Starting phenix.real_space_refine
on Tue Mar  3 14:24:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9uat_63995/03_2026/9uat_63995_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9uat_63995/03_2026/9uat_63995.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9uat_63995/03_2026/9uat_63995_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9uat_63995/03_2026/9uat_63995_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9uat_63995/03_2026/9uat_63995.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9uat_63995/03_2026/9uat_63995.map"
  }
  resolution = 3.65
  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=   0.026
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: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    3818      2.51       5
     N     937      2.21       5
     O    1070      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5865
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4014
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 531, 4014
          Classifications: {'peptide': 531}
          Link IDs: {'PTRANS': 21, 'TRANS': 509}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1733
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1733
          Classifications: {'peptide': 221}
          Link IDs: {'PTRANS': 18, 'TRANS': 202}
    Chain: "C"
      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 dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      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 dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Classifications: {'peptide': 1}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.40, per 1000 atoms: 0.24
  Number of scatterers: 5865
  At special positions: 0
  Unit cell: (115.222, 81.525, 104.352, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1070      8.00
     N     937      7.00
     C    3818      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 226 " - pdb=" SG  CYS A 309 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  80 " - pdb=" SG  CYS B 132 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 106 " - pdb=" SG  CYS B 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 107 " - pdb=" SG  CYS B 117 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 155 " - pdb=" SG  CYS B 175 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 167 " - pdb=" SG  CYS B 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 218 " 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=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
    NAG-ASN
      " NAG B 301 " - " ASN B  46 "
      " NAG C   1 " - " ASN A 229 "
      " NAG D   1 " - " ASN A 223 "
      " NAG E   1 " - " ASN B 202 "
  Time building additional restraints: 0.61
  Conformation dependent library (CDL) restraints added in 333.9 milliseconds
  

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1372

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 2 sheets defined
      63.2% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 47
      removed outlier: 3.708A  pdb=" N   THR A  45 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   GLY A  47 " --> pdb=" O   GLY A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
      removed outlier: 3.810A  pdb=" N   ALA A  56 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 64
      No H-bonds generated for 'chain 'A' and resid 62 through 64'
    Processing helix  chain 'A' and resid 65 through 89
      removed outlier: 3.656A  pdb=" N   CYS A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
      removed outlier: 4.337A  pdb=" N   TYR A 100 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   SER A 101 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   VAL A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 140
      removed outlier: 3.579A  pdb=" N   ALA A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   THR A 113 " --> pdb=" O   TRP A 109 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   ILE A 118 " --> pdb=" O   GLY A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 152
      removed outlier: 3.745A  pdb=" N   GLU A 146 " --> pdb=" O   LYS A 142 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   PHE A 147 " --> pdb=" O   PRO A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 181
      removed outlier: 3.578A  pdb=" N   VAL A 169 " --> pdb=" O   ASP A 165 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU A 181 " --> pdb=" O   GLY A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 212
    Processing helix  chain 'A' and resid 213 through 218
    Processing helix  chain 'A' and resid 243 through 260
      removed outlier: 3.619A  pdb=" N   GLY A 247 " --> pdb=" O   PHE A 243 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   THR A 254 " --> pdb=" O   SER A 250 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   TYR A 257 " --> pdb=" O   ALA A 253 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   ALA A 258 " --> pdb=" O   THR A 254 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   PHE A 259 " --> pdb=" O   CYS A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 268
      removed outlier: 4.405A  pdb=" N   ALA A 266 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 305
      removed outlier: 4.174A  pdb=" N   VAL A 281 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 324
      removed outlier: 3.731A  pdb=" N   PHE A 320 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 327
      No H-bonds generated for 'chain 'A' and resid 325 through 327'
    Processing helix  chain 'A' and resid 328 through 349
      removed outlier: 3.553A  pdb=" N   THR A 342 " --> pdb=" O   CYS A 338 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 361
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 378 through 395
      removed outlier: 3.602A  pdb=" N   THR A 384 " --> pdb=" O   ILE A 380 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ILE A 388 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   ALA A 389 " --> pdb=" O   SER A 385 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA A 390 " --> pdb=" O   GLY A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 424
      removed outlier: 3.812A  pdb=" N   ASP A 403 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A 404 " --> pdb=" O   ASP A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 475
    Processing helix  chain 'A' and resid 482 through 509
      removed outlier: 3.612A  pdb=" N   ILE A 501 " --> pdb=" O   ALA A 497 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   THR A 502 " --> pdb=" O   ALA A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 517
    Processing helix  chain 'A' and resid 518 through 542
      removed outlier: 3.538A  pdb=" N   MET A 533 " --> pdb=" O   VAL A 529 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU A 534 " --> pdb=" O   LEU A 530 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLN A 542 " --> pdb=" O   ILE A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 573
    Processing helix  chain 'A' and resid 575 through 596
      removed outlier: 3.847A  pdb=" N   TRP A 579 " --> pdb=" O   ASP A 575 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TRP A 585 " --> pdb=" O   ARG A 581 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR A 591 " --> pdb=" O   LEU A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 601
    Processing helix  chain 'B' and resid 79 through 84
      removed outlier: 3.661A  pdb=" N   LEU B  84 " --> pdb=" O   MET B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.578A  pdb=" N   TRP B  90 " --> pdb=" O   PRO B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 118 through 122
      removed outlier: 4.112A  pdb=" N   CYS B 121 " --> pdb=" O   SER B 118 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 147
    Processing helix  chain 'B' and resid 161 through 165
    Processing helix  chain 'B' and resid 169 through 173
    Processing helix  chain 'B' and resid 208 through 214
    Processing helix  chain 'B' and resid 233 through 238
      removed outlier: 4.521A  pdb=" N   THR B 236 " --> pdb=" O   THR B 233 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 66
      removed outlier: 6.657A  pdb=" N   VAL B  51 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ALA B  61 " --> pdb=" O   TRP B  49 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   TRP B  49 " --> pdb=" O   ALA B  61 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   SER B  63 " --> pdb=" O   ILE B  47 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   ILE B  47 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   ASN B  65 " --> pdb=" O   TYR B  45 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   TYR B  45 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE B 256 " --> pdb=" O   TRP B 241 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLY B 151 " --> pdb=" O   TYR B 246 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   PHE B 152 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR B 183 " --> pdb=" O   VAL B 154 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 197 through 201
      removed outlier: 3.673A  pdb=" N   THR B 198 " --> pdb=" O   GLN B 224 " (cutoff:3.500A)

    328 hydrogen bonds defined for protein.
    933 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: 0.87

  Time building geometry restraints manager: 0.75 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: 1780
        1.34 -     1.46: 1508
        1.46 -     1.58: 2676
        1.58 -     1.70: 0
        1.70 -     1.81: 56
  Bond restraints: 6020
  Sorted by residual:
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.491 -0.085 2.00e-02 2.50e+03 1.81e+01
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.465 -0.059 2.00e-02 2.50e+03 8.66e+00
  bond pdb=" CA  ORN A 701 "
       pdb=" C   ORN A 701 "
    ideal  model  delta    sigma   weight residual
    1.525  1.563 -0.038 2.10e-02 2.27e+03 3.24e+00
  bond pdb=" C   ORN A 701 "
       pdb=" O   ORN A 701 "
    ideal  model  delta    sigma   weight residual
    1.231  1.264 -0.033 2.00e-02 2.50e+03 2.79e+00
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.552 -0.033 2.00e-02 2.50e+03 2.74e+00
  ... (remaining 6015 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 7935
        1.31 -     2.63: 217
        2.63 -     3.94: 47
        3.94 -     5.26: 12
        5.26 -     6.57: 4
  Bond angle restraints: 8215
  Sorted by residual:
  angle pdb=" C   ALA A 278 "
        pdb=" N   ILE A 279 "
        pdb=" CA  ILE A 279 "
      ideal   model   delta    sigma   weight residual
     120.33  122.66   -2.33 8.00e-01 1.56e+00 8.48e+00
  angle pdb=" C   ILE A 279 "
        pdb=" CA  ILE A 279 "
        pdb=" CB  ILE A 279 "
      ideal   model   delta    sigma   weight residual
     114.00  110.58    3.42 1.31e+00 5.83e-01 6.83e+00
  angle pdb=" N   VAL A 556 "
        pdb=" CA  VAL A 556 "
        pdb=" C   VAL A 556 "
      ideal   model   delta    sigma   weight residual
     108.88  114.27   -5.39 2.16e+00 2.14e-01 6.23e+00
  angle pdb=" N   ASN B 133 "
        pdb=" CA  ASN B 133 "
        pdb=" C   ASN B 133 "
      ideal   model   delta    sigma   weight residual
     111.14  113.52   -2.38 1.08e+00 8.57e-01 4.84e+00
  angle pdb=" C   TYR A 425 "
        pdb=" N   GLN A 426 "
        pdb=" CA  GLN A 426 "
      ideal   model   delta    sigma   weight residual
     121.61  118.64    2.97 1.39e+00 5.18e-01 4.55e+00
  ... (remaining 8210 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.93: 3441
       24.93 -    49.86: 84
       49.86 -    74.79: 25
       74.79 -    99.72: 21
       99.72 -   124.65: 28
  Dihedral angle restraints: 3599
    sinusoidal: 1450
      harmonic: 2149
  Sorted by residual:
  dihedral pdb=" CB  CYS A 226 "
           pdb=" SG  CYS A 226 "
           pdb=" SG  CYS A 309 "
           pdb=" CB  CYS A 309 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  132.21  -39.21     1      1.00e+01 1.00e-02 2.16e+01
  dihedral pdb=" C2  NAG D   1 "
           pdb=" C1  NAG D   1 "
           pdb=" O5  NAG D   1 "
           pdb=" C5  NAG D   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   61.69 -124.65     1      3.00e+01 1.11e-03 1.67e+01
  dihedral pdb=" C1  NAG C   2 "
           pdb=" C5  NAG C   2 "
           pdb=" O5  NAG C   2 "
           pdb=" C6  NAG C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -76.82 -112.02     1      3.00e+01 1.11e-03 1.47e+01
  ... (remaining 3596 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 814
       0.054 -    0.108: 141
       0.108 -    0.162: 12
       0.162 -    0.215: 0
       0.215 -    0.269: 1
  Chirality restraints: 968
  Sorted by residual:
  chirality pdb=" C5  BMA D   3 "
            pdb=" C4  BMA D   3 "
            pdb=" C6  BMA D   3 "
            pdb=" O5  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 202 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.32e-01
  chirality pdb=" C2  BMA D   3 "
            pdb=" C1  BMA D   3 "
            pdb=" C3  BMA D   3 "
            pdb=" O2  BMA D   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.61   -0.14 2.00e-01 2.50e+01 5.04e-01
  ... (remaining 965 not shown)

  Planarity restraints: 1010
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 480 "    0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO A 481 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A 481 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 481 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 305 "   -0.023 5.00e-02 4.00e+02   3.53e-02 2.00e+00
        pdb=" N   PRO A 306 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 306 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 306 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 101 "   -0.021 5.00e-02 4.00e+02   3.14e-02 1.57e+00
        pdb=" N   PRO B 102 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 102 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 102 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1007 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1124
        2.77 -     3.30: 5733
        3.30 -     3.83: 9453
        3.83 -     4.37: 10196
        4.37 -     4.90: 18419
  Nonbonded interactions: 44925
  Sorted by model distance:
  nonbonded pdb=" NE  ARG B 119 "
            pdb=" OE2 GLU B 123 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" OD1 ASP A 263 "
            pdb=" OH  TYR A 413 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O3  NAG D   1 "
            pdb=" O7  NAG D   2 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   ASP A 263 "
            pdb=" OG1 THR A 267 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG1 THR A  94 "
            pdb=" O   THR A 268 "
     model   vdw
     2.307 3.040
  ... (remaining 44920 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'E'
}

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:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.480
  Find NCS groups from input model:        0.020
  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:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6964
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   0.085   6035  Z= 0.160
  Angle     :  0.560   6.571   8253  Z= 0.296
  Chirality :  0.039   0.269    968
  Planarity :  0.004   0.037   1006
  Dihedral  : 18.589 124.653   2206
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  :  5.00 %
    Favored  : 92.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.32), residues: 746
  helix:  2.22 (0.27), residues: 384
  sheet: -0.10 (0.68), residues: 59
  loop : -0.20 (0.37), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 581 
 TYR   0.012   0.001   TYR A 257 
 PHE   0.007   0.001   PHE A 367 
 TRP   0.009   0.001   TRP B 188 
 HIS   0.002   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6020)
  covalent geometry    : angle       0.55039 ( 8215)
  SS BOND              : bond        0.00166 (    7)
  SS BOND              : angle       0.74380 (   14)
  hydrogen bonds       : bond        0.18137 (  328)
  hydrogen bonds       : angle       5.87463 (  933)
  link_BETA1-4         : bond        0.00479 (    4)
  link_BETA1-4         : angle       1.48767 (   12)
  link_NAG-ASN         : bond        0.00429 (    4)
  link_NAG-ASN         : angle       2.25209 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 187
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 PHE cc_start: 0.7850 (t80) cc_final: 0.7506 (t80)
REVERT: A  147 PHE cc_start: 0.7820 (t80) cc_final: 0.7554 (t80)
REVERT: A  222 LYS cc_start: 0.8246 (mtmt) cc_final: 0.7915 (mtpp)
REVERT: A  234 LYS cc_start: 0.8097 (tttp) cc_final: 0.7670 (tttp)
REVERT: A  250 SER cc_start: 0.8594 (m) cc_final: 0.8374 (t)
REVERT: A  265 ILE cc_start: 0.7547 (mt) cc_final: 0.7304 (mm)
REVERT: A  275 PRO cc_start: 0.8633 (Cg_endo) cc_final: 0.8290 (Cg_exo)
REVERT: A  371 ILE cc_start: 0.7163 (mt) cc_final: 0.6828 (mt)
REVERT: A  410 LEU cc_start: 0.8186 (mt) cc_final: 0.7956 (mm)
REVERT: A  421 LEU cc_start: 0.6812 (tp) cc_final: 0.6595 (tp)
REVERT: A  492 SER cc_start: 0.6974 (m) cc_final: 0.6534 (p)
REVERT: A  501 ILE cc_start: 0.8190 (mt) cc_final: 0.7689 (tp)
REVERT: A  505 ILE cc_start: 0.8568 (mt) cc_final: 0.8287 (mm)
REVERT: A  533 MET cc_start: 0.6048 (mtp) cc_final: 0.5792 (mtp)
REVERT: A  553 VAL cc_start: 0.7089 (t) cc_final: 0.6846 (m)
REVERT: A  588 ILE cc_start: 0.7716 (mt) cc_final: 0.7434 (tt)
REVERT: A  593 TYR cc_start: 0.7250 (t80) cc_final: 0.6818 (t80)
REVERT: B   63 SER cc_start: 0.8223 (m) cc_final: 0.7958 (p)
REVERT: B  120 ASP cc_start: 0.7656 (m-30) cc_final: 0.7371 (m-30)
REVERT: B  142 ASP cc_start: 0.8088 (t70) cc_final: 0.7877 (t0)
REVERT: B  185 ARG cc_start: 0.7077 (ttp80) cc_final: 0.6827 (ttp80)
REVERT: B  246 TYR cc_start: 0.7680 (t80) cc_final: 0.7184 (t80)
REVERT: B  259 ARG cc_start: 0.8062 (ptt-90) cc_final: 0.7710 (ptp90)
  outliers start: 14
  outliers final: 7
  residues processed: 196
  average time/residue: 0.0706
  time to fit residues: 18.4720
Evaluate side-chains
  169 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 162
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain B residue  175 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0470
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.6478

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.139309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.123848 restraints weight = 9999.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.127569 restraints weight = 5147.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.130055 restraints weight = 3159.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.131726 restraints weight = 2193.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.132748 restraints weight = 1654.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6035  Z= 0.155
  Angle     :  0.674   8.955   8253  Z= 0.315
  Chirality :  0.044   0.280    968
  Planarity :  0.005   0.040   1006
  Dihedral  : 19.473 113.850    977
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 11.77 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.54 (0.32), residues: 746
  helix:  2.09 (0.27), residues: 400
  sheet: -0.14 (0.69), residues: 59
  loop : -0.20 (0.39), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 185 
 TYR   0.018   0.002   TYR A 257 
 PHE   0.019   0.001   PHE A 590 
 TRP   0.016   0.001   TRP B 241 
 HIS   0.002   0.001   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6020)
  covalent geometry    : angle       0.65527 ( 8215)
  SS BOND              : bond        0.00212 (    7)
  SS BOND              : angle       0.64939 (   14)
  hydrogen bonds       : bond        0.05251 (  328)
  hydrogen bonds       : angle       4.62732 (  933)
  link_BETA1-4         : bond        0.00378 (    4)
  link_BETA1-4         : angle       2.75737 (   12)
  link_NAG-ASN         : bond        0.00360 (    4)
  link_NAG-ASN         : angle       3.23712 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 157
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 PHE cc_start: 0.7780 (t80) cc_final: 0.7576 (t80)
REVERT: A  211 LYS cc_start: 0.8345 (mmmt) cc_final: 0.7676 (ttpp)
REVERT: A  222 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7910 (ttpp)
REVERT: A  234 LYS cc_start: 0.8284 (tttp) cc_final: 0.7831 (tttp)
REVERT: A  275 PRO cc_start: 0.8615 (Cg_endo) cc_final: 0.8298 (Cg_exo)
REVERT: A  305 MET cc_start: 0.7434 (ttt) cc_final: 0.7184 (ttp)
REVERT: A  371 ILE cc_start: 0.7103 (mt) cc_final: 0.6807 (mt)
REVERT: A  410 LEU cc_start: 0.8228 (mt) cc_final: 0.7746 (mm)
REVERT: A  413 TYR cc_start: 0.7077 (m-10) cc_final: 0.6788 (m-10)
REVERT: A  414 SER cc_start: 0.8142 (m) cc_final: 0.7714 (p)
REVERT: A  421 LEU cc_start: 0.6781 (tp) cc_final: 0.6520 (tp)
REVERT: A  490 ASN cc_start: 0.6673 (t0) cc_final: 0.6369 (t0)
REVERT: A  492 SER cc_start: 0.7027 (m) cc_final: 0.6494 (p)
REVERT: A  501 ILE cc_start: 0.8089 (mt) cc_final: 0.7631 (tp)
REVERT: A  505 ILE cc_start: 0.8574 (mt) cc_final: 0.8214 (mm)
REVERT: A  533 MET cc_start: 0.5954 (mtp) cc_final: 0.5728 (mtp)
REVERT: A  553 VAL cc_start: 0.7072 (OUTLIER) cc_final: 0.6830 (m)
REVERT: A  593 TYR cc_start: 0.7395 (t80) cc_final: 0.6875 (t80)
REVERT: B  120 ASP cc_start: 0.7704 (m-30) cc_final: 0.7274 (m-30)
REVERT: B  185 ARG cc_start: 0.7254 (ttp80) cc_final: 0.6760 (ttp80)
REVERT: B  241 TRP cc_start: 0.8106 (m-90) cc_final: 0.7565 (m-90)
  outliers start: 26
  outliers final: 19
  residues processed: 168
  average time/residue: 0.0793
  time to fit residues: 17.3996
Evaluate side-chains
  170 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  399 LYS
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  553 VAL
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain B residue   44 VAL
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  147 LYS
Chi-restraints excluded: chain B residue  175 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 19 optimal weight:    0.0970
   chunk 27 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 64 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
A 151 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.139799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.124118 restraints weight = 9966.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.127929 restraints weight = 5163.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.130510 restraints weight = 3185.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.132188 restraints weight = 2202.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.133233 restraints weight = 1659.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6035  Z= 0.143
  Angle     :  0.666  10.293   8253  Z= 0.306
  Chirality :  0.044   0.240    968
  Planarity :  0.004   0.040   1006
  Dihedral  : 16.670 114.705    973
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 15.00 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.32), residues: 746
  helix:  2.10 (0.26), residues: 400
  sheet: -0.10 (0.71), residues: 59
  loop : -0.22 (0.40), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 511 
 TYR   0.015   0.001   TYR A 356 
 PHE   0.021   0.001   PHE A 590 
 TRP   0.016   0.001   TRP B  71 
 HIS   0.002   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6020)
  covalent geometry    : angle       0.65057 ( 8215)
  SS BOND              : bond        0.00165 (    7)
  SS BOND              : angle       0.64870 (   14)
  hydrogen bonds       : bond        0.04874 (  328)
  hydrogen bonds       : angle       4.46834 (  933)
  link_BETA1-4         : bond        0.00678 (    4)
  link_BETA1-4         : angle       2.89079 (   12)
  link_NAG-ASN         : bond        0.00316 (    4)
  link_NAG-ASN         : angle       2.53139 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 PHE cc_start: 0.7775 (t80) cc_final: 0.7545 (t80)
REVERT: A  211 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7652 (ttpp)
REVERT: A  221 GLU cc_start: 0.7257 (tt0) cc_final: 0.6962 (tt0)
REVERT: A  222 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7885 (ttpp)
REVERT: A  224 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7683 (m-10)
REVERT: A  234 LYS cc_start: 0.8300 (tttp) cc_final: 0.7817 (tttp)
REVERT: A  275 PRO cc_start: 0.8663 (Cg_endo) cc_final: 0.8342 (Cg_exo)
REVERT: A  277 LYS cc_start: 0.4139 (mmmm) cc_final: 0.3927 (mtmm)
REVERT: A  327 GLU cc_start: 0.6790 (tp30) cc_final: 0.6543 (tp30)
REVERT: A  371 ILE cc_start: 0.7090 (mt) cc_final: 0.6869 (mt)
REVERT: A  410 LEU cc_start: 0.8280 (mt) cc_final: 0.7861 (mm)
REVERT: A  413 TYR cc_start: 0.7047 (m-10) cc_final: 0.6795 (m-10)
REVERT: A  414 SER cc_start: 0.8114 (m) cc_final: 0.7718 (p)
REVERT: A  473 ILE cc_start: 0.7140 (mp) cc_final: 0.6918 (mm)
REVERT: A  484 PHE cc_start: 0.5690 (t80) cc_final: 0.5405 (t80)
REVERT: A  488 ILE cc_start: 0.7030 (tp) cc_final: 0.6511 (pt)
REVERT: A  490 ASN cc_start: 0.6722 (t0) cc_final: 0.6440 (t0)
REVERT: A  501 ILE cc_start: 0.8035 (mt) cc_final: 0.7609 (tp)
REVERT: A  505 ILE cc_start: 0.8558 (mt) cc_final: 0.8340 (mt)
REVERT: A  533 MET cc_start: 0.5995 (mtp) cc_final: 0.5762 (mtp)
REVERT: A  581 ARG cc_start: 0.7892 (mtt90) cc_final: 0.7662 (mtt-85)
REVERT: A  593 TYR cc_start: 0.7413 (t80) cc_final: 0.6675 (t80)
REVERT: B   49 TRP cc_start: 0.7895 (m100) cc_final: 0.7651 (m100)
REVERT: B  120 ASP cc_start: 0.7753 (m-30) cc_final: 0.7368 (m-30)
REVERT: B  185 ARG cc_start: 0.7217 (ttp80) cc_final: 0.6198 (ttp80)
REVERT: B  241 TRP cc_start: 0.8153 (m-90) cc_final: 0.7529 (m-90)
  outliers start: 24
  outliers final: 16
  residues processed: 160
  average time/residue: 0.0754
  time to fit residues: 15.7695
Evaluate side-chains
  162 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  175 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0970
   chunk 70 optimal weight:    0.8980
   chunk 28 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.6178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.140077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.124271 restraints weight = 10097.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.128105 restraints weight = 5251.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.130702 restraints weight = 3236.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.132414 restraints weight = 2235.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.133629 restraints weight = 1677.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6957
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6035  Z= 0.138
  Angle     :  0.646  11.317   8253  Z= 0.297
  Chirality :  0.043   0.276    968
  Planarity :  0.004   0.039   1006
  Dihedral  : 14.318 113.708    973
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 15.32 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.57 (0.33), residues: 746
  helix:  2.16 (0.26), residues: 400
  sheet: -0.13 (0.71), residues: 59
  loop : -0.28 (0.40), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 149 
 TYR   0.021   0.001   TYR A 569 
 PHE   0.034   0.001   PHE A 590 
 TRP   0.017   0.001   TRP A 585 
 HIS   0.002   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6020)
  covalent geometry    : angle       0.62890 ( 8215)
  SS BOND              : bond        0.00283 (    7)
  SS BOND              : angle       0.59583 (   14)
  hydrogen bonds       : bond        0.04547 (  328)
  hydrogen bonds       : angle       4.34557 (  933)
  link_BETA1-4         : bond        0.00643 (    4)
  link_BETA1-4         : angle       3.18119 (   12)
  link_NAG-ASN         : bond        0.00317 (    4)
  link_NAG-ASN         : angle       2.45296 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 PHE cc_start: 0.7745 (t80) cc_final: 0.7525 (t80)
REVERT: A  149 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6507 (mtm180)
REVERT: A  211 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7644 (ttpp)
REVERT: A  221 GLU cc_start: 0.7299 (tt0) cc_final: 0.7009 (tt0)
REVERT: A  224 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7665 (m-10)
REVERT: A  234 LYS cc_start: 0.8258 (tttp) cc_final: 0.7803 (tttp)
REVERT: A  275 PRO cc_start: 0.8685 (Cg_endo) cc_final: 0.8359 (Cg_exo)
REVERT: A  327 GLU cc_start: 0.6760 (tp30) cc_final: 0.6508 (tp30)
REVERT: A  371 ILE cc_start: 0.7115 (mt) cc_final: 0.6868 (mt)
REVERT: A  410 LEU cc_start: 0.8255 (mt) cc_final: 0.7867 (mm)
REVERT: A  413 TYR cc_start: 0.7062 (m-10) cc_final: 0.6770 (m-10)
REVERT: A  414 SER cc_start: 0.8143 (m) cc_final: 0.7735 (p)
REVERT: A  473 ILE cc_start: 0.7075 (mp) cc_final: 0.6873 (mm)
REVERT: A  484 PHE cc_start: 0.5663 (t80) cc_final: 0.5394 (t80)
REVERT: A  488 ILE cc_start: 0.6985 (tp) cc_final: 0.6509 (pt)
REVERT: A  490 ASN cc_start: 0.6783 (t0) cc_final: 0.6387 (t0)
REVERT: A  492 SER cc_start: 0.6984 (m) cc_final: 0.6397 (p)
REVERT: A  501 ILE cc_start: 0.8055 (mt) cc_final: 0.7645 (tp)
REVERT: A  505 ILE cc_start: 0.8546 (mt) cc_final: 0.8269 (mt)
REVERT: A  533 MET cc_start: 0.6000 (mtp) cc_final: 0.5773 (mtp)
REVERT: A  581 ARG cc_start: 0.7910 (mtt90) cc_final: 0.7647 (mtt-85)
REVERT: A  586 MET cc_start: 0.7228 (mmm) cc_final: 0.6940 (tmm)
REVERT: B  120 ASP cc_start: 0.7695 (m-30) cc_final: 0.7317 (m-30)
REVERT: B  185 ARG cc_start: 0.7274 (ttp80) cc_final: 0.6244 (ttp80)
REVERT: B  241 TRP cc_start: 0.8127 (m-90) cc_final: 0.7477 (m-90)
  outliers start: 26
  outliers final: 19
  residues processed: 160
  average time/residue: 0.0811
  time to fit residues: 17.0477
Evaluate side-chains
  168 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  149 ARG
Chi-restraints excluded: chain A residue  217 TRP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  338 CYS
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  175 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 14 optimal weight:    0.4980
   chunk 31 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 55 optimal weight:    0.2980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 150 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 = 0.3817 r_free = 0.3817 target = 0.139995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.124122 restraints weight = 10098.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.127971 restraints weight = 5249.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.130592 restraints weight = 3233.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.132256 restraints weight = 2241.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.133504 restraints weight = 1697.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6965
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6035  Z= 0.144
  Angle     :  0.666  10.850   8253  Z= 0.304
  Chirality :  0.043   0.250    968
  Planarity :  0.004   0.040   1006
  Dihedral  : 12.793 113.508    973
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 16.94 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.32), residues: 746
  helix:  2.22 (0.26), residues: 394
  sheet: -0.22 (0.71), residues: 59
  loop : -0.43 (0.39), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 511 
 TYR   0.020   0.001   TYR A 569 
 PHE   0.023   0.001   PHE A 565 
 TRP   0.012   0.001   TRP A 585 
 HIS   0.007   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6020)
  covalent geometry    : angle       0.63903 ( 8215)
  SS BOND              : bond        0.00128 (    7)
  SS BOND              : angle       0.77178 (   14)
  hydrogen bonds       : bond        0.04513 (  328)
  hydrogen bonds       : angle       4.32193 (  933)
  link_BETA1-4         : bond        0.00729 (    4)
  link_BETA1-4         : angle       3.71878 (   12)
  link_NAG-ASN         : bond        0.00460 (    4)
  link_NAG-ASN         : angle       3.24770 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 148
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.6329 (t80) cc_final: 0.5836 (t80)
REVERT: A  136 PHE cc_start: 0.7736 (t80) cc_final: 0.7477 (t80)
REVERT: A  149 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6483 (mtm180)
REVERT: A  211 LYS cc_start: 0.8373 (mmmt) cc_final: 0.7702 (ttpp)
REVERT: A  221 GLU cc_start: 0.7303 (tt0) cc_final: 0.7041 (tt0)
REVERT: A  222 LYS cc_start: 0.8250 (mtmt) cc_final: 0.7958 (ttpp)
REVERT: A  224 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7743 (m-10)
REVERT: A  234 LYS cc_start: 0.8233 (tttp) cc_final: 0.7812 (tttp)
REVERT: A  275 PRO cc_start: 0.8678 (Cg_endo) cc_final: 0.8313 (Cg_exo)
REVERT: A  327 GLU cc_start: 0.6784 (tp30) cc_final: 0.6445 (tp30)
REVERT: A  371 ILE cc_start: 0.7093 (mt) cc_final: 0.6867 (mt)
REVERT: A  410 LEU cc_start: 0.8313 (mt) cc_final: 0.7886 (mm)
REVERT: A  414 SER cc_start: 0.8131 (m) cc_final: 0.7738 (p)
REVERT: A  490 ASN cc_start: 0.6907 (t0) cc_final: 0.6553 (t0)
REVERT: A  492 SER cc_start: 0.6990 (m) cc_final: 0.6424 (p)
REVERT: A  501 ILE cc_start: 0.8087 (mt) cc_final: 0.7659 (tp)
REVERT: A  533 MET cc_start: 0.6039 (mtp) cc_final: 0.5793 (mtp)
REVERT: B   49 TRP cc_start: 0.7883 (m100) cc_final: 0.7665 (m100)
REVERT: B  120 ASP cc_start: 0.7752 (m-30) cc_final: 0.7344 (m-30)
REVERT: B  142 ASP cc_start: 0.7943 (t0) cc_final: 0.7682 (t0)
REVERT: B  185 ARG cc_start: 0.7262 (ttp80) cc_final: 0.6267 (ttp80)
REVERT: B  241 TRP cc_start: 0.8131 (m-90) cc_final: 0.7470 (m-90)
  outliers start: 23
  outliers final: 19
  residues processed: 159
  average time/residue: 0.0787
  time to fit residues: 16.3604
Evaluate side-chains
  168 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  149 ARG
Chi-restraints excluded: chain A residue  217 TRP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  147 LYS
Chi-restraints excluded: chain B residue  175 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 59 optimal weight:    0.0000
   chunk 55 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0030
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.141063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.125928 restraints weight = 9911.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.129674 restraints weight = 5130.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.132112 restraints weight = 3153.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.133787 restraints weight = 2187.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.134960 restraints weight = 1639.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6035  Z= 0.119
  Angle     :  0.627   8.845   8253  Z= 0.290
  Chirality :  0.042   0.264    968
  Planarity :  0.004   0.045   1006
  Dihedral  : 11.757 111.895    973
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 18.23 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.33), residues: 746
  helix:  2.36 (0.26), residues: 393
  sheet: -0.14 (0.70), residues: 59
  loop : -0.41 (0.39), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 511 
 TYR   0.020   0.001   TYR A 569 
 PHE   0.018   0.001   PHE A 590 
 TRP   0.013   0.001   TRP A 585 
 HIS   0.002   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6020)
  covalent geometry    : angle       0.60591 ( 8215)
  SS BOND              : bond        0.00125 (    7)
  SS BOND              : angle       0.65077 (   14)
  hydrogen bonds       : bond        0.04091 (  328)
  hydrogen bonds       : angle       4.27580 (  933)
  link_BETA1-4         : bond        0.00625 (    4)
  link_BETA1-4         : angle       3.31036 (   12)
  link_NAG-ASN         : bond        0.00367 (    4)
  link_NAG-ASN         : angle       2.82521 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.6292 (t80) cc_final: 0.5823 (t80)
REVERT: A  136 PHE cc_start: 0.7698 (t80) cc_final: 0.7440 (t80)
REVERT: A  149 ARG cc_start: 0.6675 (OUTLIER) cc_final: 0.6401 (mtm180)
REVERT: A  211 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7709 (ttpp)
REVERT: A  221 GLU cc_start: 0.7312 (tt0) cc_final: 0.6946 (tt0)
REVERT: A  222 LYS cc_start: 0.8246 (mtmt) cc_final: 0.7965 (ttpp)
REVERT: A  234 LYS cc_start: 0.8258 (tttp) cc_final: 0.7837 (tttp)
REVERT: A  275 PRO cc_start: 0.8623 (Cg_endo) cc_final: 0.8301 (Cg_exo)
REVERT: A  327 GLU cc_start: 0.6694 (tp30) cc_final: 0.6402 (tp30)
REVERT: A  371 ILE cc_start: 0.7103 (mt) cc_final: 0.6794 (mt)
REVERT: A  410 LEU cc_start: 0.8295 (mt) cc_final: 0.7860 (mm)
REVERT: A  413 TYR cc_start: 0.7018 (m-10) cc_final: 0.6718 (m-10)
REVERT: A  414 SER cc_start: 0.8157 (m) cc_final: 0.7771 (p)
REVERT: A  473 ILE cc_start: 0.7033 (mp) cc_final: 0.6786 (mm)
REVERT: A  501 ILE cc_start: 0.8034 (mt) cc_final: 0.7704 (tp)
REVERT: A  533 MET cc_start: 0.5943 (mtp) cc_final: 0.5702 (mtp)
REVERT: B  120 ASP cc_start: 0.7701 (m-30) cc_final: 0.7312 (m-30)
REVERT: B  142 ASP cc_start: 0.7904 (t0) cc_final: 0.7690 (t0)
REVERT: B  185 ARG cc_start: 0.7269 (ttp80) cc_final: 0.6255 (ttp80)
REVERT: B  241 TRP cc_start: 0.8144 (m-90) cc_final: 0.7446 (m-90)
  outliers start: 22
  outliers final: 20
  residues processed: 157
  average time/residue: 0.0760
  time to fit residues: 15.7250
Evaluate side-chains
  166 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  149 ARG
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  147 LYS
Chi-restraints excluded: chain B residue  175 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 58 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    0.3980
   chunk 39 optimal weight:    0.7980
   chunk 27 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 8 optimal weight:    0.3980
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:    0.2980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
A 372 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.140636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.124955 restraints weight = 10131.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.128847 restraints weight = 5232.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.131353 restraints weight = 3203.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.133020 restraints weight = 2217.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.134276 restraints weight = 1677.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6939
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6035  Z= 0.119
  Angle     :  0.638   8.900   8253  Z= 0.295
  Chirality :  0.041   0.250    968
  Planarity :  0.004   0.036   1006
  Dihedral  : 11.058 111.683    973
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 17.26 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.65 (0.32), residues: 746
  helix:  2.37 (0.26), residues: 393
  sheet: -0.16 (0.70), residues: 59
  loop : -0.39 (0.39), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 511 
 TYR   0.020   0.001   TYR A 569 
 PHE   0.022   0.001   PHE A 565 
 TRP   0.011   0.001   TRP A 585 
 HIS   0.005   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6020)
  covalent geometry    : angle       0.61857 ( 8215)
  SS BOND              : bond        0.00124 (    7)
  SS BOND              : angle       0.67149 (   14)
  hydrogen bonds       : bond        0.03994 (  328)
  hydrogen bonds       : angle       4.21958 (  933)
  link_BETA1-4         : bond        0.00584 (    4)
  link_BETA1-4         : angle       3.24653 (   12)
  link_NAG-ASN         : bond        0.00344 (    4)
  link_NAG-ASN         : angle       2.56226 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.6301 (t80) cc_final: 0.5794 (t80)
REVERT: A  136 PHE cc_start: 0.7710 (t80) cc_final: 0.7440 (t80)
REVERT: A  211 LYS cc_start: 0.8362 (mmmt) cc_final: 0.7706 (ttpp)
REVERT: A  222 LYS cc_start: 0.8224 (mtmt) cc_final: 0.8018 (ttpp)
REVERT: A  224 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7717 (m-10)
REVERT: A  234 LYS cc_start: 0.8199 (tttp) cc_final: 0.7793 (tttp)
REVERT: A  241 MET cc_start: 0.7577 (ttm) cc_final: 0.7338 (ttm)
REVERT: A  275 PRO cc_start: 0.8626 (Cg_endo) cc_final: 0.8291 (Cg_exo)
REVERT: A  327 GLU cc_start: 0.6754 (tp30) cc_final: 0.6449 (tp30)
REVERT: A  371 ILE cc_start: 0.7072 (mt) cc_final: 0.6826 (mt)
REVERT: A  410 LEU cc_start: 0.8267 (mt) cc_final: 0.7856 (mm)
REVERT: A  414 SER cc_start: 0.8153 (m) cc_final: 0.7750 (p)
REVERT: A  533 MET cc_start: 0.6025 (mtp) cc_final: 0.5749 (mtp)
REVERT: B  120 ASP cc_start: 0.7747 (m-30) cc_final: 0.7363 (m-30)
REVERT: B  185 ARG cc_start: 0.7248 (ttp80) cc_final: 0.6235 (ttp80)
REVERT: B  241 TRP cc_start: 0.8127 (m-90) cc_final: 0.7451 (m-90)
  outliers start: 27
  outliers final: 23
  residues processed: 155
  average time/residue: 0.0748
  time to fit residues: 15.1220
Evaluate side-chains
  168 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  224 PHE
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  147 LYS
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  183 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 72 optimal weight:    0.5980
   chunk 13 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 58 optimal weight:    0.6980
   chunk 56 optimal weight:    0.3980
   chunk 71 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 372 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.139653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.124535 restraints weight = 9930.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.128267 restraints weight = 5167.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.130751 restraints weight = 3180.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.132414 restraints weight = 2190.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.133587 restraints weight = 1639.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6954
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6035  Z= 0.138
  Angle     :  0.656   8.829   8253  Z= 0.307
  Chirality :  0.042   0.223    968
  Planarity :  0.004   0.047   1006
  Dihedral  : 10.455 112.345    973
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 17.74 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.32), residues: 746
  helix:  2.27 (0.26), residues: 394
  sheet: -0.12 (0.70), residues: 59
  loop : -0.43 (0.39), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 511 
 TYR   0.021   0.001   TYR A 569 
 PHE   0.016   0.001   PHE A 565 
 TRP   0.011   0.001   TRP A 585 
 HIS   0.003   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6020)
  covalent geometry    : angle       0.63765 ( 8215)
  SS BOND              : bond        0.00133 (    7)
  SS BOND              : angle       0.68329 (   14)
  hydrogen bonds       : bond        0.04245 (  328)
  hydrogen bonds       : angle       4.29623 (  933)
  link_BETA1-4         : bond        0.00614 (    4)
  link_BETA1-4         : angle       3.22314 (   12)
  link_NAG-ASN         : bond        0.00347 (    4)
  link_NAG-ASN         : angle       2.51913 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 148
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 TYR cc_start: 0.6378 (t80) cc_final: 0.5848 (t80)
REVERT: A  136 PHE cc_start: 0.7688 (t80) cc_final: 0.7439 (t80)
REVERT: A  149 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.6451 (mtm180)
REVERT: A  211 LYS cc_start: 0.8302 (mmmt) cc_final: 0.7637 (ttpp)
REVERT: A  234 LYS cc_start: 0.8191 (tttp) cc_final: 0.7795 (tttp)
REVERT: A  241 MET cc_start: 0.7580 (ttm) cc_final: 0.7360 (ttm)
REVERT: A  275 PRO cc_start: 0.8639 (Cg_endo) cc_final: 0.8300 (Cg_exo)
REVERT: A  327 GLU cc_start: 0.6763 (tp30) cc_final: 0.6454 (tp30)
REVERT: A  410 LEU cc_start: 0.8286 (mt) cc_final: 0.7880 (mm)
REVERT: A  414 SER cc_start: 0.8184 (m) cc_final: 0.7777 (p)
REVERT: A  533 MET cc_start: 0.5985 (mtp) cc_final: 0.5727 (mtp)
REVERT: A  581 ARG cc_start: 0.7900 (mtt90) cc_final: 0.7649 (mtt-85)
REVERT: A  588 ILE cc_start: 0.7669 (mt) cc_final: 0.7312 (tt)
REVERT: A  592 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8323 (tt)
REVERT: B  120 ASP cc_start: 0.7740 (m-30) cc_final: 0.7346 (m-30)
REVERT: B  142 ASP cc_start: 0.7929 (t0) cc_final: 0.7669 (t0)
REVERT: B  185 ARG cc_start: 0.7282 (ttp80) cc_final: 0.6167 (ttp80)
REVERT: B  241 TRP cc_start: 0.8132 (m-90) cc_final: 0.7452 (m-90)
  outliers start: 27
  outliers final: 23
  residues processed: 161
  average time/residue: 0.0760
  time to fit residues: 16.0247
Evaluate side-chains
  174 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  149 ARG
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  217 TRP
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  480 GLU
Chi-restraints excluded: chain A residue  547 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  592 ILE
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue   52 THR
Chi-restraints excluded: chain B residue  147 LYS
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  183 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 43 optimal weight:    0.2980
   chunk 47 optimal weight:    0.0020
   chunk 7 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
A 372 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.140132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.124555 restraints weight = 10125.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.128421 restraints weight = 5219.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.131015 restraints weight = 3197.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.132794 restraints weight = 2196.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.133857 restraints weight = 1631.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   6035  Z= 0.125
  Angle     :  0.662  10.453   8253  Z= 0.308
  Chirality :  0.042   0.217    968
  Planarity :  0.004   0.039   1006
  Dihedral  : 10.055 114.230    973
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 19.68 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.33), residues: 746
  helix:  2.34 (0.27), residues: 394
  sheet: -0.14 (0.70), residues: 59
  loop : -0.41 (0.39), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 511 
 TYR   0.021   0.001   TYR A 569 
 PHE   0.010   0.001   PHE A 367 
 TRP   0.011   0.001   TRP A 585 
 HIS   0.002   0.001   HIS B  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6020)
  covalent geometry    : angle       0.64160 ( 8215)
  SS BOND              : bond        0.00131 (    7)
  SS BOND              : angle       0.63587 (   14)
  hydrogen bonds       : bond        0.04040 (  328)
  hydrogen bonds       : angle       4.18745 (  933)
  link_BETA1-4         : bond        0.00569 (    4)
  link_BETA1-4         : angle       3.33753 (   12)
  link_NAG-ASN         : bond        0.00332 (    4)
  link_NAG-ASN         : angle       2.86584 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 PHE cc_start: 0.7698 (t80) cc_final: 0.7280 (t80)
REVERT: A  149 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6416 (mtm180)
REVERT: A  211 LYS cc_start: 0.8303 (mmmt) cc_final: 0.7630 (ttpp)
REVERT: A  222 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7909 (ttpp)
REVERT: A  234 LYS cc_start: 0.8200 (tttp) cc_final: 0.7800 (tttp)
REVERT: A  241 MET cc_start: 0.7589 (ttm) cc_final: 0.7360 (ttm)
REVERT: A  275 PRO cc_start: 0.8607 (Cg_endo) cc_final: 0.8257 (Cg_exo)
REVERT: A  410 LEU cc_start: 0.8277 (mt) cc_final: 0.7863 (mm)
REVERT: A  414 SER cc_start: 0.8174 (m) cc_final: 0.7756 (p)
REVERT: A  533 MET cc_start: 0.6096 (mtp) cc_final: 0.5815 (mtp)
REVERT: A  581 ARG cc_start: 0.7883 (mtt90) cc_final: 0.7632 (mtt-85)
REVERT: A  588 ILE cc_start: 0.7677 (mt) cc_final: 0.7333 (tt)
REVERT: B  120 ASP cc_start: 0.7751 (m-30) cc_final: 0.7358 (m-30)
REVERT: B  142 ASP cc_start: 0.7956 (t0) cc_final: 0.7722 (t0)
REVERT: B  185 ARG cc_start: 0.7252 (ttp80) cc_final: 0.6099 (ttp80)
REVERT: B  241 TRP cc_start: 0.8116 (m-90) cc_final: 0.7422 (m-90)
  outliers start: 22
  outliers final: 19
  residues processed: 152
  average time/residue: 0.0780
  time to fit residues: 15.3898
Evaluate side-chains
  161 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  149 ARG
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  147 LYS
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  183 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 55 optimal weight:    0.0040
   chunk 58 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 22 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 67 optimal weight:    0.0020
   chunk 56 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.4200

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
A 372 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.141877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.126268 restraints weight = 10032.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.130118 restraints weight = 5173.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.132658 restraints weight = 3162.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.134350 restraints weight = 2174.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135548 restraints weight = 1636.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067   6035  Z= 0.124
  Angle     :  0.666  10.709   8253  Z= 0.311
  Chirality :  0.041   0.203    968
  Planarity :  0.004   0.044   1006
  Dihedral  :  9.669 112.606    972
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.65 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.32), residues: 746
  helix:  2.36 (0.26), residues: 394
  sheet: -0.18 (0.70), residues: 59
  loop : -0.43 (0.39), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 511 
 TYR   0.021   0.001   TYR A 569 
 PHE   0.024   0.001   PHE A 565 
 TRP   0.011   0.001   TRP A 217 
 HIS   0.006   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6020)
  covalent geometry    : angle       0.64648 ( 8215)
  SS BOND              : bond        0.00116 (    7)
  SS BOND              : angle       0.65020 (   14)
  hydrogen bonds       : bond        0.03997 (  328)
  hydrogen bonds       : angle       4.15702 (  933)
  link_BETA1-4         : bond        0.00560 (    4)
  link_BETA1-4         : angle       3.24040 (   12)
  link_NAG-ASN         : bond        0.00464 (    4)
  link_NAG-ASN         : angle       2.89011 (   12)

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

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

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1492 Ramachandran restraints generated.
    746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  136 PHE cc_start: 0.7672 (t80) cc_final: 0.7266 (t80)
REVERT: A  211 LYS cc_start: 0.8284 (mmmt) cc_final: 0.7629 (ttpp)
REVERT: A  222 LYS cc_start: 0.8170 (ttpp) cc_final: 0.7880 (ttpp)
REVERT: A  234 LYS cc_start: 0.8201 (tttp) cc_final: 0.7809 (tttp)
REVERT: A  241 MET cc_start: 0.7587 (ttm) cc_final: 0.7360 (ttm)
REVERT: A  275 PRO cc_start: 0.8593 (Cg_endo) cc_final: 0.8247 (Cg_exo)
REVERT: A  380 ILE cc_start: 0.7828 (mm) cc_final: 0.7511 (pt)
REVERT: A  410 LEU cc_start: 0.8287 (mt) cc_final: 0.7868 (mm)
REVERT: A  414 SER cc_start: 0.8198 (m) cc_final: 0.7780 (p)
REVERT: A  533 MET cc_start: 0.6056 (mtp) cc_final: 0.5778 (mtp)
REVERT: A  581 ARG cc_start: 0.7880 (mtt90) cc_final: 0.7644 (mtt-85)
REVERT: A  588 ILE cc_start: 0.7659 (mt) cc_final: 0.7324 (tt)
REVERT: B  120 ASP cc_start: 0.7727 (m-30) cc_final: 0.7326 (m-30)
REVERT: B  185 ARG cc_start: 0.7275 (ttp80) cc_final: 0.6154 (ttp80)
REVERT: B  241 TRP cc_start: 0.8127 (m-90) cc_final: 0.7456 (m-90)
  outliers start: 19
  outliers final: 19
  residues processed: 141
  average time/residue: 0.0828
  time to fit residues: 15.1636
Evaluate side-chains
  155 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 136
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue   84 TYR
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  149 ARG
Chi-restraints excluded: chain A residue  150 GLN
Chi-restraints excluded: chain A residue  185 GLU
Chi-restraints excluded: chain A residue  223 ASN
Chi-restraints excluded: chain A residue  292 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  325 TRP
Chi-restraints excluded: chain A residue  355 ILE
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  405 MET
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain B residue   47 ILE
Chi-restraints excluded: chain B residue  147 LYS
Chi-restraints excluded: chain B residue  175 CYS
Chi-restraints excluded: chain B residue  183 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 55 optimal weight:    0.1980
   chunk 48 optimal weight:    0.0870
   chunk 66 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
A 372 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.141680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.126153 restraints weight = 9914.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.129971 restraints weight = 5106.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.132497 restraints weight = 3124.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.134194 restraints weight = 2153.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.135383 restraints weight = 1619.441|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6944
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6035  Z= 0.130
  Angle     :  0.667  10.539   8253  Z= 0.312
  Chirality :  0.041   0.211    968
  Planarity :  0.004   0.041   1006
  Dihedral  :  9.457 112.579    972
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.32 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.60 (0.32), residues: 746
  helix:  2.34 (0.27), residues: 394
  sheet: -0.19 (0.70), residues: 59
  loop : -0.45 (0.39), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 511 
 TYR   0.021   0.001   TYR A 569 
 PHE   0.010   0.001   PHE A 367 
 TRP   0.011   0.001   TRP A 217 
 HIS   0.003   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6020)
  covalent geometry    : angle       0.64741 ( 8215)
  SS BOND              : bond        0.00124 (    7)
  SS BOND              : angle       0.65605 (   14)
  hydrogen bonds       : bond        0.04042 (  328)
  hydrogen bonds       : angle       4.16723 (  933)
  link_BETA1-4         : bond        0.00561 (    4)
  link_BETA1-4         : angle       3.15296 (   12)
  link_NAG-ASN         : bond        0.00448 (    4)
  link_NAG-ASN         : angle       2.89958 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1126.75 seconds
wall clock time: 20 minutes 3.92 seconds (1203.92 seconds total)