Starting phenix.real_space_refine
on Thu Jul  2 04:56:28 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7mgw_23830/07_2026/7mgw_23830.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mgw_23830/07_2026/7mgw_23830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mgw_23830/07_2026/7mgw_23830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mgw_23830/07_2026/7mgw_23830.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mgw_23830/07_2026/7mgw_23830.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mgw_23830/07_2026/7mgw_23830.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7mgw_23830/07_2026/7mgw_23830.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7mgw_23830/07_2026/7mgw_23830.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.041
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
     S      34      5.16       5
     Cl      1      4.86       5
     C    4140      2.51       5
     N     964      2.21       5
     O    1084      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6223
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4292
          Classifications: {'peptide': 537}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 514}
    Chain: "B"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 913
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "C"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 830
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 16, 160
          Unusual residues: {' CL': 1, 'CLR': 1, 'D10': 1, 'D12': 4, 'HP6': 6, 'LNK': 1, 'SRO': 2}
          Classifications: {'undetermined': 16}
          Link IDs: {None: 15}
  Time building chain proxies: 1.52, per 1000 atoms: 0.24
  Number of scatterers: 6223
  At special positions: 0
  Unit cell: (69.336, 73.224, 121.824, 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)
     Cl      1     17.00
     S      34     16.00
     O    1084      8.00
     N     964      7.00
     C    4140      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 112 " distance=2.03

  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=3, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 208 "
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 365.0 milliseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 7 sheets defined
      54.9% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 3.846A  pdb=" N   PHE A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 113
      Proline residue:  A 106  - end of helix
    Processing helix  chain 'A' and resid 114 through 120
      removed outlier: 3.809A  pdb=" N   LEU A 118 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   LEU A 119 " --> pdb=" O   ALA A 116 " (cutoff:3.500A)
      Proline residue:  A 120  - end of helix
    Processing helix  chain 'A' and resid 121 through 144
      Proline residue:  A 131  - end of helix
    Processing helix  chain 'A' and resid 148 through 152
      removed outlier: 3.524A  pdb=" N   TRP A 151 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 159
      removed outlier: 3.598A  pdb=" N   LYS A 159 " --> pdb=" O   PRO A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 190
      removed outlier: 4.145A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
      removed outlier: 3.668A  pdb=" N   HIS A 235 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 252 through 272
      removed outlier: 4.364A  pdb=" N   LYS A 272 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 284
      removed outlier: 3.642A  pdb=" N   VAL A 281 " --> pdb=" O   SER A 277 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   TRP A 282 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   VAL A 283 " --> pdb=" O   LYS A 279 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   THR A 284 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 300
      removed outlier: 4.228A  pdb=" N   TYR A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 313
    Processing helix  chain 'A' and resid 325 through 338
    Processing helix  chain 'A' and resid 342 through 349
    Processing helix  chain 'A' and resid 356 through 391
    Processing helix  chain 'A' and resid 393 through 397
      removed outlier: 3.783A  pdb=" N   GLU A 396 " --> pdb=" O   ASP A 393 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 397 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 393 through 397'
    Processing helix  chain 'A' and resid 403 through 417
      removed outlier: 4.749A  pdb=" N   PHE A 407 " --> pdb=" O   PRO A 403 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ALA A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 454
      removed outlier: 3.807A  pdb=" N   VAL A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ALA A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASP A 452 " --> pdb=" O   THR A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 461
      removed outlier: 4.511A  pdb=" N   LYS A 460 " --> pdb=" O   HIS A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 482
      removed outlier: 3.852A  pdb=" N   VAL A 479 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   THR A 480 " --> pdb=" O   GLY A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 496
      removed outlier: 4.318A  pdb=" N   VAL A 489 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
    Processing helix  chain 'A' and resid 517 through 530
      removed outlier: 4.432A  pdb=" N   ASP A 524 " --> pdb=" O   GLN A 520 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL A 525 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   GLU A 527 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 541
    Processing helix  chain 'A' and resid 543 through 559
    Processing helix  chain 'A' and resid 571 through 585
    Processing helix  chain 'A' and resid 587 through 600
    Processing helix  chain 'A' and resid 603 through 612
    Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25
      removed outlier: 3.515A  pdb=" N   ILE B  39 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 30
      removed outlier: 5.352A  pdb=" N   GLU B  29 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL B 112 " --> pdb=" O   GLN B  58 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG B  69 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 30
      removed outlier: 5.352A  pdb=" N   GLU B  29 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL B 112 " --> pdb=" O   GLN B  58 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 25 through 27
      removed outlier: 3.616A  pdb=" N   ALA C  39 " --> pdb=" O   ILE C  99 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   CYS C  43 " --> pdb=" O   PHE C  95 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   PHE C  95 " --> pdb=" O   CYS C  43 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TYR C  94 " --> pdb=" O   SER C  91 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31
    Processing sheet with id=AA6, first strand: chain 'C' and resid 50 through 51
      removed outlier: 3.605A  pdb=" N   ASN C  51 " --> pdb=" O   ILE C  54 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78
      removed outlier: 6.930A  pdb=" N   TRP C  59 " --> pdb=" O   LEU C  71 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR C 121 " --> pdb=" O   GLN C 114 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    912 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: 0.96

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1816
        1.34 -     1.46: 1680
        1.46 -     1.58: 2849
        1.58 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 6394
  Sorted by residual:
  bond pdb=" CD1 SRO A 712 "
       pdb=" NE1 SRO A 712 "
    ideal  model  delta    sigma   weight residual
    1.377  1.324  0.053 2.00e-02 2.50e+03 7.13e+00
  bond pdb=" CD1 SRO A 715 "
       pdb=" NE1 SRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.377  1.324  0.053 2.00e-02 2.50e+03 7.07e+00
  bond pdb=" CD2 SRO A 712 "
       pdb=" CE2 SRO A 712 "
    ideal  model  delta    sigma   weight residual
    1.419  1.370  0.049 2.00e-02 2.50e+03 6.00e+00
  bond pdb=" CD2 SRO A 715 "
       pdb=" CE2 SRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.419  1.370  0.049 2.00e-02 2.50e+03 5.91e+00
  bond pdb=" CB  SRO A 715 "
       pdb=" CG  SRO A 715 "
    ideal  model  delta    sigma   weight residual
    1.498  1.527 -0.029 2.00e-02 2.50e+03 2.14e+00
  ... (remaining 6389 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 8486
        2.07 -     4.13: 161
        4.13 -     6.20: 16
        6.20 -     8.27: 1
        8.27 -    10.34: 1
  Bond angle restraints: 8665
  Sorted by residual:
  angle pdb=" C   GLU C  47 "
        pdb=" N   SER C  48 "
        pdb=" CA  SER C  48 "
      ideal   model   delta    sigma   weight residual
     121.70  132.04  -10.34 1.80e+00 3.09e-01 3.30e+01
  angle pdb=" C   LEU A 119 "
        pdb=" N   PRO A 120 "
        pdb=" CA  PRO A 120 "
      ideal   model   delta    sigma   weight residual
     121.65  119.11    2.54 1.01e+00 9.80e-01 6.34e+00
  angle pdb=" CA  GLU C  47 "
        pdb=" C   GLU C  47 "
        pdb=" N   SER C  48 "
      ideal   model   delta    sigma   weight residual
     115.60  118.96   -3.36 1.48e+00 4.57e-01 5.16e+00
  angle pdb=" C20 CLR A 716 "
        pdb=" C22 CLR A 716 "
        pdb=" C23 CLR A 716 "
      ideal   model   delta    sigma   weight residual
     115.57  109.14    6.43 3.00e+00 1.11e-01 4.59e+00
  angle pdb=" N   VAL A 236 "
        pdb=" CA  VAL A 236 "
        pdb=" C   VAL A 236 "
      ideal   model   delta    sigma   weight residual
     113.39  110.26    3.13 1.47e+00 4.63e-01 4.53e+00
  ... (remaining 8660 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.69: 3268
       15.69 -    31.37: 291
       31.37 -    47.06: 60
       47.06 -    62.75: 7
       62.75 -    78.44: 5
  Dihedral angle restraints: 3631
    sinusoidal: 1431
      harmonic: 2200
  Sorted by residual:
  dihedral pdb=" CA  ASN A 177 "
           pdb=" CB  ASN A 177 "
           pdb=" CG  ASN A 177 "
           pdb=" OD1 ASN A 177 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -176.99  -63.01     2      2.00e+01 2.50e-03 9.53e+00
  dihedral pdb=" CA  ASP A 328 "
           pdb=" CB  ASP A 328 "
           pdb=" CG  ASP A 328 "
           pdb=" OD1 ASP A 328 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.17   52.17     1      2.00e+01 2.50e-03 9.28e+00
  dihedral pdb=" CA  ARG B 117 "
           pdb=" CB  ARG B 117 "
           pdb=" CG  ARG B 117 "
           pdb=" CD  ARG B 117 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -114.09   54.09     3      1.50e+01 4.44e-03 9.26e+00
  ... (remaining 3628 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 869
       0.068 -    0.137: 74
       0.137 -    0.205: 2
       0.205 -    0.273: 2
       0.273 -    0.341: 1
  Chirality restraints: 948
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-02 2.50e+03 7.95e+01
  chirality pdb=" C14 CLR A 716 "
            pdb=" C13 CLR A 716 "
            pdb=" C15 CLR A 716 "
            pdb=" C8  CLR A 716 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.66    0.34 2.00e-01 2.50e+01 2.91e+00
  chirality pdb=" C9  CLR A 716 "
            pdb=" C10 CLR A 716 "
            pdb=" C11 CLR A 716 "
            pdb=" C8  CLR A 716 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.68    0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 945 not shown)

  Planarity restraints: 1050
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 570 "    0.020 5.00e-02 4.00e+02   3.06e-02 1.50e+00
        pdb=" N   PRO A 571 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 571 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 571 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C 100 "   -0.020 5.00e-02 4.00e+02   3.05e-02 1.48e+00
        pdb=" N   PRO C 101 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO C 101 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 101 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 589 "    0.018 5.00e-02 4.00e+02   2.71e-02 1.17e+00
        pdb=" N   PRO A 590 "   -0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO A 590 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 590 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1047 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1875
        2.81 -     3.34: 5836
        3.34 -     3.86: 10538
        3.86 -     4.38: 11412
        4.38 -     4.90: 19850
  Nonbonded interactions: 49511
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B 106 "
            pdb=" OD1 ASP B 109 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" O   ILE A 108 "
            pdb=" ND2 ASN A 112 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" OG  SER C  76 "
            pdb=" OD1 ASN C  77 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OG  SER C  55 "
            pdb=" O   ALA C  74 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   SER A 190 "
            pdb=" OG  SER A 190 "
     model   vdw
     2.323 3.040
  ... (remaining 49506 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:             4.640
  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:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.250
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5281
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   0.064   6402  Z= 0.144
  Angle     :  0.646  10.607   8677  Z= 0.303
  Chirality :  0.041   0.341    948
  Planarity :  0.003   0.031   1049
  Dihedral  : 12.278  78.436   2226
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  9.66 %
    Favored  : 88.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.28), residues: 759
  helix: -0.76 (0.23), residues: 354
  sheet: -1.78 (0.51), residues: 93
  loop : -2.62 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 564 
 TYR   0.009   0.000   TYR A 176 
 PHE   0.015   0.001   PHE A 474 
 TRP   0.006   0.000   TRP A 317 
 HIS   0.001   0.000   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.14 ( 6394)
  covalent geometry    : angle       0.63619 /  0.30 ( 8665)
  SS BOND              : bond        0.00154 /  0.08 (    3)
  SS BOND              : angle       0.24093 /  0.14 (    6)
  hydrogen bonds       : bond        0.11025 /  7.16 (  318)
  hydrogen bonds       : angle       5.13441 /  3.53 (  912)
  Misc. bond           : bond        0.00043 /  0.02 (    3)
  link_BETA1-4         : bond        0.06372 /  3.35 (    1)
  link_BETA1-4         : angle       6.18196 /  3.26 (    3)
  link_NAG-ASN         : bond        0.00526 /  0.28 (    1)
  link_NAG-ASN         : angle       1.21940 /  0.64 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 144
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  144 ARG cc_start: 0.6293 (mtm110) cc_final: 0.6074 (ttm110)
REVERT: A  145 ASN cc_start: 0.6110 (t0) cc_final: 0.5464 (t0)
REVERT: A  243 LYS cc_start: 0.7231 (mtmm) cc_final: 0.7008 (mmtm)
REVERT: A  267 TYR cc_start: 0.5156 (t80) cc_final: 0.4873 (t80)
REVERT: A  370 MET cc_start: 0.6126 (mmp) cc_final: 0.4205 (ttm)
REVERT: A  391 ASN cc_start: 0.7447 (t0) cc_final: 0.7161 (t0)
REVERT: A  430 MET cc_start: 0.6275 (ttm) cc_final: 0.6050 (tmm)
REVERT: A  466 VAL cc_start: 0.3865 (p) cc_final: 0.3450 (t)
REVERT: A  508 GLU cc_start: 0.6099 (tm-30) cc_final: 0.5663 (tm-30)
REVERT: A  572 TYR cc_start: 0.6178 (t80) cc_final: 0.5765 (t80)
REVERT: B   76 ASP cc_start: 0.7630 (t0) cc_final: 0.6898 (t0)
REVERT: C   78 GLN cc_start: 0.7740 (mt0) cc_final: 0.7485 (mt0)
  outliers start: 9
  outliers final: 4
  residues processed: 151
  average time/residue: 0.0830
  time to fit residues: 16.1065
Evaluate side-chains
  101 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 ASN
A 316 ASN
A 332 GLN
A 355 ASN
A 368 ASN
B  25 GLN
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 101 GLN
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.199716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.163312 restraints weight = 7695.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.168638 restraints weight = 4698.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.172151 restraints weight = 3419.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.174136 restraints weight = 2775.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.175894 restraints weight = 2439.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   6402  Z= 0.165
  Angle     :  0.594   9.882   8677  Z= 0.305
  Chirality :  0.042   0.188    948
  Planarity :  0.004   0.032   1049
  Dihedral  :  6.202  76.097    920
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.36 %
    Allowed  : 17.45 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.29), residues: 759
  helix:  0.14 (0.25), residues: 354
  sheet: -1.47 (0.50), residues: 96
  loop : -2.41 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 564 
 TYR   0.015   0.002   TYR A 358 
 PHE   0.025   0.002   PHE A 428 
 TRP   0.021   0.002   TRP A 326 
 HIS   0.002   0.001   HIS A 235 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.16 ( 6394)
  covalent geometry    : angle       0.59264 /  0.31 ( 8665)
  SS BOND              : bond        0.00825 /  0.41 (    3)
  SS BOND              : angle       0.34467 /  0.21 (    6)
  hydrogen bonds       : bond        0.03474 /  2.24 (  318)
  hydrogen bonds       : angle       4.45392 /  3.08 (  912)
  Misc. bond           : bond        0.00054 /  0.03 (    3)
  link_BETA1-4         : bond        0.00239 /  0.13 (    1)
  link_BETA1-4         : angle       1.51378 /  0.79 (    3)
  link_NAG-ASN         : bond        0.00127 /  0.07 (    1)
  link_NAG-ASN         : angle       1.46196 /  0.79 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 104
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  391 ASN cc_start: 0.6437 (t0) cc_final: 0.6147 (m-40)
REVERT: A  478 LEU cc_start: 0.7542 (tt) cc_final: 0.7265 (tp)
REVERT: A  508 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7313 (tm-30)
  outliers start: 28
  outliers final: 15
  residues processed: 122
  average time/residue: 0.0717
  time to fit residues: 11.8486
Evaluate side-chains
  108 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 44 optimal weight:    1.9990
   chunk 55 optimal weight:    0.4980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 416 ASN
B  54 ASN
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  78 GLN
C 113 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.186513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.146678 restraints weight = 7626.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.152041 restraints weight = 4648.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.155584 restraints weight = 3420.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.157985 restraints weight = 2797.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.159172 restraints weight = 2453.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   6402  Z= 0.172
  Angle     :  0.588  10.020   8677  Z= 0.306
  Chirality :  0.042   0.202    948
  Planarity :  0.004   0.032   1049
  Dihedral  :  5.893  65.679    918
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 18.85 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.29), residues: 759
  helix:  0.10 (0.25), residues: 362
  sheet: -1.15 (0.51), residues: 96
  loop : -2.25 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 144 
 TYR   0.012   0.002   TYR A 267 
 PHE   0.023   0.002   PHE A 428 
 TRP   0.016   0.001   TRP A 197 
 HIS   0.004   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00415 /  0.17 ( 6394)
  covalent geometry    : angle       0.58562 /  0.31 ( 8665)
  SS BOND              : bond        0.01351 /  0.68 (    3)
  SS BOND              : angle       0.45331 /  0.23 (    6)
  hydrogen bonds       : bond        0.03574 /  2.29 (  318)
  hydrogen bonds       : angle       4.46934 /  3.12 (  912)
  Misc. bond           : bond        0.00040 /  0.02 (    3)
  link_BETA1-4         : bond        0.00412 /  0.22 (    1)
  link_BETA1-4         : angle       2.42402 /  1.26 (    3)
  link_NAG-ASN         : bond        0.00359 /  0.19 (    1)
  link_NAG-ASN         : angle       1.46427 /  0.78 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.7003 (pttm) cc_final: 0.6160 (ptpt)
REVERT: A   98 ASP cc_start: 0.7739 (t0) cc_final: 0.7517 (t70)
REVERT: A  391 ASN cc_start: 0.6628 (t0) cc_final: 0.6265 (m-40)
REVERT: A  454 PHE cc_start: 0.6451 (m-10) cc_final: 0.6016 (m-80)
REVERT: A  508 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7401 (tm-30)
  outliers start: 31
  outliers final: 19
  residues processed: 129
  average time/residue: 0.0653
  time to fit residues: 11.7697
Evaluate side-chains
  117 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  341 PHE
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  107 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0170
   chunk 9 optimal weight:    0.5980
   chunk 48 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   overall best weight:    0.5818

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 101 ASN
A 141 GLN
A 177 ASN
B  25 GLN
B 101 GLN
** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.186417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.146895 restraints weight = 7624.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.152099 restraints weight = 4710.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.155646 restraints weight = 3485.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.157584 restraints weight = 2861.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.157586 restraints weight = 2537.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6402  Z= 0.137
  Angle     :  0.553   9.934   8677  Z= 0.289
  Chirality :  0.041   0.211    948
  Planarity :  0.004   0.051   1049
  Dihedral  :  5.510  50.799    918
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 19.47 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.32 (0.30), residues: 759
  helix:  0.26 (0.26), residues: 361
  sheet: -1.13 (0.51), residues: 101
  loop : -2.18 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B  38 
 TYR   0.010   0.001   TYR A 358 
 PHE   0.021   0.001   PHE A 407 
 TRP   0.016   0.001   TRP A 271 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 6394)
  covalent geometry    : angle       0.55066 /  0.29 ( 8665)
  SS BOND              : bond        0.00509 /  0.25 (    3)
  SS BOND              : angle       0.25117 /  0.13 (    6)
  hydrogen bonds       : bond        0.03243 /  2.10 (  318)
  hydrogen bonds       : angle       4.42424 /  3.10 (  912)
  Misc. bond           : bond        0.00031 /  0.02 (    3)
  link_BETA1-4         : bond        0.00501 /  0.26 (    1)
  link_BETA1-4         : angle       2.20857 /  1.14 (    3)
  link_NAG-ASN         : bond        0.00300 /  0.16 (    1)
  link_NAG-ASN         : angle       1.66210 /  0.87 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A   84 LYS cc_start: 0.7030 (pttm) cc_final: 0.6259 (ptpt)
REVERT: A  391 ASN cc_start: 0.6653 (t0) cc_final: 0.6231 (m-40)
REVERT: A  454 PHE cc_start: 0.6557 (m-10) cc_final: 0.6187 (m-80)
REVERT: A  508 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7475 (tm-30)
  outliers start: 32
  outliers final: 25
  residues processed: 124
  average time/residue: 0.0633
  time to fit residues: 10.9257
Evaluate side-chains
  124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 43 optimal weight:    0.0970
   chunk 65 optimal weight:    0.7980
   chunk 22 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0870
   chunk 47 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.5356

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.184275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.144728 restraints weight = 7799.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.150160 restraints weight = 4616.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.153804 restraints weight = 3350.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.156252 restraints weight = 2720.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.157600 restraints weight = 2362.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.4295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6402  Z= 0.136
  Angle     :  0.555   9.914   8677  Z= 0.291
  Chirality :  0.040   0.212    948
  Planarity :  0.004   0.048   1049
  Dihedral  :  5.156  49.413    918
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 20.56 %
    Favored  : 73.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.30), residues: 759
  helix:  0.29 (0.26), residues: 366
  sheet: -1.08 (0.51), residues: 101
  loop : -1.98 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 607 
 TYR   0.011   0.001   TYR B  99 
 PHE   0.018   0.001   PHE A 407 
 TRP   0.022   0.001   TRP A 220 
 HIS   0.002   0.000   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 ( 6394)
  covalent geometry    : angle       0.55271 /  0.29 ( 8665)
  SS BOND              : bond        0.00249 /  0.12 (    3)
  SS BOND              : angle       0.22547 /  0.15 (    6)
  hydrogen bonds       : bond        0.03195 /  2.05 (  318)
  hydrogen bonds       : angle       4.45566 /  3.13 (  912)
  Misc. bond           : bond        0.00033 /  0.02 (    3)
  link_BETA1-4         : bond        0.00547 /  0.29 (    1)
  link_BETA1-4         : angle       2.18671 /  1.13 (    3)
  link_NAG-ASN         : bond        0.00265 /  0.14 (    1)
  link_NAG-ASN         : angle       1.67044 /  0.87 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 97
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.7020 (pttm) cc_final: 0.6246 (ptpt)
REVERT: A  220 TRP cc_start: 0.5708 (m-90) cc_final: 0.5390 (m-90)
REVERT: A  259 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6464 (mm)
REVERT: A  391 ASN cc_start: 0.6702 (t0) cc_final: 0.6243 (m-40)
REVERT: A  508 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7476 (tm-30)
  outliers start: 35
  outliers final: 29
  residues processed: 119
  average time/residue: 0.0589
  time to fit residues: 9.9226
Evaluate side-chains
  125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  103 GLU
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0370
   chunk 13 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 63 optimal weight:    3.9990
   overall best weight:    0.6858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 141 GLN ** 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 = 0.4099 r_free = 0.4099 target = 0.181198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142128 restraints weight = 7699.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.147391 restraints weight = 4603.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.150860 restraints weight = 3363.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.152909 restraints weight = 2755.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.154630 restraints weight = 2428.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.4656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   6402  Z= 0.152
  Angle     :  0.572   9.896   8677  Z= 0.300
  Chirality :  0.041   0.209    948
  Planarity :  0.004   0.048   1049
  Dihedral  :  5.141  49.703    918
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 20.25 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.20 (0.30), residues: 759
  helix:  0.25 (0.26), residues: 364
  sheet: -1.15 (0.50), residues: 101
  loop : -1.95 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 564 
 TYR   0.012   0.001   TYR A 110 
 PHE   0.020   0.001   PHE A 407 
 TRP   0.014   0.001   TRP A 151 
 HIS   0.002   0.001   HIS A 235 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.15 ( 6394)
  covalent geometry    : angle       0.57013 /  0.30 ( 8665)
  SS BOND              : bond        0.00267 /  0.13 (    3)
  SS BOND              : angle       0.23598 /  0.15 (    6)
  hydrogen bonds       : bond        0.03361 /  2.20 (  318)
  hydrogen bonds       : angle       4.49851 /  3.16 (  912)
  Misc. bond           : bond        0.00036 /  0.02 (    3)
  link_BETA1-4         : bond        0.00504 /  0.27 (    1)
  link_BETA1-4         : angle       2.24607 /  1.16 (    3)
  link_NAG-ASN         : bond        0.00257 /  0.14 (    1)
  link_NAG-ASN         : angle       1.65608 /  0.87 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 106
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
REVERT: A   84 LYS cc_start: 0.7082 (pttm) cc_final: 0.6365 (ptpt)
REVERT: A  220 TRP cc_start: 0.5788 (m-90) cc_final: 0.5499 (m-90)
REVERT: A  259 ILE cc_start: 0.7299 (OUTLIER) cc_final: 0.6807 (mm)
REVERT: A  391 ASN cc_start: 0.6654 (t0) cc_final: 0.6182 (m-40)
REVERT: A  508 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7581 (tm-30)
REVERT: C   85 ARG cc_start: 0.8408 (mtm110) cc_final: 0.8194 (mtm110)
  outliers start: 41
  outliers final: 33
  residues processed: 130
  average time/residue: 0.0746
  time to fit residues: 13.3065
Evaluate side-chains
  133 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  280 VAL
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 67 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0870
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.5158

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 562 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.180926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.142581 restraints weight = 7558.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.147638 restraints weight = 4589.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.151044 restraints weight = 3367.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.153257 restraints weight = 2756.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.154767 restraints weight = 2410.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.4831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6402  Z= 0.135
  Angle     :  0.563   9.873   8677  Z= 0.294
  Chirality :  0.041   0.213    948
  Planarity :  0.004   0.048   1049
  Dihedral  :  5.073  49.643    918
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 21.18 %
    Favored  : 73.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.16 (0.30), residues: 759
  helix:  0.28 (0.26), residues: 364
  sheet: -1.15 (0.50), residues: 101
  loop : -1.92 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.011   0.001   TYR A 110 
 PHE   0.025   0.001   PHE A 407 
 TRP   0.013   0.001   TRP A 514 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.13 ( 6394)
  covalent geometry    : angle       0.56102 /  0.29 ( 8665)
  SS BOND              : bond        0.00260 /  0.13 (    3)
  SS BOND              : angle       0.25411 /  0.16 (    6)
  hydrogen bonds       : bond        0.03245 /  2.10 (  318)
  hydrogen bonds       : angle       4.47799 /  3.15 (  912)
  Misc. bond           : bond        0.00039 /  0.02 (    3)
  link_BETA1-4         : bond        0.00649 /  0.34 (    1)
  link_BETA1-4         : angle       2.25978 /  1.17 (    3)
  link_NAG-ASN         : bond        0.00306 /  0.16 (    1)
  link_NAG-ASN         : angle       1.68932 /  0.89 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 99
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A   84 LYS cc_start: 0.7046 (pttm) cc_final: 0.6362 (ptpt)
REVERT: A  220 TRP cc_start: 0.5750 (m-90) cc_final: 0.5492 (m-90)
REVERT: A  259 ILE cc_start: 0.7278 (OUTLIER) cc_final: 0.6633 (mm)
REVERT: A  282 TRP cc_start: 0.5761 (OUTLIER) cc_final: 0.4753 (m100)
REVERT: A  391 ASN cc_start: 0.6662 (t0) cc_final: 0.6171 (m-40)
REVERT: A  454 PHE cc_start: 0.6433 (m-10) cc_final: 0.5953 (m-80)
REVERT: A  508 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7627 (tm-30)
  outliers start: 36
  outliers final: 32
  residues processed: 122
  average time/residue: 0.0684
  time to fit residues: 11.5782
Evaluate side-chains
  130 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 96
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  282 TRP
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 27 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 38 optimal weight:    0.3980
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 141 GLN ** 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 = 0.4062 r_free = 0.4062 target = 0.177359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.138824 restraints weight = 7709.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.143873 restraints weight = 4690.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.147183 restraints weight = 3451.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.149389 restraints weight = 2829.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.150665 restraints weight = 2492.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.5170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6402  Z= 0.162
  Angle     :  0.601   9.887   8677  Z= 0.313
  Chirality :  0.042   0.194    948
  Planarity :  0.004   0.049   1049
  Dihedral  :  5.300  49.967    918
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 22.12 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.30), residues: 759
  helix:  0.30 (0.26), residues: 358
  sheet: -1.19 (0.50), residues: 101
  loop : -1.92 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 523 
 TYR   0.022   0.002   TYR B 120 
 PHE   0.025   0.001   PHE A 407 
 TRP   0.015   0.001   TRP A 151 
 HIS   0.002   0.001   HIS A 235 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.16 ( 6394)
  covalent geometry    : angle       0.59915 /  0.31 ( 8665)
  SS BOND              : bond        0.00260 /  0.13 (    3)
  SS BOND              : angle       0.31143 /  0.18 (    6)
  hydrogen bonds       : bond        0.03465 /  2.26 (  318)
  hydrogen bonds       : angle       4.54953 /  3.21 (  912)
  Misc. bond           : bond        0.00038 /  0.02 (    3)
  link_BETA1-4         : bond        0.00622 /  0.33 (    1)
  link_BETA1-4         : angle       2.43183 /  1.26 (    3)
  link_NAG-ASN         : bond        0.00102 /  0.05 (    1)
  link_NAG-ASN         : angle       1.51610 /  0.79 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 102
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A   84 LYS cc_start: 0.7147 (pttm) cc_final: 0.6447 (ptpt)
REVERT: A  220 TRP cc_start: 0.5801 (m-90) cc_final: 0.5504 (m-90)
REVERT: A  259 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.7021 (mm)
REVERT: A  282 TRP cc_start: 0.5923 (OUTLIER) cc_final: 0.4918 (m100)
REVERT: A  328 ASP cc_start: 0.8556 (OUTLIER) cc_final: 0.8242 (t0)
REVERT: A  391 ASN cc_start: 0.6679 (t0) cc_final: 0.6148 (m-40)
REVERT: A  508 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7857 (tm-30)
REVERT: A  537 TRP cc_start: 0.6882 (m100) cc_final: 0.6365 (m100)
  outliers start: 37
  outliers final: 34
  residues processed: 124
  average time/residue: 0.0655
  time to fit residues: 11.2669
Evaluate side-chains
  136 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 99
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  282 TRP
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain A residue  612 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 72 optimal weight:    8.9990
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 113 GLN ** 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 = 0.4063 r_free = 0.4063 target = 0.177825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.139171 restraints weight = 7720.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.144288 restraints weight = 4685.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.147637 restraints weight = 3430.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.149564 restraints weight = 2814.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.151243 restraints weight = 2488.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.5325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6402  Z= 0.152
  Angle     :  0.593   9.988   8677  Z= 0.310
  Chirality :  0.042   0.216    948
  Planarity :  0.004   0.050   1049
  Dihedral  :  5.306  49.742    918
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 22.43 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.30), residues: 759
  helix:  0.33 (0.26), residues: 358
  sheet: -1.29 (0.50), residues: 102
  loop : -1.87 (0.37), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  38 
 TYR   0.011   0.001   TYR A 110 
 PHE   0.025   0.001   PHE A 407 
 TRP   0.014   0.001   TRP A 151 
 HIS   0.002   0.001   HIS A 235 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00373 /  0.15 ( 6394)
  covalent geometry    : angle       0.59109 /  0.31 ( 8665)
  SS BOND              : bond        0.00302 /  0.15 (    3)
  SS BOND              : angle       0.47253 /  0.27 (    6)
  hydrogen bonds       : bond        0.03420 /  2.22 (  318)
  hydrogen bonds       : angle       4.57209 /  3.22 (  912)
  Misc. bond           : bond        0.00034 /  0.02 (    3)
  link_BETA1-4         : bond        0.00683 /  0.36 (    1)
  link_BETA1-4         : angle       2.34452 /  1.21 (    3)
  link_NAG-ASN         : bond        0.00223 /  0.12 (    1)
  link_NAG-ASN         : angle       1.84230 /  0.96 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.209 
Fit side-chains
REVERT: A   84 LYS cc_start: 0.7114 (pttm) cc_final: 0.6471 (ptpt)
REVERT: A  101 ASN cc_start: 0.4832 (t0) cc_final: 0.3487 (t0)
REVERT: A  220 TRP cc_start: 0.5839 (m-90) cc_final: 0.5559 (m-90)
REVERT: A  259 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7029 (mm)
REVERT: A  282 TRP cc_start: 0.5911 (OUTLIER) cc_final: 0.4969 (m100)
REVERT: A  328 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8181 (t0)
REVERT: A  391 ASN cc_start: 0.6648 (t0) cc_final: 0.6112 (m-40)
REVERT: A  508 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7856 (tm-30)
REVERT: A  537 TRP cc_start: 0.6919 (m100) cc_final: 0.6371 (m100)
  outliers start: 34
  outliers final: 28
  residues processed: 121
  average time/residue: 0.0617
  time to fit residues: 10.5654
Evaluate side-chains
  125 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  282 TRP
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain B residue   30 LEU
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 51 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 562 GLN
** C 113 GLN ** 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 = 0.4057 r_free = 0.4057 target = 0.177249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.138906 restraints weight = 7558.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.143907 restraints weight = 4612.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.147237 restraints weight = 3387.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.149193 restraints weight = 2779.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.150823 restraints weight = 2453.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.5453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   6402  Z= 0.154
  Angle     :  0.608  10.088   8677  Z= 0.315
  Chirality :  0.042   0.210    948
  Planarity :  0.004   0.050   1049
  Dihedral  :  5.348  50.176    918
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 11.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 22.43 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.17 (0.30), residues: 759
  helix:  0.32 (0.26), residues: 357
  sheet: -1.17 (0.52), residues: 96
  loop : -1.93 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 523 
 TYR   0.010   0.001   TYR B 120 
 PHE   0.024   0.001   PHE A 407 
 TRP   0.014   0.001   TRP A 151 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00378 /  0.15 ( 6394)
  covalent geometry    : angle       0.60564 /  0.31 ( 8665)
  SS BOND              : bond        0.00317 /  0.16 (    3)
  SS BOND              : angle       0.45769 /  0.26 (    6)
  hydrogen bonds       : bond        0.03438 /  2.23 (  318)
  hydrogen bonds       : angle       4.59724 /  3.24 (  912)
  Misc. bond           : bond        0.00033 /  0.02 (    3)
  link_BETA1-4         : bond        0.00634 /  0.33 (    1)
  link_BETA1-4         : angle       2.38345 /  1.23 (    3)
  link_NAG-ASN         : bond        0.00270 /  0.14 (    1)
  link_NAG-ASN         : angle       1.80211 /  0.94 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 92
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A   84 LYS cc_start: 0.7130 (pttm) cc_final: 0.6465 (ptpt)
REVERT: A  101 ASN cc_start: 0.4910 (t0) cc_final: 0.3605 (t0)
REVERT: A  220 TRP cc_start: 0.5859 (m-90) cc_final: 0.5579 (m-90)
REVERT: A  259 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7017 (mm)
REVERT: A  282 TRP cc_start: 0.5955 (OUTLIER) cc_final: 0.5035 (m100)
REVERT: A  328 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8176 (t0)
REVERT: A  391 ASN cc_start: 0.6641 (t0) cc_final: 0.6089 (m-40)
REVERT: A  454 PHE cc_start: 0.6579 (m-10) cc_final: 0.6298 (m-10)
REVERT: A  508 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7891 (tm-30)
REVERT: B   38 ARG cc_start: 0.8601 (ttt-90) cc_final: 0.8255 (ttt90)
REVERT: B  127 MET cc_start: 0.8322 (mtt) cc_final: 0.7966 (mtt)
  outliers start: 35
  outliers final: 29
  residues processed: 115
  average time/residue: 0.0662
  time to fit residues: 10.8180
Evaluate side-chains
  123 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 91
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  175 TYR
Chi-restraints excluded: chain A residue  200 CYS
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  239 ILE
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  282 TRP
Chi-restraints excluded: chain A residue  301 THR
Chi-restraints excluded: chain A residue  328 ASP
Chi-restraints excluded: chain A residue  362 LEU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  379 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  386 MET
Chi-restraints excluded: chain A residue  410 TYR
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  554 CYS
Chi-restraints excluded: chain A residue  574 SER
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  599 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain C residue   40 THR
Chi-restraints excluded: chain C residue   42 SER
Chi-restraints excluded: chain C residue   98 ASN
Chi-restraints excluded: chain C residue  107 THR
Chi-restraints excluded: chain C residue  118 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0670
   chunk 33 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 47 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.5918

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 GLN
** C 113 GLN ** 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 = 0.4102 r_free = 0.4102 target = 0.181738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.143806 restraints weight = 7721.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.148683 restraints weight = 4772.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.151999 restraints weight = 3535.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.153785 restraints weight = 2908.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.155436 restraints weight = 2579.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.5526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6402  Z= 0.144
  Angle     :  0.601  10.101   8677  Z= 0.310
  Chirality :  0.042   0.211    948
  Planarity :  0.004   0.050   1049
  Dihedral  :  5.333  50.282    918
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 22.43 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.10 (0.30), residues: 759
  helix:  0.36 (0.26), residues: 357
  sheet: -1.14 (0.52), residues: 96
  loop : -1.87 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  38 
 TYR   0.010   0.001   TYR C  73 
 PHE   0.024   0.001   PHE A 407 
 TRP   0.013   0.001   TRP A 151 
 HIS   0.002   0.001   HIS A 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.14 ( 6394)
  covalent geometry    : angle       0.59850 /  0.31 ( 8665)
  SS BOND              : bond        0.00291 /  0.15 (    3)
  SS BOND              : angle       0.39068 /  0.23 (    6)
  hydrogen bonds       : bond        0.03368 /  2.17 (  318)
  hydrogen bonds       : angle       4.59725 /  3.24 (  912)
  Misc. bond           : bond        0.00030 /  0.02 (    3)
  link_BETA1-4         : bond        0.00654 /  0.34 (    1)
  link_BETA1-4         : angle       2.37049 /  1.23 (    3)
  link_NAG-ASN         : bond        0.00286 /  0.15 (    1)
  link_NAG-ASN         : angle       1.84137 /  0.97 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1322.15 seconds
wall clock time: 23 minutes 37.82 seconds (1417.82 seconds total)