Starting phenix.real_space_refine
on Thu Feb 13 06:55:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zip_60125/02_2025/8zip_60125.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zip_60125/02_2025/8zip_60125.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zip_60125/02_2025/8zip_60125.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zip_60125/02_2025/8zip_60125.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zip_60125/02_2025/8zip_60125.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zip_60125/02_2025/8zip_60125.cif"
  }
  resolution = 4.9
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      52      5.16       5
     C    5511      2.51       5
     N    1465      2.21       5
     O    1632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8662
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "J"
      Number of atoms: 2887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 2887
          Classifications: {'peptide': 370}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 350}
    Chain: "C"
      Number of atoms: 5748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 714, 5748
          Classifications: {'peptide': 714}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PTRANS': 24, 'TRANS': 687}
          Chain breaks: 6
    Chain: "J"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'ADP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.62, per 1000 atoms: 0.76
  Number of scatterers: 8662
  At special positions: 0
  Unit cell: (127.82, 95.45, 112.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     P       2     15.00
     O    1632      8.00
     N    1465      7.00
     C    5511      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: 2.30
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2028

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 13 sheets defined
      51.2% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'J' and resid 58 through 63
    Processing helix  chain 'J' and resid 80 through 94
    Processing helix  chain 'J' and resid 99 through 103
      removed outlier: 3.639A  pdb=" N   HIS J 103 " --> pdb=" O   PRO J 100 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 114 through 129
      removed outlier: 4.175A  pdb=" N   ARG J 118 " --> pdb=" O   PRO J 114 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 139 through 148
    Processing helix  chain 'J' and resid 174 through 177
      removed outlier: 3.703A  pdb=" N   ILE J 177 " --> pdb=" O   PRO J 174 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'J' and resid 174 through 177'
    Processing helix  chain 'J' and resid 183 through 195
    Processing helix  chain 'J' and resid 196 through 199
    Processing helix  chain 'J' and resid 204 through 219
      removed outlier: 3.538A  pdb=" N   CYS J 219 " --> pdb=" O   LYS J 215 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 224 through 235
    Processing helix  chain 'J' and resid 254 through 259
    Processing helix  chain 'J' and resid 260 through 264
    Processing helix  chain 'J' and resid 265 through 270
      removed outlier: 3.537A  pdb=" N   ILE J 269 " --> pdb=" O   PRO J 266 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 275 through 286
    Processing helix  chain 'J' and resid 291 through 296
    Processing helix  chain 'J' and resid 303 through 307
    Processing helix  chain 'J' and resid 310 through 323
    Processing helix  chain 'J' and resid 336 through 338
      No H-bonds generated for 'chain 'J' and resid 336 through 338'
    Processing helix  chain 'J' and resid 339 through 351
    Processing helix  chain 'J' and resid 352 through 355
    Processing helix  chain 'J' and resid 361 through 368
    Processing helix  chain 'J' and resid 370 through 376
    Processing helix  chain 'C' and resid 6 through 11
      removed outlier: 6.927A  pdb=" N   ALA C  11 " --> pdb=" O   ASP C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 12 through 17
    Processing helix  chain 'C' and resid 19 through 27
      removed outlier: 3.695A  pdb=" N   ARG C  23 " --> pdb=" O   SER C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 85
      removed outlier: 3.710A  pdb=" N   ASP C  85 " --> pdb=" O   PRO C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 93
      removed outlier: 3.578A  pdb=" N   MET C  92 " --> pdb=" O   ASP C  89 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU C  93 " --> pdb=" O   MET C  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 89 through 93'
    Processing helix  chain 'C' and resid 97 through 111
    Processing helix  chain 'C' and resid 136 through 141
      removed outlier: 3.753A  pdb=" N   ALA C 140 " --> pdb=" O   ALA C 136 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 153 through 169
    Processing helix  chain 'C' and resid 183 through 199
    Processing helix  chain 'C' and resid 216 through 232
      removed outlier: 3.867A  pdb=" N   ALA C 224 " --> pdb=" O   GLN C 220 " (cutoff:3.500A)
      Proline residue:  C 226  - end of helix
    Processing helix  chain 'C' and resid 271 through 275
    Processing helix  chain 'C' and resid 284 through 292
      removed outlier: 4.475A  pdb=" N   TYR C 288 " --> pdb=" O   TYR C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 295 through 302
      removed outlier: 3.724A  pdb=" N   LEU C 299 " --> pdb=" O   LYS C 295 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 311
      removed outlier: 3.585A  pdb=" N   ASP C 310 " --> pdb=" O   ASN C 307 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 326 through 340
    Processing helix  chain 'C' and resid 344 through 361
      removed outlier: 4.896A  pdb=" N   VAL C 350 " --> pdb=" O   GLU C 346 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   GLY C 361 " --> pdb=" O   ILE C 357 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 379 through 390
    Processing helix  chain 'C' and resid 392 through 402
    Processing helix  chain 'C' and resid 417 through 448
    Processing helix  chain 'C' and resid 473 through 505
    Processing helix  chain 'C' and resid 516 through 521
      removed outlier: 4.051A  pdb=" N   CYS C 521 " --> pdb=" O   ASP C 517 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 530 through 541
    Processing helix  chain 'C' and resid 545 through 558
    Processing helix  chain 'C' and resid 593 through 599
    Processing helix  chain 'C' and resid 603 through 611
    Processing helix  chain 'C' and resid 615 through 622
    Processing helix  chain 'C' and resid 648 through 666
      removed outlier: 3.759A  pdb=" N   THR C 666 " --> pdb=" O   THR C 662 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 687 through 699
    Processing helix  chain 'C' and resid 699 through 708
    Processing helix  chain 'C' and resid 716 through 724
      removed outlier: 4.052A  pdb=" N   PHE C 720 " --> pdb=" O   LEU C 716 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 744 through 750
    Processing sheet with id=AA1, first strand: chain 'J' and resid 31 through 34
      removed outlier: 6.870A  pdb=" N   LEU J  10 " --> pdb=" O   LEU J 106 " (cutoff:3.500A)
      removed outlier: 8.355A  pdb=" N   THR J 108 " --> pdb=" O   LEU J  10 " (cutoff:3.500A)
      removed outlier: 8.115A  pdb=" N   CYS J  12 " --> pdb=" O   THR J 108 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'J' and resid 55 through 56
    Processing sheet with id=AA3, first strand: chain 'J' and resid 171 through 172
    Processing sheet with id=AA4, first strand: chain 'J' and resid 171 through 172
      removed outlier: 6.369A  pdb=" N   ASN J 299 " --> pdb=" O   ILE J 332 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'J' and resid 240 through 244
      removed outlier: 3.704A  pdb=" N   LEU J 244 " --> pdb=" O   GLN J 248 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   GLN J 248 " --> pdb=" O   LEU J 244 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 47 through 49
    Processing sheet with id=AA7, first strand: chain 'C' and resid 62 through 64
    Processing sheet with id=AA8, first strand: chain 'C' and resid 115 through 118
      removed outlier: 3.559A  pdb=" N   SER C 118 " --> pdb=" O   PHE C 121 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   CYS C 122 " --> pdb=" O   ARG C 673 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   ILE C 675 " --> pdb=" O   CYS C 122 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   THR C 124 " --> pdb=" O   ILE C 675 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   SER C 173 " --> pdb=" O   HIS C 670 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   VAL C 672 " --> pdb=" O   SER C 173 " (cutoff:3.500A)
      removed outlier: 6.115A  pdb=" N   LEU C 175 " --> pdb=" O   VAL C 672 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   CYS C 674 " --> pdb=" O   LEU C 175 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   THR C 177 " --> pdb=" O   CYS C 674 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   GLN C 172 " --> pdb=" O   GLY C 459 " (cutoff:3.500A)
      removed outlier: 7.274A  pdb=" N   LEU C 461 " --> pdb=" O   GLN C 172 " (cutoff:3.500A)
      removed outlier: 5.974A  pdb=" N   ILE C 174 " --> pdb=" O   LEU C 461 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   ILE C 463 " --> pdb=" O   ILE C 174 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   ILE C 176 " --> pdb=" O   ILE C 463 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   GLY C 246 " --> pdb=" O   THR C 266 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   THR C 266 " --> pdb=" O   GLY C 246 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   PHE C 248 " --> pdb=" O   ILE C 264 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   ILE C 264 " --> pdb=" O   PHE C 248 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ARG C 250 " --> pdb=" O   ALA C 262 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   ALA C 262 " --> pdb=" O   ARG C 250 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   HIS C 252 " --> pdb=" O   ALA C 260 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 233 through 234
      removed outlier: 3.608A  pdb=" N   ALA C 234 " --> pdb=" O   SER C 242 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   SER C 242 " --> pdb=" O   ALA C 234 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 365 through 367
    Processing sheet with id=AB2, first strand: chain 'C' and resid 404 through 407
      removed outlier: 3.566A  pdb=" N   VAL C 412 " --> pdb=" O   VAL C 405 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 564 through 565
      removed outlier: 3.654A  pdb=" N   PHE C 578 " --> pdb=" O   TYR C 589 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   GLY C 585 " --> pdb=" O   HIS C 582 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 713 through 715

    411 hydrogen bonds defined for protein.
    1131 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: 2.98

  Time building geometry restraints manager: 2.55 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: 2815
        1.34 -     1.46: 1599
        1.46 -     1.58: 4338
        1.58 -     1.69: 3
        1.69 -     1.81: 90
  Bond restraints: 8845
  Sorted by residual:
  bond pdb=" N   GLU C 410 "
       pdb=" CA  GLU C 410 "
    ideal  model  delta    sigma   weight residual
    1.455  1.484 -0.029 1.25e-02 6.40e+03 5.38e+00
  bond pdb=" C   GLN C 452 "
       pdb=" N   PRO C 453 "
    ideal  model  delta    sigma   weight residual
    1.331  1.353 -0.022 1.20e-02 6.94e+03 3.33e+00
  bond pdb=" C   GLN J 265 "
       pdb=" N   PRO J 266 "
    ideal  model  delta    sigma   weight residual
    1.337  1.319  0.018 9.80e-03 1.04e+04 3.19e+00
  bond pdb=" C4  ADP J 401 "
       pdb=" C5  ADP J 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.457  0.033 2.00e-02 2.50e+03 2.67e+00
  bond pdb=" CB  ARG J  64 "
       pdb=" CG  ARG J  64 "
    ideal  model  delta    sigma   weight residual
    1.520  1.472  0.048 3.00e-02 1.11e+03 2.52e+00
  ... (remaining 8840 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 11630
        1.80 -     3.59: 273
        3.59 -     5.39: 32
        5.39 -     7.19: 6
        7.19 -     8.98: 2
  Bond angle restraints: 11943
  Sorted by residual:
  angle pdb=" N   GLY C  66 "
        pdb=" CA  GLY C  66 "
        pdb=" C   GLY C  66 "
      ideal   model   delta    sigma   weight residual
     114.85  107.98    6.87 1.35e+00 5.49e-01 2.59e+01
  angle pdb=" C   GLY C 710 "
        pdb=" N   PHE C 711 "
        pdb=" CA  PHE C 711 "
      ideal   model   delta    sigma   weight residual
     121.70  127.94   -6.24 1.80e+00 3.09e-01 1.20e+01
  angle pdb=" N   ASN C 688 "
        pdb=" CA  ASN C 688 "
        pdb=" C   ASN C 688 "
      ideal   model   delta    sigma   weight residual
     109.81  117.31   -7.50 2.21e+00 2.05e-01 1.15e+01
  angle pdb=" CA  GLY C 710 "
        pdb=" C   GLY C 710 "
        pdb=" N   PHE C 711 "
      ideal   model   delta    sigma   weight residual
     115.50  120.35   -4.85 1.45e+00 4.76e-01 1.12e+01
  angle pdb=" N   PHE C 711 "
        pdb=" CA  PHE C 711 "
        pdb=" C   PHE C 711 "
      ideal   model   delta    sigma   weight residual
     111.00  119.98   -8.98 2.80e+00 1.28e-01 1.03e+01
  ... (remaining 11938 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.62: 4968
       21.62 -    43.25: 311
       43.25 -    64.87: 36
       64.87 -    86.49: 13
       86.49 -   108.12: 4
  Dihedral angle restraints: 5332
    sinusoidal: 2179
      harmonic: 3153
  Sorted by residual:
  dihedral pdb=" C5' ADP J 401 "
           pdb=" O5' ADP J 401 "
           pdb=" PA  ADP J 401 "
           pdb=" O2A ADP J 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   48.12 -108.12     1      2.00e+01 2.50e-03 3.15e+01
  dihedral pdb=" CA  ALA C 111 "
           pdb=" C   ALA C 111 "
           pdb=" N   TRP C 112 "
           pdb=" CA  TRP C 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.24  -26.76     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  ASP J 181 "
           pdb=" C   ASP J 181 "
           pdb=" N   LEU J 182 "
           pdb=" CA  LEU J 182 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.70   19.30     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 5329 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 942
       0.047 -    0.094: 288
       0.094 -    0.141: 69
       0.141 -    0.188: 2
       0.188 -    0.235: 1
  Chirality restraints: 1302
  Sorted by residual:
  chirality pdb=" CA  ASN C 688 "
            pdb=" N   ASN C 688 "
            pdb=" C   ASN C 688 "
            pdb=" CB  ASN C 688 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  PHE C 711 "
            pdb=" N   PHE C 711 "
            pdb=" C   PHE C 711 "
            pdb=" CB  PHE C 711 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.55e-01
  chirality pdb=" CA  PRO J 114 "
            pdb=" N   PRO J 114 "
            pdb=" C   PRO J 114 "
            pdb=" CB  PRO J 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.14 2.00e-01 2.50e+01 5.23e-01
  ... (remaining 1299 not shown)

  Planarity restraints: 1537
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  98 "    0.034 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO C  99 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO C  99 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C  99 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 225 "   -0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO C 226 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C 226 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 226 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 409 "    0.008 2.00e-02 2.50e+03   1.53e-02 2.34e+00
        pdb=" C   ASN C 409 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   ASN C 409 "    0.010 2.00e-02 2.50e+03
        pdb=" N   GLU C 410 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1534 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.09: 2
        2.09 -     2.79: 2259
        2.79 -     3.49: 12294
        3.49 -     4.20: 20711
        4.20 -     4.90: 36440
  Nonbonded interactions: 71706
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP J  27 "
            pdb=" OG  SER C 644 "
     model   vdw
     1.384 3.040
  nonbonded pdb=" N   THR J 353 "
            pdb=" OE2 GLU C 537 "
     model   vdw
     1.995 3.120
  nonbonded pdb=" O   HIS C 153 "
            pdb=" OG  SER C 156 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" O   MET C 389 "
            pdb=" OG  SER C 613 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" OD1 ASP J 159 "
            pdb=" O3' ADP J 401 "
     model   vdw
     2.183 3.040
  ... (remaining 71701 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.570
  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:             0.020
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.000
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058   8845  Z= 0.401
  Angle     :  0.694   8.983  11943  Z= 0.395
  Chirality :  0.045   0.235   1302
  Planarity :  0.004   0.051   1537
  Dihedral  : 14.309 108.115   3304
  Min Nonbonded Distance : 1.384

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.74 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    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: -3.13 (0.22), residues: 1069
  helix: -1.51 (0.21), residues: 471
  sheet: -2.31 (0.43), residues: 132
  loop : -2.52 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP J 342 
 HIS   0.010   0.001   HIS C 359 
 PHE   0.016   0.002   PHE C 253 
 TYR   0.013   0.001   TYR C 311 
 ARG   0.007   0.001   ARG J 258 

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   26 ASP cc_start: 0.8234 (m-30) cc_final: 0.7635 (t0)
REVERT: J  113 ASN cc_start: 0.7586 (p0) cc_final: 0.7330 (p0)
REVERT: J  159 ASP cc_start: 0.5642 (t70) cc_final: 0.4382 (t70)
REVERT: J  218 LEU cc_start: 0.9000 (mt) cc_final: 0.8768 (tp)
REVERT: J  252 ILE cc_start: 0.8076 (pt) cc_final: 0.7624 (mm)
REVERT: J  300 VAL cc_start: 0.8962 (t) cc_final: 0.8200 (t)
REVERT: J  347 ILE cc_start: 0.8946 (mt) cc_final: 0.8728 (mm)
REVERT: C   75 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8286 (tm-30)
REVERT: C   77 MET cc_start: 0.7941 (mpp) cc_final: 0.7737 (mpp)
REVERT: C  113 MET cc_start: 0.7663 (mtp) cc_final: 0.7331 (mtt)
REVERT: C  290 ILE cc_start: 0.9520 (mt) cc_final: 0.9303 (tp)
REVERT: C  358 MET cc_start: 0.8844 (mtm) cc_final: 0.8586 (mtp)
REVERT: C  363 MET cc_start: 0.9113 (mtp) cc_final: 0.8903 (tpp)
REVERT: C  489 PHE cc_start: 0.9032 (t80) cc_final: 0.8797 (t80)
REVERT: C  517 ASP cc_start: 0.8857 (m-30) cc_final: 0.8553 (t0)
REVERT: C  529 MET cc_start: 0.8368 (tpp) cc_final: 0.8168 (tpp)
REVERT: C  547 MET cc_start: 0.9090 (tmm) cc_final: 0.8807 (tmm)
REVERT: C  687 ASP cc_start: 0.8803 (m-30) cc_final: 0.8573 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 172
  average time/residue: 0.2364
  time to fit residues: 54.5479
Evaluate side-chains
  104 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.4980
   chunk 27 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
J  14 ASN
J  75 HIS
J 355 GLN
J 356 GLN
** C  80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 223 GLN
C 285 HIS
C 487 GLN
C 488 GLN
C 493 HIS
** C 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 658 ASN
C 693 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.046001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.038195 restraints weight = 75418.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.039395 restraints weight = 49549.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.040279 restraints weight = 35807.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8845  Z= 0.205
  Angle     :  0.648   8.741  11943  Z= 0.343
  Chirality :  0.044   0.234   1302
  Planarity :  0.005   0.062   1537
  Dihedral  :  6.087  75.607   1185
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    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: -1.53 (0.24), residues: 1069
  helix: -0.10 (0.23), residues: 477
  sheet: -1.74 (0.41), residues: 144
  loop : -1.68 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP J  81 
 HIS   0.008   0.001   HIS J 373 
 PHE   0.018   0.001   PHE C 671 
 TYR   0.014   0.001   TYR C 456 
 ARG   0.004   0.000   ARG C 244 

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   49 MET cc_start: 0.4028 (ptt) cc_final: 0.3697 (ptp)
REVERT: J  117 ASN cc_start: 0.8938 (t0) cc_final: 0.8523 (t0)
REVERT: J  125 MET cc_start: 0.9001 (mmm) cc_final: 0.8690 (mtt)
REVERT: J  128 THR cc_start: 0.8926 (t) cc_final: 0.8220 (t)
REVERT: J  134 MET cc_start: 0.8015 (tmm) cc_final: 0.7740 (tmm)
REVERT: J  252 ILE cc_start: 0.9506 (pt) cc_final: 0.9301 (mm)
REVERT: J  271 MET cc_start: 0.6964 (tpt) cc_final: 0.6511 (tpt)
REVERT: J  294 ASP cc_start: 0.9485 (m-30) cc_final: 0.9104 (m-30)
REVERT: J  307 MET cc_start: 0.7915 (mmp) cc_final: 0.7495 (mmm)
REVERT: C    6 MET cc_start: 0.8572 (mtm) cc_final: 0.8371 (mtm)
REVERT: C   77 MET cc_start: 0.7826 (mpp) cc_final: 0.7620 (mpp)
REVERT: C  113 MET cc_start: 0.7783 (mtp) cc_final: 0.7171 (mtt)
REVERT: C  267 TYR cc_start: 0.7081 (m-80) cc_final: 0.6758 (m-80)
REVERT: C  363 MET cc_start: 0.9147 (mtp) cc_final: 0.8939 (tpp)
REVERT: C  389 MET cc_start: 0.8552 (mpp) cc_final: 0.8286 (mpp)
REVERT: C  486 LEU cc_start: 0.9261 (mt) cc_final: 0.8852 (tt)
REVERT: C  517 ASP cc_start: 0.9064 (m-30) cc_final: 0.8704 (t0)
REVERT: C  547 MET cc_start: 0.9237 (tmm) cc_final: 0.8840 (tmm)
REVERT: C  575 GLU cc_start: 0.8923 (pt0) cc_final: 0.8456 (pp20)
REVERT: C  581 VAL cc_start: 0.8939 (t) cc_final: 0.8495 (t)
REVERT: C  767 PHE cc_start: 0.7629 (m-80) cc_final: 0.7425 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2135
  time to fit residues: 36.9449
Evaluate side-chains
  91 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
C 293 ASN
C 402 HIS
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 663 ASN
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 755 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.044220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.036643 restraints weight = 79289.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.037750 restraints weight = 52004.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.038610 restraints weight = 37862.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.3299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8845  Z= 0.279
  Angle     :  0.689   8.831  11943  Z= 0.361
  Chirality :  0.045   0.223   1302
  Planarity :  0.005   0.063   1537
  Dihedral  :  5.881  49.728   1185
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.08 %
    Favored  : 93.92 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.44 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    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: -1.07 (0.25), residues: 1069
  helix:  0.22 (0.24), residues: 479
  sheet: -1.60 (0.40), residues: 145
  loop : -1.34 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP J  81 
 HIS   0.007   0.002   HIS J  75 
 PHE   0.013   0.002   PHE C 541 
 TYR   0.015   0.001   TYR C 288 
 ARG   0.010   0.001   ARG J 185 

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.5952 (ptp) cc_final: 0.5601 (ptp)
REVERT: J  125 MET cc_start: 0.9079 (mmm) cc_final: 0.8795 (ttm)
REVERT: J  128 THR cc_start: 0.8993 (t) cc_final: 0.8235 (t)
REVERT: J  167 ILE cc_start: 0.8922 (mm) cc_final: 0.8684 (mm)
REVERT: J  192 MET cc_start: 0.8948 (ttm) cc_final: 0.8643 (tpt)
REVERT: J  242 TYR cc_start: 0.7919 (t80) cc_final: 0.7371 (t80)
REVERT: J  252 ILE cc_start: 0.9393 (pt) cc_final: 0.9160 (mm)
REVERT: J  271 MET cc_start: 0.7170 (tpt) cc_final: 0.6637 (tpt)
REVERT: J  307 MET cc_start: 0.8084 (mmp) cc_final: 0.7630 (mmm)
REVERT: C  113 MET cc_start: 0.7779 (mtp) cc_final: 0.7223 (mtt)
REVERT: C  389 MET cc_start: 0.8485 (mpp) cc_final: 0.8260 (mpp)
REVERT: C  486 LEU cc_start: 0.9221 (mt) cc_final: 0.8835 (tt)
REVERT: C  517 ASP cc_start: 0.9055 (m-30) cc_final: 0.8741 (t0)
REVERT: C  547 MET cc_start: 0.9212 (tmm) cc_final: 0.8814 (tmm)
REVERT: C  575 GLU cc_start: 0.8880 (pt0) cc_final: 0.8415 (pp20)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1804
  time to fit residues: 28.0940
Evaluate side-chains
  76 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 70 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 14 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 64 optimal weight:    0.4980
   chunk 74 optimal weight:    0.3980
   chunk 18 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 91 optimal weight:    0.0870
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.045355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.037531 restraints weight = 76585.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.038669 restraints weight = 49982.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.039572 restraints weight = 36184.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8845  Z= 0.163
  Angle     :  0.600   8.686  11943  Z= 0.308
  Chirality :  0.042   0.218   1302
  Planarity :  0.004   0.062   1537
  Dihedral  :  5.477  44.457   1185
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    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: -0.49 (0.26), residues: 1069
  helix:  0.74 (0.24), residues: 479
  sheet: -1.39 (0.41), residues: 148
  loop : -1.03 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP J  81 
 HIS   0.005   0.001   HIS C 359 
 PHE   0.014   0.001   PHE C 490 
 TYR   0.015   0.001   TYR C 267 
 ARG   0.003   0.000   ARG J 185 

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.6893 (ptp) cc_final: 0.6471 (ptp)
REVERT: J  121 MET cc_start: 0.8411 (mtm) cc_final: 0.8180 (mtm)
REVERT: J  192 MET cc_start: 0.9023 (ttm) cc_final: 0.8686 (tpp)
REVERT: J  242 TYR cc_start: 0.7917 (t80) cc_final: 0.7374 (t80)
REVERT: J  252 ILE cc_start: 0.9373 (pt) cc_final: 0.9139 (mm)
REVERT: J  271 MET cc_start: 0.7151 (tpt) cc_final: 0.6629 (tpt)
REVERT: J  305 THR cc_start: 0.8839 (m) cc_final: 0.8594 (m)
REVERT: J  307 MET cc_start: 0.8036 (mmp) cc_final: 0.7579 (mmm)
REVERT: C    6 MET cc_start: 0.8429 (mtt) cc_final: 0.8194 (mtt)
REVERT: C   77 MET cc_start: 0.7965 (mpp) cc_final: 0.7744 (mpp)
REVERT: C  113 MET cc_start: 0.7770 (mtp) cc_final: 0.7217 (mtt)
REVERT: C  389 MET cc_start: 0.8429 (mpp) cc_final: 0.8217 (mpp)
REVERT: C  486 LEU cc_start: 0.9181 (mt) cc_final: 0.8755 (tt)
REVERT: C  517 ASP cc_start: 0.8999 (m-30) cc_final: 0.8748 (t0)
REVERT: C  575 GLU cc_start: 0.8930 (pt0) cc_final: 0.8398 (pp20)
REVERT: C  581 VAL cc_start: 0.8879 (t) cc_final: 0.8458 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1760
  time to fit residues: 27.6811
Evaluate side-chains
  75 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 75 optimal weight:    0.0770
   chunk 82 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0570
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.5656

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

Flipped N/Q/H residues before XYZ refinement:
J  42 HIS
J 362 GLN
** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.045566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.037729 restraints weight = 75925.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.038927 restraints weight = 49555.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.039822 restraints weight = 35561.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8845  Z= 0.164
  Angle     :  0.594   8.493  11943  Z= 0.303
  Chirality :  0.043   0.252   1302
  Planarity :  0.004   0.058   1537
  Dihedral  :  5.312  45.116   1185
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    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: -0.20 (0.26), residues: 1069
  helix:  0.96 (0.24), residues: 478
  sheet: -1.23 (0.41), residues: 152
  loop : -0.86 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP J  81 
 HIS   0.004   0.001   HIS J  75 
 PHE   0.017   0.001   PHE C 767 
 TYR   0.013   0.001   TYR C 288 
 ARG   0.006   0.000   ARG C 404 

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.6852 (ptp) cc_final: 0.6505 (ptp)
REVERT: J  192 MET cc_start: 0.9011 (ttm) cc_final: 0.8771 (tpp)
REVERT: J  242 TYR cc_start: 0.7938 (t80) cc_final: 0.7363 (t80)
REVERT: J  252 ILE cc_start: 0.9360 (pt) cc_final: 0.9138 (mm)
REVERT: J  271 MET cc_start: 0.7296 (tpt) cc_final: 0.6749 (tpt)
REVERT: J  286 LYS cc_start: 0.9146 (mttp) cc_final: 0.8800 (tttm)
REVERT: J  307 MET cc_start: 0.8096 (mmp) cc_final: 0.7629 (mmm)
REVERT: C    6 MET cc_start: 0.8345 (mtt) cc_final: 0.8052 (mtt)
REVERT: C  113 MET cc_start: 0.7750 (mtp) cc_final: 0.7170 (mtt)
REVERT: C  486 LEU cc_start: 0.9188 (mt) cc_final: 0.8768 (tt)
REVERT: C  517 ASP cc_start: 0.8977 (m-30) cc_final: 0.8735 (t0)
REVERT: C  575 GLU cc_start: 0.8959 (pt0) cc_final: 0.8435 (pp20)
REVERT: C  581 VAL cc_start: 0.8903 (t) cc_final: 0.8507 (t)
REVERT: C  686 MET cc_start: 0.7100 (pmm) cc_final: 0.6805 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1753
  time to fit residues: 27.2637
Evaluate side-chains
  79 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 106 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
J 299 ASN
** C 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.044250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.036662 restraints weight = 79190.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.037834 restraints weight = 51501.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.038703 restraints weight = 36900.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.4286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8845  Z= 0.289
  Angle     :  0.702   8.446  11943  Z= 0.362
  Chirality :  0.045   0.241   1302
  Planarity :  0.005   0.058   1537
  Dihedral  :  5.938  47.811   1185
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 15.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    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: -0.43 (0.26), residues: 1069
  helix:  0.61 (0.24), residues: 486
  sheet: -0.99 (0.42), residues: 150
  loop : -0.95 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP J  81 
 HIS   0.014   0.001   HIS J  75 
 PHE   0.016   0.002   PHE C 671 
 TYR   0.013   0.002   TYR C  46 
 ARG   0.005   0.001   ARG C 244 

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.6809 (ptp) cc_final: 0.6507 (ptp)
REVERT: J  178 MET cc_start: 0.7415 (tmm) cc_final: 0.7012 (tmm)
REVERT: J  192 MET cc_start: 0.8929 (ttm) cc_final: 0.8406 (tpp)
REVERT: J  242 TYR cc_start: 0.8176 (t80) cc_final: 0.7482 (t80)
REVERT: J  252 ILE cc_start: 0.9252 (pt) cc_final: 0.9043 (mm)
REVERT: J  271 MET cc_start: 0.7196 (tpt) cc_final: 0.6627 (tpt)
REVERT: J  286 LYS cc_start: 0.9143 (mttp) cc_final: 0.8748 (tptm)
REVERT: J  305 THR cc_start: 0.8822 (m) cc_final: 0.8528 (m)
REVERT: J  307 MET cc_start: 0.8230 (mmp) cc_final: 0.7696 (mmm)
REVERT: C    6 MET cc_start: 0.8394 (mtt) cc_final: 0.8066 (mtt)
REVERT: C   77 MET cc_start: 0.8066 (mpp) cc_final: 0.7779 (mpp)
REVERT: C  113 MET cc_start: 0.7780 (mtp) cc_final: 0.7178 (mtt)
REVERT: C  358 MET cc_start: 0.8731 (mmt) cc_final: 0.8348 (mmm)
REVERT: C  517 ASP cc_start: 0.9020 (m-30) cc_final: 0.8776 (t0)
REVERT: C  540 MET cc_start: 0.7488 (mmp) cc_final: 0.6857 (mtm)
REVERT: C  575 GLU cc_start: 0.8880 (pt0) cc_final: 0.8389 (pp20)
REVERT: C  581 VAL cc_start: 0.8756 (t) cc_final: 0.8322 (t)
REVERT: C  686 MET cc_start: 0.7129 (pmm) cc_final: 0.6878 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1916
  time to fit residues: 27.3032
Evaluate side-chains
  72 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 1.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 64 optimal weight:    0.9990
   chunk 100 optimal weight:    0.0020
   chunk 39 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0570
   chunk 10 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5108

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

Flipped N/Q/H residues before XYZ refinement:
J  75 HIS
C 223 GLN
C 556 ASN
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.045480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.037816 restraints weight = 77233.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.039014 restraints weight = 50569.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.039889 restraints weight = 36247.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.4458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8845  Z= 0.153
  Angle     :  0.608   8.427  11943  Z= 0.307
  Chirality :  0.042   0.238   1302
  Planarity :  0.004   0.056   1537
  Dihedral  :  5.351  41.870   1185
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  1.29 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    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:  0.04 (0.27), residues: 1069
  helix:  0.97 (0.24), residues: 487
  sheet: -0.77 (0.44), residues: 148
  loop : -0.66 (0.32), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP J  81 
 HIS   0.010   0.001   HIS J  75 
 PHE   0.012   0.001   PHE C 671 
 TYR   0.012   0.001   TYR C 288 
 ARG   0.002   0.000   ARG C 244 

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.989 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.6927 (ptp) cc_final: 0.6644 (ptp)
REVERT: J  178 MET cc_start: 0.7446 (tmm) cc_final: 0.7146 (tmm)
REVERT: J  242 TYR cc_start: 0.7828 (t80) cc_final: 0.7297 (t80)
REVERT: J  271 MET cc_start: 0.7021 (tpt) cc_final: 0.6541 (tpt)
REVERT: J  286 LYS cc_start: 0.9095 (mttp) cc_final: 0.8769 (tttm)
REVERT: J  305 THR cc_start: 0.8786 (m) cc_final: 0.8494 (m)
REVERT: J  307 MET cc_start: 0.8160 (mmp) cc_final: 0.7598 (mmm)
REVERT: C    6 MET cc_start: 0.8419 (mtt) cc_final: 0.8079 (mtm)
REVERT: C   29 ARG cc_start: 0.8203 (mmm160) cc_final: 0.7916 (mmm160)
REVERT: C  113 MET cc_start: 0.7829 (mtp) cc_final: 0.7194 (mtt)
REVERT: C  358 MET cc_start: 0.8731 (mmt) cc_final: 0.8326 (mmm)
REVERT: C  389 MET cc_start: 0.8592 (mpp) cc_final: 0.8142 (mpp)
REVERT: C  486 LEU cc_start: 0.9199 (mt) cc_final: 0.8752 (tt)
REVERT: C  517 ASP cc_start: 0.8997 (m-30) cc_final: 0.8778 (t0)
REVERT: C  540 MET cc_start: 0.7485 (mmp) cc_final: 0.6730 (mtm)
REVERT: C  575 GLU cc_start: 0.8898 (pt0) cc_final: 0.8428 (pp20)
REVERT: C  581 VAL cc_start: 0.8849 (t) cc_final: 0.8511 (t)
REVERT: C  660 LEU cc_start: 0.8725 (tt) cc_final: 0.8444 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1991
  time to fit residues: 29.9617
Evaluate side-chains
  75 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 31 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 73 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 29 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0470
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.045257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.037479 restraints weight = 76784.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.038696 restraints weight = 49926.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.039620 restraints weight = 35674.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.4624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8845  Z= 0.164
  Angle     :  0.601   8.398  11943  Z= 0.306
  Chirality :  0.043   0.232   1302
  Planarity :  0.004   0.056   1537
  Dihedral  :  5.310  43.948   1185
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.75 %
    Favored  : 99.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    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:  0.21 (0.27), residues: 1069
  helix:  1.06 (0.24), residues: 488
  sheet: -0.56 (0.45), residues: 150
  loop : -0.56 (0.32), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J  81 
 HIS   0.004   0.001   HIS C 359 
 PHE   0.011   0.001   PHE C 671 
 TYR   0.023   0.001   TYR C 267 
 ARG   0.003   0.000   ARG C 654 

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.6986 (ptp) cc_final: 0.6698 (ptp)
REVERT: J  125 MET cc_start: 0.8688 (mtt) cc_final: 0.8410 (mtm)
REVERT: J  128 THR cc_start: 0.9005 (t) cc_final: 0.8636 (t)
REVERT: J  178 MET cc_start: 0.7390 (tmm) cc_final: 0.7142 (tmm)
REVERT: J  192 MET cc_start: 0.9036 (tpp) cc_final: 0.8578 (tpp)
REVERT: J  242 TYR cc_start: 0.7861 (t80) cc_final: 0.7352 (t80)
REVERT: J  271 MET cc_start: 0.7115 (tpt) cc_final: 0.6610 (tpt)
REVERT: J  286 LYS cc_start: 0.9070 (mttp) cc_final: 0.8732 (tttm)
REVERT: J  305 THR cc_start: 0.8767 (m) cc_final: 0.8463 (m)
REVERT: J  307 MET cc_start: 0.8193 (mmp) cc_final: 0.7673 (mmm)
REVERT: C    6 MET cc_start: 0.8391 (mtt) cc_final: 0.8022 (mtm)
REVERT: C   29 ARG cc_start: 0.8190 (mmm160) cc_final: 0.7904 (mmm160)
REVERT: C  113 MET cc_start: 0.7782 (mtp) cc_final: 0.7178 (mtt)
REVERT: C  165 MET cc_start: 0.7281 (tpp) cc_final: 0.7057 (tpt)
REVERT: C  389 MET cc_start: 0.8586 (mpp) cc_final: 0.8201 (mpp)
REVERT: C  486 LEU cc_start: 0.9225 (mt) cc_final: 0.8768 (tt)
REVERT: C  517 ASP cc_start: 0.9013 (m-30) cc_final: 0.8731 (t0)
REVERT: C  540 MET cc_start: 0.7423 (mmp) cc_final: 0.6711 (mtm)
REVERT: C  575 GLU cc_start: 0.8917 (pt0) cc_final: 0.8521 (pp20)
REVERT: C  581 VAL cc_start: 0.8853 (t) cc_final: 0.8523 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1783
  time to fit residues: 26.8632
Evaluate side-chains
  77 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0870
   chunk 83 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 94 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   overall best weight:    1.4162

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

Flipped N/Q/H residues before XYZ refinement:
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 663 ASN
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.043861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.036277 restraints weight = 78242.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.037436 restraints weight = 51614.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.038317 restraints weight = 37436.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.4856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8845  Z= 0.260
  Angle     :  0.685   8.499  11943  Z= 0.351
  Chirality :  0.044   0.235   1302
  Planarity :  0.004   0.057   1537
  Dihedral  :  5.706  45.058   1185
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    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: -0.05 (0.27), residues: 1069
  helix:  0.87 (0.24), residues: 481
  sheet: -0.64 (0.45), residues: 147
  loop : -0.73 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C 594 
 HIS   0.003   0.001   HIS C 359 
 PHE   0.017   0.002   PHE C 671 
 TYR   0.026   0.002   TYR C 267 
 ARG   0.005   0.001   ARG C 244 

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   26 ASP cc_start: 0.8677 (m-30) cc_final: 0.7370 (t0)
REVERT: J   46 MET cc_start: 0.7270 (ptp) cc_final: 0.7054 (ptp)
REVERT: J  125 MET cc_start: 0.8737 (mtt) cc_final: 0.8467 (mtm)
REVERT: J  128 THR cc_start: 0.9110 (t) cc_final: 0.8713 (t)
REVERT: J  192 MET cc_start: 0.9002 (tpp) cc_final: 0.8593 (tpp)
REVERT: J  271 MET cc_start: 0.7381 (tpt) cc_final: 0.6806 (tpt)
REVERT: J  307 MET cc_start: 0.8174 (mmp) cc_final: 0.7673 (mmm)
REVERT: C    6 MET cc_start: 0.8390 (mtt) cc_final: 0.8046 (mtm)
REVERT: C   29 ARG cc_start: 0.8130 (mmm160) cc_final: 0.7863 (mmm160)
REVERT: C  113 MET cc_start: 0.7815 (mtp) cc_final: 0.7263 (mtt)
REVERT: C  267 TYR cc_start: 0.7187 (m-10) cc_final: 0.6952 (m-10)
REVERT: C  358 MET cc_start: 0.8631 (mmt) cc_final: 0.8326 (mmm)
REVERT: C  389 MET cc_start: 0.8656 (mpp) cc_final: 0.8276 (mpp)
REVERT: C  517 ASP cc_start: 0.8994 (m-30) cc_final: 0.8765 (t0)
REVERT: C  581 VAL cc_start: 0.8784 (t) cc_final: 0.8313 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1898
  time to fit residues: 27.0123
Evaluate side-chains
  70 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 3 optimal weight:    0.5980
   chunk 37 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 762 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.044889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.037455 restraints weight = 79220.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.038619 restraints weight = 52049.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.039468 restraints weight = 37502.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.4975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8845  Z= 0.193
  Angle     :  0.654   8.436  11943  Z= 0.333
  Chirality :  0.044   0.231   1302
  Planarity :  0.004   0.056   1537
  Dihedral  :  5.659  50.804   1185
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    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:  0.02 (0.27), residues: 1069
  helix:  0.89 (0.24), residues: 493
  sheet: -0.62 (0.47), residues: 140
  loop : -0.68 (0.31), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP J  81 
 HIS   0.004   0.001   HIS C 359 
 PHE   0.016   0.001   PHE C 767 
 TYR   0.023   0.001   TYR C 267 
 ARG   0.005   0.000   ARG J 292 

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

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

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2138 Ramachandran restraints generated.
    1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: J   46 MET cc_start: 0.7223 (ptp) cc_final: 0.7020 (ptp)
REVERT: J  178 MET cc_start: 0.7310 (tmm) cc_final: 0.7058 (tmm)
REVERT: J  192 MET cc_start: 0.8977 (tpp) cc_final: 0.8619 (tpp)
REVERT: J  271 MET cc_start: 0.7210 (tpt) cc_final: 0.6687 (tpt)
REVERT: J  286 LYS cc_start: 0.9048 (mttp) cc_final: 0.8725 (tptm)
REVERT: J  305 THR cc_start: 0.8795 (m) cc_final: 0.8489 (m)
REVERT: J  307 MET cc_start: 0.8189 (mmp) cc_final: 0.7670 (mmm)
REVERT: C    6 MET cc_start: 0.8416 (mtt) cc_final: 0.8031 (mtm)
REVERT: C   29 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7902 (mmm160)
REVERT: C  113 MET cc_start: 0.7825 (mtp) cc_final: 0.7231 (mtt)
REVERT: C  389 MET cc_start: 0.8515 (mpp) cc_final: 0.8190 (mpp)
REVERT: C  486 LEU cc_start: 0.9243 (mt) cc_final: 0.8783 (tt)
REVERT: C  517 ASP cc_start: 0.8969 (m-30) cc_final: 0.8697 (t0)
REVERT: C  575 GLU cc_start: 0.8891 (pt0) cc_final: 0.8495 (pp20)
REVERT: C  581 VAL cc_start: 0.8846 (t) cc_final: 0.8461 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1810
  time to fit residues: 25.9058
Evaluate side-chains
  75 residues out of total 931 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 72 optimal weight:    7.9990
   chunk 32 optimal weight:    0.0010
   chunk 52 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0570
   chunk 28 optimal weight:    0.5980
   chunk 96 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 98 optimal weight:    0.0980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.3104

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

Flipped N/Q/H residues before XYZ refinement:
** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.045733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.038201 restraints weight = 76896.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.039363 restraints weight = 50966.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.040208 restraints weight = 36947.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.5129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8845  Z= 0.149
  Angle     :  0.620   8.419  11943  Z= 0.310
  Chirality :  0.043   0.228   1302
  Planarity :  0.004   0.054   1537
  Dihedral  :  5.306  45.512   1185
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.19 %
    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:  0.41 (0.27), residues: 1069
  helix:  1.25 (0.24), residues: 486
  sheet: -0.45 (0.48), residues: 135
  loop : -0.50 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP J  81 
 HIS   0.004   0.001   HIS C 493 
 PHE   0.017   0.001   PHE C 767 
 TYR   0.017   0.001   TYR C 267 
 ARG   0.002   0.000   ARG J  64 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2443.35 seconds
wall clock time: 45 minutes 9.07 seconds (2709.07 seconds total)