Starting phenix.real_space_refine
on Wed Sep 25 00:25:41 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/09_2024/7tqd_26066.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/09_2024/7tqd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/09_2024/7tqd_26066.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/09_2024/7tqd_26066.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/09_2024/7tqd_26066.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tqd_26066/09_2024/7tqd_26066.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

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

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 11.61, per 1000 atoms: 1.34
  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: 3.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.04
  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: 2.41

  Time building geometry restraints manager: 3.69 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:             23.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     30.850
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   65.250
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.900 
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: 1.5789
  time to fit residues: 261.1212
Evaluate side-chains
  69 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
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 fitting.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8132 (mtm180) cc_final: 0.7813 (mtm-85)
REVERT: A  479 ASP cc_start: 0.7822 (t0) cc_final: 0.7536 (t0)
REVERT: A  595 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7902 (tttp)
REVERT: B   11 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8167 (tp30)
REVERT: B  102 GLU cc_start: 0.8459 (mt-10) cc_final: 0.7799 (tp30)
REVERT: B  150 GLU cc_start: 0.7240 (tp30) cc_final: 0.6534 (tt0)
REVERT: B  216 LYS cc_start: 0.9147 (mmtt) cc_final: 0.8880 (mptt)
REVERT: B  231 LYS cc_start: 0.8651 (mtmt) cc_final: 0.8113 (pptt)
REVERT: B  259 GLN cc_start: 0.8042 (tp40) cc_final: 0.7749 (tp40)
REVERT: B  507 GLU cc_start: 0.8605 (tt0) cc_final: 0.8060 (pt0)
REVERT: B  527 ARG cc_start: 0.7503 (mmp80) cc_final: 0.6122 (mmm-85)
REVERT: C  325 GLU cc_start: 0.8554 (tt0) cc_final: 0.8272 (tp30)
  outliers start: 16
  outliers final: 3
  residues processed: 82
  average time/residue: 1.5553
  time to fit residues: 134.9520
Evaluate side-chains
  61 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
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 54 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 87 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    0.7780

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8902  Z= 0.226
  Angle     :  0.573  10.133  12114  Z= 0.276
  Chirality :  0.040   0.151   1330
  Planarity :  0.004   0.042   1551
  Dihedral  :  8.572 138.204   1224
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.18 %
    Favored  : 86.17 %
  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:  0.93 (0.26), residues: 1078
  helix:  2.59 (0.26), residues: 408
  sheet:  0.40 (0.32), residues: 234
  loop : -1.24 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C  24 
 HIS   0.005   0.001   HIS C 206 
 PHE   0.013   0.002   PHE A 510 
 TYR   0.009   0.001   TYR C 250 
 ARG   0.005   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
  74 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8083 (mtm180) cc_final: 0.7875 (ttp-110)
REVERT: A  539 ASP cc_start: 0.7796 (m-30) cc_final: 0.7556 (m-30)
REVERT: A  595 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8044 (tttp)
REVERT: B   11 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8064 (tp30)
REVERT: B  216 LYS cc_start: 0.9156 (mmtt) cc_final: 0.8881 (mptt)
REVERT: B  218 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.7052 (ttpp)
REVERT: B  231 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8156 (pptt)
REVERT: B  259 GLN cc_start: 0.8123 (tp40) cc_final: 0.7654 (tm-30)
REVERT: B  267 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7348 (mp10)
REVERT: B  507 GLU cc_start: 0.8580 (tt0) cc_final: 0.7997 (pt0)
REVERT: B  527 ARG cc_start: 0.7707 (mmp80) cc_final: 0.6317 (mmm-85)
REVERT: C  194 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7335 (pt)
  outliers start: 15
  outliers final: 5
  residues processed: 71
  average time/residue: 1.6704
  time to fit residues: 125.4346
Evaluate side-chains
  61 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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  218 LYS
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  375 ASP
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 97 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0170
   chunk 50 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   chunk 65 optimal weight:    2.9990
   chunk 98 optimal weight:    0.5980
   chunk 104 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 28 optimal weight:    6.9990
   overall best weight:    0.5218

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8902  Z= 0.176
  Angle     :  0.541  11.081  12114  Z= 0.258
  Chirality :  0.039   0.150   1330
  Planarity :  0.004   0.040   1551
  Dihedral  :  7.975 124.982   1224
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.84 %
    Favored  : 85.40 %
  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:  1.06 (0.26), residues: 1078
  helix:  2.76 (0.26), residues: 408
  sheet:  0.43 (0.32), residues: 236
  loop : -1.23 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.012   0.001   PHE A 510 
 TYR   0.008   0.001   TYR C 250 
 ARG   0.004   0.000   ARG B 450 

*********************** 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
  74 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.876 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7780 (ttp-110)
REVERT: A  539 ASP cc_start: 0.7811 (m-30) cc_final: 0.7574 (m-30)
REVERT: A  595 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8075 (tttp)
REVERT: B   11 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8050 (tp30)
REVERT: B  150 GLU cc_start: 0.7211 (tp30) cc_final: 0.6433 (tt0)
REVERT: B  216 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8891 (mptt)
REVERT: B  231 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8177 (pptt)
REVERT: B  259 GLN cc_start: 0.8069 (tp40) cc_final: 0.7591 (tm-30)
REVERT: B  267 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7312 (mp10)
REVERT: B  507 GLU cc_start: 0.8594 (tt0) cc_final: 0.8020 (pt0)
REVERT: B  527 ARG cc_start: 0.7821 (mmp80) cc_final: 0.6439 (mmm-85)
  outliers start: 16
  outliers final: 7
  residues processed: 71
  average time/residue: 1.5005
  time to fit residues: 113.0420
Evaluate side-chains
  64 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain A residue  595 LYS
Chi-restraints excluded: chain B residue  127 GLU
Chi-restraints excluded: chain B residue  137 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0980
   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 561 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8902  Z= 0.347
  Angle     :  0.626  11.268  12114  Z= 0.304
  Chirality :  0.043   0.161   1330
  Planarity :  0.004   0.041   1551
  Dihedral  :  7.897 112.317   1224
  Min Nonbonded Distance : 1.919

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 13.17 %
    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 (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:  0.81 (0.26), residues: 1078
  helix:  2.49 (0.26), residues: 407
  sheet:  0.34 (0.32), residues: 239
  loop : -1.33 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C  24 
 HIS   0.005   0.001   HIS C 206 
 PHE   0.018   0.002   PHE C  10 
 TYR   0.011   0.002   TYR C 250 
 ARG   0.004   0.001   ARG B 281 

*********************** 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
  78 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 1.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8038 (mtm180) cc_final: 0.7753 (ttp-110)
REVERT: A  539 ASP cc_start: 0.7704 (m-30) cc_final: 0.7467 (m-30)
REVERT: A  595 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8136 (tttp)
REVERT: B   11 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8073 (tp30)
REVERT: B  216 LYS cc_start: 0.9124 (mmtt) cc_final: 0.8904 (mptt)
REVERT: B  231 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8499 (ptpp)
REVERT: B  259 GLN cc_start: 0.8000 (tp40) cc_final: 0.7555 (tm-30)
REVERT: B  267 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7400 (mp10)
REVERT: B  507 GLU cc_start: 0.8590 (tt0) cc_final: 0.7944 (pt0)
REVERT: B  527 ARG cc_start: 0.7924 (mmp80) cc_final: 0.6486 (mmm-85)
REVERT: C   83 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7622 (mtp)
  outliers start: 21
  outliers final: 7
  residues processed: 75
  average time/residue: 1.4836
  time to fit residues: 118.1595
Evaluate side-chains
  62 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
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  137 LEU
Chi-restraints excluded: chain B residue  267 GLN
Chi-restraints excluded: chain B residue  375 ASP
Chi-restraints excluded: chain B residue  594 GLU
Chi-restraints excluded: chain C residue   83 MET
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 35 optimal weight:    0.5980
   chunk 94 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 104 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   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
B 149 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8902  Z= 0.193
  Angle     :  0.550  12.032  12114  Z= 0.264
  Chirality :  0.040   0.155   1330
  Planarity :  0.004   0.039   1551
  Dihedral  :  7.516  97.094   1224
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 3.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 14.27 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.26), residues: 1078
  helix:  2.69 (0.26), residues: 407
  sheet:  0.30 (0.32), residues: 237
  loop : -1.19 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.013   0.001   PHE A 510 
 TYR   0.009   0.001   TYR C 250 
 ARG   0.005   0.000   ARG C  82 

*********************** 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
  71 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.7995 (mtm180) cc_final: 0.7712 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8117 (mtmt)
REVERT: A  444 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8145 (pp)
REVERT: A  535 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8083 (mm-30)
REVERT: A  539 ASP cc_start: 0.7730 (m-30) cc_final: 0.7480 (m-30)
REVERT: A  595 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8117 (tttp)
REVERT: B   11 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8046 (tp30)
REVERT: B  216 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8904 (mptt)
REVERT: B  231 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8474 (ptpp)
REVERT: B  259 GLN cc_start: 0.7937 (tp40) cc_final: 0.7516 (tm-30)
REVERT: B  267 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7458 (mp10)
REVERT: B  507 GLU cc_start: 0.8509 (tt0) cc_final: 0.7845 (pt0)
REVERT: B  527 ARG cc_start: 0.7929 (mmp80) cc_final: 0.6550 (mmm-85)
  outliers start: 17
  outliers final: 7
  residues processed: 66
  average time/residue: 1.5201
  time to fit residues: 106.5605
Evaluate side-chains
  64 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
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  535 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 100 optimal weight:    0.4980
   chunk 11 optimal weight:    0.0370
   chunk 59 optimal weight:    3.9990
   chunk 76 optimal weight:    0.3980
   chunk 87 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 104 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.4458

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   8902  Z= 0.160
  Angle     :  0.535  12.211  12114  Z= 0.253
  Chirality :  0.039   0.152   1330
  Planarity :  0.004   0.036   1551
  Dihedral  :  7.227  86.564   1224
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.60 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.26), residues: 1078
  helix:  2.82 (0.26), residues: 408
  sheet:  0.35 (0.32), residues: 237
  loop : -1.08 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  24 
 HIS   0.003   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
  66 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.7999 (mtm180) cc_final: 0.7714 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8109 (mtmt)
REVERT: A  444 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7923 (pp)
REVERT: A  539 ASP cc_start: 0.7709 (m-30) cc_final: 0.7463 (m-30)
REVERT: B   11 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8097 (tp30)
REVERT: B  216 LYS cc_start: 0.9121 (mmtt) cc_final: 0.8895 (mptt)
REVERT: B  507 GLU cc_start: 0.8469 (tt0) cc_final: 0.7781 (pt0)
REVERT: B  527 ARG cc_start: 0.7828 (mmp80) cc_final: 0.6355 (mmm-85)
REVERT: B  594 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7747 (mm-30)
  outliers start: 12
  outliers final: 3
  residues processed: 62
  average time/residue: 1.5481
  time to fit residues: 101.8971
Evaluate side-chains
  56 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
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 B residue  127 GLU
Chi-restraints excluded: chain B residue  594 GLU
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 41 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 94 optimal weight:    2.9990
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8902  Z= 0.229
  Angle     :  0.565  12.166  12114  Z= 0.273
  Chirality :  0.041   0.151   1330
  Planarity :  0.004   0.036   1551
  Dihedral  :  7.198  83.794   1224
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  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 (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:  1.06 (0.26), residues: 1078
  helix:  2.72 (0.26), residues: 407
  sheet:  0.28 (0.32), residues: 238
  loop : -1.07 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.013   0.002   PHE C  10 
 TYR   0.009   0.001   TYR C 250 
 ARG   0.003   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
  60 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8020 (mtm180) cc_final: 0.7763 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8125 (mtmt)
REVERT: A  444 LEU cc_start: 0.8253 (pp) cc_final: 0.8014 (pp)
REVERT: A  446 ASP cc_start: 0.8503 (t0) cc_final: 0.8215 (m-30)
REVERT: A  539 ASP cc_start: 0.7722 (m-30) cc_final: 0.7465 (m-30)
REVERT: B   11 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8039 (tp30)
REVERT: B  216 LYS cc_start: 0.9107 (mmtt) cc_final: 0.8883 (mptt)
REVERT: B  507 GLU cc_start: 0.8475 (tt0) cc_final: 0.7746 (pt0)
REVERT: B  527 ARG cc_start: 0.7912 (mmp80) cc_final: 0.6532 (mmm-85)
  outliers start: 10
  outliers final: 6
  residues processed: 58
  average time/residue: 1.5978
  time to fit residues: 98.9225
Evaluate side-chains
  57 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LYS
Chi-restraints excluded: chain A residue  425 MET
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  179 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    0.0770
   chunk 97 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.5938

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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.3603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8902  Z= 0.182
  Angle     :  0.542  12.372  12114  Z= 0.260
  Chirality :  0.040   0.150   1330
  Planarity :  0.004   0.035   1551
  Dihedral  :  7.105  86.291   1224
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  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:  1.12 (0.26), residues: 1078
  helix:  2.77 (0.26), residues: 408
  sheet:  0.31 (0.32), residues: 238
  loop : -1.05 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C  24 
 HIS   0.004   0.001   HIS C 206 
 PHE   0.013   0.001   PHE A 510 
 TYR   0.012   0.001   TYR B 582 
 ARG   0.004   0.000   ARG B 281 

*********************** 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 fitting.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8012 (mtm180) cc_final: 0.7745 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8107 (mtmt)
REVERT: A  539 ASP cc_start: 0.7710 (m-30) cc_final: 0.7459 (m-30)
REVERT: B   11 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8039 (tp30)
REVERT: B  216 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8855 (mptt)
REVERT: B  507 GLU cc_start: 0.8443 (tt0) cc_final: 0.7732 (pt0)
REVERT: B  527 ARG cc_start: 0.7769 (mmp80) cc_final: 0.6392 (mmm-85)
REVERT: B  586 LYS cc_start: 0.8510 (tttt) cc_final: 0.8247 (ttpm)
REVERT: B  594 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7732 (mm-30)
  outliers start: 11
  outliers final: 3
  residues processed: 62
  average time/residue: 1.6492
  time to fit residues: 108.3221
Evaluate side-chains
  55 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LYS
Chi-restraints excluded: chain A residue  425 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0670
   chunk 71 optimal weight:    0.0980
   chunk 107 optimal weight:    0.0980
   chunk 99 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 66 optimal weight:    0.3980
   chunk 52 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.2918

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8902  Z= 0.143
  Angle     :  0.543  16.665  12114  Z= 0.256
  Chirality :  0.039   0.151   1330
  Planarity :  0.004   0.033   1551
  Dihedral  :  6.982  88.833   1224
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 15.15 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.26), residues: 1078
  helix:  2.82 (0.26), residues: 408
  sheet:  0.30 (0.32), residues: 240
  loop : -0.98 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C  24 
 HIS   0.003   0.001   HIS C 206 
 PHE   0.012   0.001   PHE A 510 
 TYR   0.012   0.001   TYR B 582 
 ARG   0.007   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
  60 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 1.031 
Fit side-chains
   revert: symmetry clash
REVERT: A  377 ARG cc_start: 0.8003 (mtm180) cc_final: 0.7743 (ttp-110)
REVERT: A  380 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8106 (mtmt)
REVERT: A  539 ASP cc_start: 0.7698 (m-30) cc_final: 0.7444 (m-30)
REVERT: B   11 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8036 (tp30)
REVERT: B  216 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8831 (mptt)
REVERT: B  259 GLN cc_start: 0.7911 (tp40) cc_final: 0.7512 (tm-30)
REVERT: B  527 ARG cc_start: 0.7737 (mmp80) cc_final: 0.6329 (mpt-90)
REVERT: B  586 LYS cc_start: 0.8495 (tttt) cc_final: 0.8250 (ttpm)
REVERT: B  594 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7757 (mm-30)
  outliers start: 6
  outliers final: 1
  residues processed: 58
  average time/residue: 1.5375
  time to fit residues: 94.8115
Evaluate side-chains
  52 residues out of total 922 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.971 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LYS
Chi-restraints excluded: chain B residue  594 GLU
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 91 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0870
   chunk 12 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0770
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.3316

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

Flipped N/Q/H residues before XYZ refinement:
A 561 GLN
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.101132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.080175 restraints weight = 16917.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 3.13
r_work: 0.3101 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    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 = 0.3143 r_free = 0.3143    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3143
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   8902  Z= 0.146
  Angle     :  0.540  13.899  12114  Z= 0.256
  Chirality :  0.039   0.150   1330
  Planarity :  0.004   0.033   1551
  Dihedral  :  6.856  86.092   1224
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 15.48 %
    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:  1.20 (0.26), residues: 1078
  helix:  2.84 (0.26), residues: 408
  sheet:  0.31 (0.32), residues: 240
  loop : -0.98 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C  24 
 HIS   0.010   0.001   HIS B 263 
 PHE   0.012   0.001   PHE A 510 
 TYR   0.012   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: 3182.67 seconds
wall clock time: 58 minutes 29.56 seconds (3509.56 seconds total)