
    Processing helix  chain 'A' and resid 520 through 531
      removed outlier: 3.838A  pdb=" N   ALA A 524 " --> pdb=" O   PRO A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 577
    Processing helix  chain 'B' and resid 9 through 22
    Processing helix  chain 'B' and resid 118 through 123
    Processing helix  chain 'B' and resid 128 through 150
    Processing helix  chain 'B' and resid 178 through 180
      No H-bonds generated for 'chain 'B' and resid 178 through 180'
    Processing helix  chain 'B' and resid 181 through 187
      removed outlier: 3.512A  pdb=" N   TRP B 185 " --> pdb=" O   ASP B 181 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   SER B 187 " --> pdb=" O   PRO B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 231
      removed outlier: 3.707A  pdb=" N   LYS B 231 " --> pdb=" O   PRO B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 269
    Processing helix  chain 'B' and resid 271 through 286
    Processing helix  chain 'B' and resid 362 through 366
    Processing helix  chain 'B' and resid 373 through 378
    Processing helix  chain 'B' and resid 387 through 401
      removed outlier: 3.662A  pdb=" N   SER B 391 " --> pdb=" O   GLY B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 442
    Processing helix  chain 'B' and resid 460 through 469
    Processing helix  chain 'B' and resid 479 through 489
      removed outlier: 3.584A  pdb=" N   LEU B 483 " --> pdb=" O   ASP B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 506
      No H-bonds generated for 'chain 'B' and resid 504 through 506'
    Processing helix  chain 'B' and resid 520 through 530
      removed outlier: 3.839A  pdb=" N   ALA B 524 " --> pdb=" O   PRO B 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 577
    Processing helix  chain 'C' and resid 3 through 14
    Processing helix  chain 'C' and resid 17 through 38
    Processing helix  chain 'C' and resid 52 through 56
    Processing helix  chain 'C' and resid 84 through 91
    Processing helix  chain 'C' and resid 92 through 100
    Processing helix  chain 'C' and resid 131 through 142
    Processing helix  chain 'C' and resid 206 through 221
      removed outlier: 3.948A  pdb=" N   GLN C 210 " --> pdb=" O   HIS C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 239
    Processing helix  chain 'C' and resid 249 through 260
    Processing helix  chain 'C' and resid 266 through 282
    Processing helix  chain 'C' and resid 282 through 288
    Processing helix  chain 'C' and resid 303 through 307
      removed outlier: 3.604A  pdb=" N   ALA C 306 " --> pdb=" O   ASP C 303 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ARG C 307 " --> pdb=" O   VAL C 304 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 303 through 307'
    Processing helix  chain 'C' and resid 309 through 333
      removed outlier: 3.589A  pdb=" N   ALA C 332 " --> pdb=" O   ARG C 328 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER C 333 " --> pdb=" O   ASN C 329 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 335 through 348
      removed outlier: 3.919A  pdb=" N   LEU C 346 " --> pdb=" O   LEU C 342 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 448 through 452
      removed outlier: 6.624A  pdb=" N   GLN A 405 " --> pdb=" O   ARG A 450 " (cutoff:3.500A)
      removed outlier: 8.025A  pdb=" N   PHE A 452 " --> pdb=" O   GLN A 405 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   ILE A 407 " --> pdb=" O   PHE A 452 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   LEU A 382 " --> pdb=" O   ILE A 474 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 26
    Processing sheet with id=AA3, first strand: chain 'B' and resid 25 through 26
    Processing sheet with id=AA4, first strand: chain 'B' and resid 221 through 222
      removed outlier: 3.624A  pdb=" N   ARG B 221 " --> pdb=" O   PHE B 212 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   SER B 196 " --> pdb=" O   ARG B 210 " (cutoff:3.500A)
      removed outlier: 5.164A  pdb=" N   PHE B 212 " --> pdb=" O   PHE B 194 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   PHE B 194 " --> pdb=" O   PHE B 212 " (cutoff:3.500A)
      removed outlier: 7.079A  pdb=" N   SER B 197 " --> pdb=" O   THR B 236 " (cutoff:3.500A)
      removed outlier: 5.700A  pdb=" N   THR B 236 " --> pdb=" O   SER B 197 " (cutoff:3.500A)
      removed outlier: 9.363A  pdb=" N   LEU B 294 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 7.269A  pdb=" N   ASN B 237 " --> pdb=" O   LEU B 294 " (cutoff:3.500A)
      removed outlier: 7.975A  pdb=" N   LEU B 296 " --> pdb=" O   ASN B 237 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   VAL B 239 " --> pdb=" O   LEU B 296 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   GLY B 298 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   SER B 241 " --> pdb=" O   GLY B 298 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ARG B 311 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 11.311A  pdb=" N   ILE B 312 " --> pdb=" O   ASN B 360 " (cutoff:3.500A)
      removed outlier: 8.189A  pdb=" N   ASN B 360 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   TRP B 314 " --> pdb=" O   THR B 358 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   THR B 358 " --> pdb=" O   TRP B 314 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   ALA B 316 " --> pdb=" O   VAL B 356 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   ARG B 354 " --> pdb=" O   ARG B 318 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   TRP B 355 " --> pdb=" O   GLN B 167 " (cutoff:3.500A)
      removed outlier: 8.586A  pdb=" N   ARG B 357 " --> pdb=" O   PRO B 169 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   THR B 171 " --> pdb=" O   ARG B 357 " (cutoff:3.500A)
      removed outlier: 7.954A  pdb=" N   GLN B 359 " --> pdb=" O   THR B 171 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ILE B 173 " --> pdb=" O   GLN B 359 " (cutoff:3.500A)
      removed outlier: 7.438A  pdb=" N   LEU B 207 " --> pdb=" O   PHE B 170 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   VAL B 172 " --> pdb=" O   LEU B 207 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   LEU B 209 " --> pdb=" O   VAL B 172 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   GLY B 174 " --> pdb=" O   LEU B 209 " (cutoff:3.500A)
      removed outlier: 8.710A  pdb=" N   GLU B 211 " --> pdb=" O   GLY B 174 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 448 through 452
      removed outlier: 6.607A  pdb=" N   VAL B 381 " --> pdb=" O   GLY B 406 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   LEU B 408 " --> pdb=" O   VAL B 381 " (cutoff:3.500A)
      removed outlier: 6.201A  pdb=" N   ILE B 383 " --> pdb=" O   LEU B 408 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 45 through 51
      removed outlier: 6.728A  pdb=" N   VAL C  75 " --> pdb=" O   VAL C  46 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   THR C  48 " --> pdb=" O   VAL C  73 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   VAL C  73 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   LEU C  50 " --> pdb=" O   ASP C  71 " (cutoff:3.500A)
      removed outlier: 7.623A  pdb=" N   ASP C  71 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 192 through 195

    400 hydrogen bonds defined for protein.
    1149 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.44

  Time building geometry restraints manager: 2.71 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=" 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
  bond pdb=" C2' ADP C 405 "
       pdb=" C3' ADP C 405 "
    ideal  model  delta    sigma   weight residual
    1.524  1.506  0.018 2.00e-02 2.50e+03 8.31e-01
  ... (remaining 8897 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 11890
        1.46 -     2.92: 163
        2.92 -     4.38: 41
        4.38 -     5.84: 18
        5.84 -     7.30: 2
  Bond angle restraints: 12114
  Sorted by residual:
  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=" 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
  angle pdb=" C   ILE B 144 "
        pdb=" N   ASP B 145 "
        pdb=" CA  ASP B 145 "
      ideal   model   delta    sigma   weight residual
     120.29  117.48    2.81 1.42e+00 4.96e-01 3.93e+00
  angle pdb=" O1B ADP C 405 "
        pdb=" PB  ADP C 405 "
        pdb=" O3B ADP C 405 "
      ideal   model   delta    sigma   weight residual
     119.90  114.10    5.80 3.00e+00 1.11e-01 3.74e+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 -    0.028: 847
       0.028 -    0.056: 325
       0.056 -    0.084: 74
       0.084 -    0.113: 66
       0.113 -    0.141: 18
  Chirality restraints: 1330
  Sorted by residual:
  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
  chirality pdb=" CA  VAL B  49 "
            pdb=" N   VAL B  49 "
            pdb=" C   VAL B  49 "
            pdb=" CB  VAL B  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.16e-01
  ... (remaining 1327 not shown)

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

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 20
        2.55 -     3.14: 6196
        3.14 -     3.72: 12740
        3.72 -     4.31: 18284
        4.31 -     4.90: 31305
  Nonbonded interactions: 68545
  Sorted by model distance:
  nonbonded pdb="MG    MG C 403 "
            pdb=" O2B ATP C 404 "
     model   vdw
     1.960 2.170
  nonbonded pdb=" OD2 ASP C  69 "
            pdb="MG    MG C 402 "
     model   vdw
     1.995 2.170
  nonbonded pdb=" OD2 ASP C  71 "
            pdb="MG    MG C 403 "
     model   vdw
     2.254 2.170
  nonbonded pdb=" O   ARG B 468 "
            pdb=" NZ  LYS B 495 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" OD1 ASN B 374 "
            pdb=" NH2 ARG B 377 "
     model   vdw
     2.314 3.120
  ... (remaining 68540 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.710
  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:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.870
  Find NCS groups from input model:        0.070
  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:             0.010
  Load rotamer database and sin/cos tables:12.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.740
-------------------------------------------------------------------------------
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      :  0.003   0.031   8902  Z= 0.201
  Angle     :  0.520   7.302  12114  Z= 0.262
  Chirality :  0.039   0.141   1330
  Planarity :  0.004   0.049   1551
  Dihedral  : 12.102 173.252   3248
  Min Nonbonded Distance : 1.960

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

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

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

*********************** 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  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8183 (mtm180) cc_final: 0.7872 (mtm-85)
REVERT: A  479 ASP cc_start: 0.7808 (t0) cc_final: 0.7472 (t0)
REVERT: B   11 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8218 (tp30)
REVERT: B   37 LYS cc_start: 0.9298 (mttt) cc_final: 0.8972 (mmmt)
REVERT: B   73 ARG cc_start: 0.7616 (mmm160) cc_final: 0.7397 (mmm160)
REVERT: B  102 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7811 (tp30)
REVERT: B  216 LYS cc_start: 0.9139 (mmtt) cc_final: 0.8924 (mptt)
REVERT: B  231 LYS cc_start: 0.8682 (mtmt) cc_final: 0.8117 (pptt)
REVERT: B  276 PHE cc_start: 0.7312 (m-80) cc_final: 0.7054 (m-80)
REVERT: B  388 SER cc_start: 0.8518 (m) cc_final: 0.8267 (p)
REVERT: B  507 GLU cc_start: 0.8605 (tt0) cc_final: 0.8027 (pt0)
REVERT: B  527 ARG cc_start: 0.7413 (mmp80) cc_final: 0.5999 (mmm-85)
REVERT: C  342 LEU cc_start: 0.8196 (mt) cc_final: 0.7914 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 1.6872
  time to fit residues: 278.1957
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  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.0370
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.5858

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.102960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.081885 restraints weight = 16148.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 3.08
r_work: 0.3137 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3141 r_free = 0.3141    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3141
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8902  Z= 0.199
  Angle     :  0.580   7.835  12114  Z= 0.283
  Chirality :  0.040   0.168   1330
  Planarity :  0.004   0.046   1551
  Dihedral  :  9.480 147.234   1224
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 10.87 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1078
  helix:  2.63 (0.26), residues: 408
  sheet:  0.59 (0.33), residues: 228
  loop : -1.21 (0.27), residues: 442

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

*********************** 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
  87 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8270 (mtm180) cc_final: 0.7810 (mtm-85)
REVERT: A  479 ASP cc_start: 0.7893 (t0) cc_final: 0.7609 (t0)
REVERT: A  595 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7932 (tttp)
REVERT: B   11 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8174 (tp30)
REVERT: B   37 LYS cc_start: 0.9227 (mttt) cc_final: 0.9005 (mmmt)
REVERT: B  102 GLU cc_start: 0.8668 (mt-10) cc_final: 0.7862 (tp30)
REVERT: B  150 GLU cc_start: 0.7229 (tp30) cc_final: 0.6559 (tt0)
REVERT: B  216 LYS cc_start: 0.9218 (mmtt) cc_final: 0.8898 (mptt)
REVERT: B  231 LYS cc_start: 0.8631 (mtmt) cc_final: 0.8031 (pptt)
REVERT: B  259 GLN cc_start: 0.8137 (tp40) cc_final: 0.7894 (tp40)
REVERT: B  507 GLU cc_start: 0.8824 (tt0) cc_final: 0.8152 (pt0)
REVERT: B  527 ARG cc_start: 0.7465 (mmp80) cc_final: 0.6091 (mmm-85)
REVERT: B  588 MET cc_start: 0.7773 (mmm) cc_final: 0.7573 (mmm)
REVERT: C  325 GLU cc_start: 0.8597 (tt0) cc_final: 0.8287 (tp30)
  outliers start: 16
  outliers final: 3
  residues processed: 82
  average time/residue: 1.5982
  time to fit residues: 138.6051
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  : 0.966 
-------------------------------------------------------------------------------
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 35 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0570
   chunk 88 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0470
   chunk 53 optimal weight:    0.3980
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.102164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.081056 restraints weight = 16395.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 3.12
r_work: 0.3121 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3131
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8902  Z= 0.169
  Angle     :  0.544  10.392  12114  Z= 0.259
  Chirality :  0.039   0.153   1330
  Planarity :  0.004   0.041   1551
  Dihedral  :  8.540 136.743   1224
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.29 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.26), residues: 1078
  helix:  2.73 (0.26), residues: 408
  sheet:  0.54 (0.33), residues: 230
  loop : -1.19 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.011   0.001   PHE A 510 
 TYR   0.008   0.001   TYR C 250 
 ARG   0.006   0.000   ARG B 450 

*********************** 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
  75 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 64
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8222 (mtm180) cc_final: 0.7702 (mtm-85)
REVERT: A  479 ASP cc_start: 0.7893 (t0) cc_final: 0.7604 (t0)
REVERT: A  539 ASP cc_start: 0.8037 (m-30) cc_final: 0.7814 (m-30)
REVERT: A  595 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.8065 (tttp)
REVERT: B   11 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8020 (tp30)
REVERT: B   37 LYS cc_start: 0.9235 (mttt) cc_final: 0.8985 (mmmt)
REVERT: B  102 GLU cc_start: 0.8660 (mt-10) cc_final: 0.7840 (tp30)
REVERT: B  150 GLU cc_start: 0.7279 (tp30) cc_final: 0.6619 (tt0)
REVERT: B  216 LYS cc_start: 0.9217 (mmtt) cc_final: 0.8911 (mptt)
REVERT: B  231 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8028 (pptt)
REVERT: B  259 GLN cc_start: 0.8200 (tp40) cc_final: 0.7963 (tp40)
REVERT: B  267 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7358 (mp10)
REVERT: B  507 GLU cc_start: 0.8797 (tt0) cc_final: 0.8112 (pt0)
REVERT: B  527 ARG cc_start: 0.7610 (mmp80) cc_final: 0.6261 (mmm-85)
  outliers start: 11
  outliers final: 5
  residues processed: 72
  average time/residue: 1.6246
  time to fit residues: 123.5473
Evaluate side-chains
  64 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  122 LEU
Chi-restraints excluded: chain C residue  179 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.096974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.076003 restraints weight = 17092.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3194 rms_B_bonded: 3.08
r_work: 0.3072 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3091
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3091 r_free = 0.3091    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3091
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8158
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   8902  Z= 0.349
  Angle     :  0.657  11.612  12114  Z= 0.321
  Chirality :  0.044   0.159   1330
  Planarity :  0.005   0.050   1551
  Dihedral  :  8.172 124.923   1224
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 12.73 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.25), residues: 1078
  helix:  2.34 (0.26), residues: 413
  sheet:  0.25 (0.32), residues: 237
  loop : -1.45 (0.27), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C  24 
 HIS   0.007   0.002   HIS C 206 
 PHE   0.017   0.002   PHE A 489 
 TYR   0.013   0.002   TYR C 250 
 ARG   0.004   0.001   ARG B 281 

*********************** 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
  83 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8196 (mtm180) cc_final: 0.7871 (ttp-110)
REVERT: A  539 ASP cc_start: 0.8002 (m-30) cc_final: 0.7782 (m-30)
REVERT: A  595 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8218 (tttp)
REVERT: B   11 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8085 (tp30)
REVERT: B   37 LYS cc_start: 0.9292 (mttt) cc_final: 0.9057 (mmmt)
REVERT: B  216 LYS cc_start: 0.9219 (mmtt) cc_final: 0.8961 (mptt)
REVERT: B  231 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8562 (ptpp)
REVERT: B  259 GLN cc_start: 0.8140 (tp40) cc_final: 0.7639 (tm-30)
REVERT: B  267 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7493 (mp10)
REVERT: B  507 GLU cc_start: 0.8851 (tt0) cc_final: 0.8221 (pt0)
REVERT: B  527 ARG cc_start: 0.7954 (mmp80) cc_final: 0.6494 (mmm-85)
REVERT: B  561 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7825 (mp10)
REVERT: B  594 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7901 (mm-30)
  outliers start: 20
  outliers final: 6
  residues processed: 79
  average time/residue: 1.5480
  time to fit residues: 129.9564
Evaluate side-chains
  65 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
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  127 GLU
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  561 GLN
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue   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 63 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.098113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.077139 restraints weight = 16958.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 3.07
r_work: 0.3091 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3094
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8902  Z= 0.240
  Angle     :  0.583  11.372  12114  Z= 0.279
  Chirality :  0.041   0.163   1330
  Planarity :  0.004   0.040   1551
  Dihedral  :  7.795 112.709   1224
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 13.94 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.25), residues: 1078
  helix:  2.51 (0.26), residues: 407
  sheet:  0.20 (0.32), residues: 235
  loop : -1.31 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  24 
 HIS   0.005   0.001   HIS C 206 
 PHE   0.014   0.002   PHE A 510 
 TYR   0.010   0.001   TYR C 250 
 ARG   0.004   0.000   ARG C  82 

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

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

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

  2156 Ramachandran restraints generated.
    1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7780 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8099 (mtmt)
REVERT: A  444 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8392 (pp)
REVERT: A  516 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6885 (mm-30)
REVERT: A  539 ASP cc_start: 0.7925 (m-30) cc_final: 0.7688 (m-30)
REVERT: A  595 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8163 (tttp)
REVERT: B   11 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8055 (tp30)
REVERT: B   37 LYS cc_start: 0.9297 (mttt) cc_final: 0.9089 (mmmt)
REVERT: B  216 LYS cc_start: 0.9207 (mmtt) cc_final: 0.8947 (mptt)
REVERT: B  231 LYS cc_start: 0.8838 (mtmt) cc_final: 0.8479 (ptpp)
REVERT: B  259 GLN cc_start: 0.8079 (tp40) cc_final: 0.7597 (tm-30)
REVERT: B  267 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7511 (mp10)
REVERT: B  484 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7231 (mttt)
REVERT: B  507 GLU cc_start: 0.8794 (tt0) cc_final: 0.8062 (pt0)
REVERT: B  527 ARG cc_start: 0.7902 (mmp80) cc_final: 0.6467 (mmm-85)
  outliers start: 20
  outliers final: 6
  residues processed: 72
  average time/residue: 1.5221
  time to fit residues: 116.2510
Evaluate side-chains
  66 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 1.037 
-------------------------------------------------------------------------------
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  484 LYS
Chi-restraints excluded: chain C residue  106 THR
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 52 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 102 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0670
   chunk 41 optimal weight:    2.9990
   chunk 83 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.6520

-------------------------------------------------------------------------------
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 = 0.3554 r_free = 0.3554 target = 0.098975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.078078 restraints weight = 16825.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 3.06
r_work: 0.3107 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3119
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.63   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3119 r_free = 0.3119    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3119
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8902  Z= 0.196
  Angle     :  0.547  12.113  12114  Z= 0.261
  Chirality :  0.040   0.165   1330
  Planarity :  0.004   0.037   1551
  Dihedral  :  7.430  93.661   1224
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 13.94 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.26), residues: 1078
  helix:  2.68 (0.26), residues: 407
  sheet:  0.22 (0.32), residues: 238
  loop : -1.20 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.014   0.001   PHE A 510 
 TYR   0.010   0.001   TYR B 582 
 ARG   0.004   0.000   ARG B 357 

*********************** 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
  73 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8198 (mtm180) cc_final: 0.7854 (ttp-110)
REVERT: A  444 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8227 (pp)
REVERT: A  516 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6771 (mm-30)
REVERT: A  539 ASP cc_start: 0.7938 (m-30) cc_final: 0.7685 (m-30)
REVERT: B   11 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8084 (tp30)
REVERT: B  216 LYS cc_start: 0.9212 (mmtt) cc_final: 0.8972 (mptt)
REVERT: B  259 GLN cc_start: 0.8065 (tp40) cc_final: 0.7624 (tm-30)
REVERT: B  484 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7259 (mttt)
REVERT: B  507 GLU cc_start: 0.8719 (tt0) cc_final: 0.8000 (pt0)
REVERT: B  527 ARG cc_start: 0.7880 (mmp80) cc_final: 0.6397 (mmm-85)
  outliers start: 19
  outliers final: 8
  residues processed: 68
  average time/residue: 1.6162
  time to fit residues: 116.5933
Evaluate side-chains
  61 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 50
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue  127 GLU
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  484 LYS
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  179 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 76 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9990
   chunk 79 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0980
   chunk 101 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3567 r_free = 0.3567 target = 0.099736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.078864 restraints weight = 16941.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 3.08
r_work: 0.3123 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3134
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.71   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3134 r_free = 0.3134    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3134
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8902  Z= 0.161
  Angle     :  0.538  12.228  12114  Z= 0.255
  Chirality :  0.039   0.152   1330
  Planarity :  0.004   0.036   1551
  Dihedral  :  7.196  85.060   1224
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.26), residues: 1078
  helix:  2.79 (0.26), residues: 408
  sheet:  0.26 (0.32), residues: 239
  loop : -1.04 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.013   0.001   PHE A 510 
 TYR   0.011   0.001   TYR B 582 
 ARG   0.005   0.000   ARG B 281 

*********************** 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
  64 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8155 (mtm180) cc_final: 0.7845 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8155 (mtmt)
REVERT: A  539 ASP cc_start: 0.7936 (m-30) cc_final: 0.7700 (m-30)
REVERT: B   11 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8077 (tp30)
REVERT: B  216 LYS cc_start: 0.9214 (mmtt) cc_final: 0.8958 (mptt)
REVERT: B  259 GLN cc_start: 0.8067 (tp40) cc_final: 0.7602 (tm-30)
REVERT: B  484 LYS cc_start: 0.7472 (OUTLIER) cc_final: 0.7252 (mttt)
REVERT: B  507 GLU cc_start: 0.8695 (tt0) cc_final: 0.7934 (pt0)
REVERT: B  527 ARG cc_start: 0.7861 (mmp80) cc_final: 0.6382 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7875 (mm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 61
  average time/residue: 1.5350
  time to fit residues: 99.6037
Evaluate side-chains
  58 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
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  590 ASP
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  484 LYS
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  179 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 7 optimal weight:    0.0170
   chunk 17 optimal weight:    0.0000
   chunk 87 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 46 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9990
   chunk 55 optimal weight:    0.6980
   chunk 75 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.4022

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.100028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.079064 restraints weight = 17091.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 3.10
r_work: 0.3126 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3133
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3133 r_free = 0.3133    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3133
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8902  Z= 0.151
  Angle     :  0.531  12.349  12114  Z= 0.251
  Chirality :  0.039   0.149   1330
  Planarity :  0.004   0.035   1551
  Dihedral  :  7.078  88.677   1224
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.26), residues: 1078
  helix:  2.86 (0.26), residues: 408
  sheet:  0.28 (0.32), residues: 240
  loop : -1.00 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C  24 
 HIS   0.003   0.001   HIS C 206 
 PHE   0.012   0.001   PHE A 510 
 TYR   0.010   0.001   TYR B 582 
 ARG   0.004   0.000   ARG B 281 

*********************** 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
  63 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8135 (mtm180) cc_final: 0.7802 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8092 (mtmt)
REVERT: A  539 ASP cc_start: 0.7937 (m-30) cc_final: 0.7681 (m-30)
REVERT: B   11 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8023 (tp30)
REVERT: B  216 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8922 (mptt)
REVERT: B  259 GLN cc_start: 0.8001 (tp40) cc_final: 0.7552 (tm-30)
REVERT: B  484 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7219 (mttt)
REVERT: B  507 GLU cc_start: 0.8703 (tt0) cc_final: 0.7916 (pt0)
REVERT: B  527 ARG cc_start: 0.7815 (mmp80) cc_final: 0.6353 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7879 (mm-30)
  outliers start: 13
  outliers final: 5
  residues processed: 61
  average time/residue: 1.5797
  time to fit residues: 102.4257
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  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LYS
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  484 LYS
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue  106 THR
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 36 optimal weight:    0.4980
   chunk 87 optimal weight:    0.0060
   chunk 93 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 64 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 9 optimal weight:    0.1980
   chunk 70 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   chunk 44 optimal weight:    0.4980
   overall best weight:    0.3596

-------------------------------------------------------------------------------
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 = 0.3580 r_free = 0.3580 target = 0.100486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.079623 restraints weight = 16975.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 3.09
r_work: 0.3133 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3148
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3148 r_free = 0.3148    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3148
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.3622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8902  Z= 0.145
  Angle     :  0.526  12.439  12114  Z= 0.248
  Chirality :  0.039   0.148   1330
  Planarity :  0.004   0.034   1551
  Dihedral  :  6.924  87.263   1224
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 14.93 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.26), residues: 1078
  helix:  2.91 (0.26), residues: 408
  sheet:  0.36 (0.32), residues: 239
  loop : -0.95 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C  24 
 HIS   0.003   0.001   HIS C 206 
 PHE   0.012   0.001   PHE A 510 
 TYR   0.011   0.001   TYR B 582 
 ARG   0.005   0.000   ARG C  82 

*********************** 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
  64 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8169 (mtm180) cc_final: 0.7872 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8192 (mtmt)
REVERT: A  539 ASP cc_start: 0.7943 (m-30) cc_final: 0.7689 (m-30)
REVERT: B   11 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8007 (tp30)
REVERT: B  216 LYS cc_start: 0.9204 (mmtt) cc_final: 0.8944 (mptt)
REVERT: B  484 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7272 (mttt)
REVERT: B  527 ARG cc_start: 0.7815 (mmp80) cc_final: 0.6435 (mmm-85)
REVERT: B  586 LYS cc_start: 0.8603 (tttt) cc_final: 0.8396 (ttpm)
REVERT: B  594 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7929 (mm-30)
  outliers start: 11
  outliers final: 4
  residues processed: 62
  average time/residue: 1.5792
  time to fit residues: 103.9369
Evaluate side-chains
  56 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 1.030 
-------------------------------------------------------------------------------
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  590 ASP
Chi-restraints excluded: chain B residue  484 LYS
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue  106 THR
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 82 optimal weight:    0.9980
   chunk 35 optimal weight:    0.8980
   chunk 58 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 9 optimal weight:    0.3980
   chunk 71 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0020
   chunk 86 optimal weight:    0.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.100092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.079147 restraints weight = 17016.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 3.09
r_work: 0.3133 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3136
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3136 r_free = 0.3136    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3136
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8902  Z= 0.167
  Angle     :  0.553  16.547  12114  Z= 0.260
  Chirality :  0.039   0.149   1330
  Planarity :  0.004   0.034   1551
  Dihedral  :  6.886  87.053   1224
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 15.26 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.26), residues: 1078
  helix:  2.82 (0.26), residues: 408
  sheet:  0.35 (0.32), residues: 239
  loop : -0.95 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP C  24 
 HIS   0.012   0.001   HIS B 263 
 PHE   0.012   0.001   PHE A 510 
 TYR   0.010   0.001   TYR B 582 
 ARG   0.006   0.000   ARG B 281 

********************** 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
  56 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8137 (mtm180) cc_final: 0.7798 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.8085 (mtmt)
REVERT: A  539 ASP cc_start: 0.7920 (m-30) cc_final: 0.7663 (m-30)
REVERT: B   11 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8018 (tp30)
REVERT: B  216 LYS cc_start: 0.9178 (mmtt) cc_final: 0.8898 (mptt)
REVERT: B  527 ARG cc_start: 0.7764 (mmp80) cc_final: 0.6389 (mmm-85)
REVERT: B  586 LYS cc_start: 0.8548 (tttt) cc_final: 0.8321 (ttpm)
REVERT: B  594 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7925 (mm-30)
  outliers start: 8
  outliers final: 4
  residues processed: 54
  average time/residue: 1.7104
  time to fit residues: 98.4520
Evaluate side-chains
  53 residues out of total 922 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
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  590 ASP
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue  106 THR
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 83 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 47 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 48 optimal weight:    0.1980
   chunk 25 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3553 r_free = 0.3553 target = 0.098874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.077836 restraints weight = 17056.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 3.10
r_work: 0.3110 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3111
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3111 r_free = 0.3111    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3111
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8902  Z= 0.200
  Angle     :  0.559  13.836  12114  Z= 0.268
  Chirality :  0.040   0.149   1330
  Planarity :  0.004   0.034   1551
  Dihedral  :  6.954  89.654   1224
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 15.37 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.26), residues: 1078
  helix:  2.67 (0.26), residues: 408
  sheet:  0.36 (0.32), residues: 237
  loop : -1.00 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP C  24 
 HIS   0.015   0.001   HIS B 263 
 PHE   0.013   0.001   PHE A 510 
 TYR   0.011   0.001   TYR B 582 
 ARG   0.006   0.000   ARG B 281 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5105.18 seconds
wall clock time: 91 minutes 11.91 seconds (5471.91 seconds total)