Starting phenix.real_space_refine
on Sat Aug 23 11:16:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fqt_50668/08_2025/9fqt_50668_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fqt_50668/08_2025/9fqt_50668.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fqt_50668/08_2025/9fqt_50668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fqt_50668/08_2025/9fqt_50668.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fqt_50668/08_2025/9fqt_50668_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fqt_50668/08_2025/9fqt_50668_trim.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    3854      2.51       5
     N     936      2.21       5
     O    1092      1.98       5
     H    5667      0.53       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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11589
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 8104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 8104
          Classifications: {'peptide': 537}
          Link IDs: {'PTRANS': 22, 'TRANS': 514}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 3320
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 3320
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 18, 'TRANS': 204}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 60
          Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "I"
      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: "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: "A"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 49
          Unusual residues: {'NAG': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 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: 2.35, per 1000 atoms: 0.20
  Number of scatterers: 11589
  At special positions: 0
  Unit cell: (108.9, 80.025, 106.425, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     O    1092      8.00
     N     936      7.00
     C    3854      6.00
     H    5667      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  46 " - pdb=" SG  CYS B  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  72 " - pdb=" SG  CYS B  87 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  73 " - pdb=" SG  CYS B  83 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 121 " - pdb=" SG  CYS B 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 146 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 178 " - pdb=" SG  CYS B 184 " 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
    ALPHA1-3
      " BMA D   3 " - " MAN D   4 "
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG I   1 " - " NAG I   2 "
    BETA1-6
      " NAG D   1 " - " FUC D   5 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A1001 " - " ASN A 229 "
      " NAG C   1 " - " ASN A 223 "
      " NAG D   1 " - " ASN B  12 "
      " NAG I   1 " - " ASN B 168 "
  Time building additional restraints: 1.13
  Conformation dependent library (CDL) restraints added in 319.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1386

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      66.2% alpha, 6.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 33 through 45
    Processing helix  chain 'A' and resid 48 through 61
      removed outlier: 3.750A  pdb=" N   VAL A  52 " --> pdb=" O   ALA A  48 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   GLY A  55 " --> pdb=" O   TYR A  51 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ALA A  56 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 91
      removed outlier: 3.686A  pdb=" N   LEU A  71 " --> pdb=" O   VAL A  67 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 105
    Processing helix  chain 'A' and resid 106 through 141
    Processing helix  chain 'A' and resid 141 through 152
      removed outlier: 3.687A  pdb=" N   GLY A 145 " --> pdb=" O   GLY A 141 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   SER A 148 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ARG A 149 " --> pdb=" O   GLY A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 182
    Processing helix  chain 'A' and resid 186 through 212
    Processing helix  chain 'A' and resid 213 through 218
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 243 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 5.838A  pdb=" N   GLY A 261 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 267
      removed outlier: 3.874A  pdb=" N   ALA A 266 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 305
      Proline residue:  A 280  - end of helix
    Processing helix  chain 'A' and resid 306 through 310
    Processing helix  chain 'A' and resid 314 through 323
      removed outlier: 3.595A  pdb=" N   GLY A 318 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 349
      removed outlier: 3.906A  pdb=" N   ALA A 331 " --> pdb=" O   GLU A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 361
      removed outlier: 3.848A  pdb=" N   ILE A 355 " --> pdb=" O   MET A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
      removed outlier: 3.827A  pdb=" N   ALA A 369 " --> pdb=" O   PHE A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 396
    Processing helix  chain 'A' and resid 397 through 424
    Processing helix  chain 'A' and resid 469 through 475
    Processing helix  chain 'A' and resid 482 through 509
    Processing helix  chain 'A' and resid 510 through 517
    Processing helix  chain 'A' and resid 518 through 542
    Processing helix  chain 'A' and resid 558 through 574
      removed outlier: 3.658A  pdb=" N   LEU A 574 " --> pdb=" O   LEU A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 596
    Processing helix  chain 'A' and resid 596 through 601
    Processing helix  chain 'B' and resid 44 through 49
      removed outlier: 3.620A  pdb=" N   ALA B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 57
    Processing helix  chain 'B' and resid 100 through 113
    Processing helix  chain 'B' and resid 127 through 134
      removed outlier: 4.489A  pdb=" N   SER B 132 " --> pdb=" O   GLU B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 139
    Processing helix  chain 'B' and resid 170 through 180
      removed outlier: 3.985A  pdb=" N   GLN B 176 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   VAL B 177 " --> pdb=" O   GLN B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 198
    Processing helix  chain 'B' and resid 199 through 204
      removed outlier: 4.130A  pdb=" N   THR B 202 " --> pdb=" O   THR B 199 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 33
      removed outlier: 6.718A  pdb=" N   VAL B  17 " --> pdb=" O   VAL B  25 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ALA B  27 " --> pdb=" O   TRP B  15 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   TRP B  15 " --> pdb=" O   ALA B  27 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   SER B  29 " --> pdb=" O   ILE B  13 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   ILE B  13 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   ASN B  31 " --> pdb=" O   TYR B  11 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   TYR B  11 " --> pdb=" O   ASN B  31 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLY B 117 " --> pdb=" O   TYR B 212 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 163 through 167

    368 hydrogen bonds defined for protein.
    1047 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.76

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 5656
        1.03 -     1.23: 24
        1.23 -     1.42: 2527
        1.42 -     1.62: 3485
        1.62 -     1.82: 56
  Bond restraints: 11748
  Sorted by residual:
  bond pdb=" N   CYS A 255 "
       pdb=" CA  CYS A 255 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.33e-02 5.65e+03 7.36e+00
  bond pdb=" N   THR A 254 "
       pdb=" H   THR A 254 "
    ideal  model  delta    sigma   weight residual
    0.860  0.912 -0.052 2.00e-02 2.50e+03 6.68e+00
  bond pdb=" N   PHE A 259 "
       pdb=" H   PHE A 259 "
    ideal  model  delta    sigma   weight residual
    0.860  0.911 -0.051 2.00e-02 2.50e+03 6.60e+00
  bond pdb=" N   ALA A 258 "
       pdb=" H   ALA A 258 "
    ideal  model  delta    sigma   weight residual
    0.860  0.911 -0.051 2.00e-02 2.50e+03 6.57e+00
  bond pdb=" N   PHE A 256 "
       pdb=" H   PHE A 256 "
    ideal  model  delta    sigma   weight residual
    0.860  0.911 -0.051 2.00e-02 2.50e+03 6.45e+00
  ... (remaining 11743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 21010
        2.32 -     4.64: 141
        4.64 -     6.96: 9
        6.96 -     9.27: 2
        9.27 -    11.59: 2
  Bond angle restraints: 21164
  Sorted by residual:
  angle pdb=" CZ  TYR A 257 "
        pdb=" OH  TYR A 257 "
        pdb=" HH  TYR A 257 "
      ideal   model   delta    sigma   weight residual
     110.00  119.91   -9.91 3.00e+00 1.11e-01 1.09e+01
  angle pdb=" CA  PRO A 275 "
        pdb=" N   PRO A 275 "
        pdb=" CD  PRO A 275 "
      ideal   model   delta    sigma   weight residual
     112.00  107.93    4.07 1.40e+00 5.10e-01 8.47e+00
  angle pdb=" CA  ALA A 258 "
        pdb=" C   ALA A 258 "
        pdb=" O   ALA A 258 "
      ideal   model   delta    sigma   weight residual
     120.42  117.35    3.07 1.06e+00 8.90e-01 8.37e+00
  angle pdb=" CA  TYR A 257 "
        pdb=" C   TYR A 257 "
        pdb=" O   TYR A 257 "
      ideal   model   delta    sigma   weight residual
     120.10  117.18    2.92 1.13e+00 7.83e-01 6.69e+00
  angle pdb=" CB  MET A 533 "
        pdb=" CG  MET A 533 "
        pdb=" SD  MET A 533 "
      ideal   model   delta    sigma   weight residual
     112.70  120.03   -7.33 3.00e+00 1.11e-01 5.96e+00
  ... (remaining 21159 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.86: 5387
       20.86 -    41.72: 271
       41.72 -    62.58: 129
       62.58 -    83.44: 8
       83.44 -   104.29: 6
  Dihedral angle restraints: 5801
    sinusoidal: 3171
      harmonic: 2630
  Sorted by residual:
  dihedral pdb=" CB  CYS B  72 "
           pdb=" SG  CYS B  72 "
           pdb=" SG  CYS B  87 "
           pdb=" CB  CYS B  87 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -51.14  -34.86     1      1.00e+01 1.00e-02 1.72e+01
  dihedral pdb=" CB  CYS B 121 "
           pdb=" SG  CYS B 121 "
           pdb=" SG  CYS B 141 "
           pdb=" CB  CYS B 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  124.35  -31.35     1      1.00e+01 1.00e-02 1.40e+01
  dihedral pdb=" O4  BMA D   3 "
           pdb=" C4  BMA D   3 "
           pdb=" C5  BMA D   3 "
           pdb=" O5  BMA D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -175.58  104.29     1      3.00e+01 1.11e-03 1.33e+01
  ... (remaining 5798 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 846
       0.057 -    0.114: 128
       0.114 -    0.172: 12
       0.172 -    0.229: 3
       0.229 -    0.286: 1
  Chirality restraints: 990
  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   -2.56    0.29 2.00e-01 2.50e+01 2.04e+00
  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    2.68   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" C1  NAG I   1 "
            pdb=" ND2 ASN B 168 "
            pdb=" C2  NAG I   1 "
            pdb=" O5  NAG I   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 7.90e-01
  ... (remaining 987 not shown)

  Planarity restraints: 1735
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 274 "   -0.088 5.00e-02 4.00e+02   1.32e-01 2.79e+01
        pdb=" N   PRO A 275 "    0.228 5.00e-02 4.00e+02
        pdb=" CA  PRO A 275 "   -0.071 5.00e-02 4.00e+02
        pdb=" CD  PRO A 275 "   -0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 279 "   -0.052 5.00e-02 4.00e+02   7.81e-02 9.76e+00
        pdb=" N   PRO A 280 "    0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO A 280 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 280 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 367 "   -0.016 2.00e-02 2.50e+03   1.18e-02 4.16e+00
        pdb=" CG  PHE A 367 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 367 "    0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 367 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 367 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 367 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 367 "    0.000 2.00e-02 2.50e+03
        pdb=" HD1 PHE A 367 "   -0.005 2.00e-02 2.50e+03
        pdb=" HD2 PHE A 367 "    0.002 2.00e-02 2.50e+03
        pdb=" HE1 PHE A 367 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE2 PHE A 367 "   -0.003 2.00e-02 2.50e+03
        pdb=" HZ  PHE A 367 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1732 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 465
        2.16 -     2.77: 22086
        2.77 -     3.38: 34179
        3.38 -     3.99: 42326
        3.99 -     4.60: 67156
  Nonbonded interactions: 166212
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 237 "
            pdb=" H   THR B  95 "
     model   vdw
     1.549 2.450
  nonbonded pdb="HD22 ASN A 216 "
            pdb=" O   LEU A 303 "
     model   vdw
     1.558 2.450
  nonbonded pdb=" H   GLY A 236 "
            pdb=" OD2 ASP B  86 "
     model   vdw
     1.567 2.450
  nonbonded pdb=" OE1 GLU B 147 "
            pdb=" H   GLU B 147 "
     model   vdw
     1.601 2.450
  nonbonded pdb=" O   LEU A 337 "
            pdb=" HG  SER A 341 "
     model   vdw
     1.647 2.450
  ... (remaining 166207 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 'I'
}

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:             3.090
  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:             0.070
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.080
  Find NCS groups from input model:        0.040
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
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      :  0.004   0.069   6097  Z= 0.189
  Angle     :  0.688  10.273   8358  Z= 0.346
  Chirality :  0.042   0.286    990
  Planarity :  0.007   0.132   1016
  Dihedral  : 13.959 104.295   2296
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.33 %
    Favored  : 99.51 %
  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 aren not related in a simple way.
  whole:  1.28 (0.31), residues: 754
  helix:  1.32 (0.25), residues: 410
  sheet:  0.35 (0.70), residues: 58
  loop :  0.45 (0.39), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 130 
 TYR   0.021   0.001   TYR A 235 
 PHE   0.034   0.001   PHE A 367 
 TRP   0.024   0.001   TRP A 109 
 HIS   0.005   0.001   HIS B 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6081)
  covalent geometry    : angle       0.66304 ( 8316)
  SS BOND              : bond        0.00330 (    6)
  SS BOND              : angle       1.44398 (   12)
  hydrogen bonds       : bond        0.14500 (  368)
  hydrogen bonds       : angle       6.37340 ( 1047)
  link_ALPHA1-3        : bond        0.00566 (    1)
  link_ALPHA1-3        : angle       1.49053 (    3)
  link_BETA1-4         : bond        0.01238 (    4)
  link_BETA1-4         : angle       3.46825 (   12)
  link_BETA1-6         : bond        0.00424 (    1)
  link_BETA1-6         : angle       1.46120 (    3)
  link_NAG-ASN         : bond        0.00471 (    4)
  link_NAG-ASN         : angle       3.12925 (   12)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   46 is missing expected H atoms. Skipping.
Residue VAL  159 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Evaluate side-chains
  123 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 122
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 ARG cc_start: 0.7853 (mmm160) cc_final: 0.7630 (mmt-90)
  outliers start: 1
  outliers final: 1
  residues processed: 123
  average time/residue: 0.1339
  time to fit residues: 22.8131
Evaluate side-chains
  105 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 TYR
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:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
B 103 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.193175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.163865 restraints weight = 23384.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.171255 restraints weight = 10771.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.175846 restraints weight = 6614.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.178754 restraints weight = 4736.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.180746 restraints weight = 3714.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.1249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6097  Z= 0.200
  Angle     :  0.613   5.806   8358  Z= 0.319
  Chirality :  0.040   0.204    990
  Planarity :  0.005   0.085   1016
  Dihedral  :  8.458  61.991   1080
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  6.69 %
    Favored  : 91.84 %
  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 aren not related in a simple way.
  whole:  1.64 (0.31), residues: 754
  helix:  1.97 (0.25), residues: 415
  sheet:  0.24 (0.75), residues: 52
  loop :  0.01 (0.38), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 353 
 TYR   0.019   0.002   TYR B 153 
 PHE   0.014   0.001   PHE B 222 
 TRP   0.011   0.001   TRP B 154 
 HIS   0.003   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 6081)
  covalent geometry    : angle       0.59715 ( 8316)
  SS BOND              : bond        0.00543 (    6)
  SS BOND              : angle       1.19355 (   12)
  hydrogen bonds       : bond        0.05125 (  368)
  hydrogen bonds       : angle       4.97987 ( 1047)
  link_ALPHA1-3        : bond        0.00684 (    1)
  link_ALPHA1-3        : angle       3.25339 (    3)
  link_BETA1-4         : bond        0.01042 (    4)
  link_BETA1-4         : angle       2.01555 (   12)
  link_BETA1-6         : bond        0.00070 (    1)
  link_BETA1-6         : angle       1.54092 (    3)
  link_NAG-ASN         : bond        0.00570 (    4)
  link_NAG-ASN         : angle       2.40174 (   12)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   46 is missing expected H atoms. Skipping.
Residue VAL  159 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 GLU cc_start: 0.8373 (pm20) cc_final: 0.8170 (pm20)
  outliers start: 9
  outliers final: 8
  residues processed: 112
  average time/residue: 0.1447
  time to fit residues: 21.9271
Evaluate side-chains
  107 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  257 TYR
Chi-restraints excluded: chain A residue  478 ASN
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   87 CYS
Chi-restraints excluded: chain B residue  164 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 10 optimal weight:    0.2980
   chunk 49 optimal weight:    0.4980
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 63 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 64 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.191914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.163582 restraints weight = 23470.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.171002 restraints weight = 10534.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.175513 restraints weight = 6345.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.178371 restraints weight = 4508.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.180194 restraints weight = 3517.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6097  Z= 0.121
  Angle     :  0.543   5.830   8358  Z= 0.276
  Chirality :  0.038   0.210    990
  Planarity :  0.004   0.064   1016
  Dihedral  :  7.072  54.966   1080
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  :  8.32 %
    Favored  : 90.21 %
  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 aren not related in a simple way.
  whole:  1.89 (0.31), residues: 754
  helix:  2.24 (0.26), residues: 413
  sheet:  0.20 (0.81), residues: 47
  loop :  0.07 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  90 
 TYR   0.017   0.001   TYR B 153 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.009   0.001   TRP B 154 
 HIS   0.005   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6081)
  covalent geometry    : angle       0.52948 ( 8316)
  SS BOND              : bond        0.00334 (    6)
  SS BOND              : angle       0.76899 (   12)
  hydrogen bonds       : bond        0.04528 (  368)
  hydrogen bonds       : angle       4.63269 ( 1047)
  link_ALPHA1-3        : bond        0.01023 (    1)
  link_ALPHA1-3        : angle       2.72941 (    3)
  link_BETA1-4         : bond        0.00811 (    4)
  link_BETA1-4         : angle       1.90741 (   12)
  link_BETA1-6         : bond        0.00179 (    1)
  link_BETA1-6         : angle       1.25261 (    3)
  link_NAG-ASN         : bond        0.00474 (    4)
  link_NAG-ASN         : angle       2.17272 (   12)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   46 is missing expected H atoms. Skipping.
Residue VAL  159 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Evaluate side-chains
  114 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.6245 (mm-30)
  outliers start: 9
  outliers final: 7
  residues processed: 110
  average time/residue: 0.1460
  time to fit residues: 21.7577
Evaluate side-chains
  106 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  257 TYR
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0270
   chunk 39 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.7242

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.188953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.160225 restraints weight = 23398.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.167559 restraints weight = 10528.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.172053 restraints weight = 6391.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.174920 restraints weight = 4554.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.176854 restraints weight = 3569.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6097  Z= 0.138
  Angle     :  0.544   6.268   8358  Z= 0.276
  Chirality :  0.038   0.210    990
  Planarity :  0.004   0.058   1016
  Dihedral  :  6.228  55.464   1080
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  7.99 %
    Favored  : 90.05 %
  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 aren not related in a simple way.
  whole:  2.05 (0.31), residues: 754
  helix:  2.43 (0.26), residues: 413
  sheet:  0.18 (0.76), residues: 52
  loop :  0.04 (0.37), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  90 
 TYR   0.020   0.001   TYR B 153 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.009   0.001   TRP A 520 
 HIS   0.004   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6081)
  covalent geometry    : angle       0.53186 ( 8316)
  SS BOND              : bond        0.00311 (    6)
  SS BOND              : angle       1.01160 (   12)
  hydrogen bonds       : bond        0.04232 (  368)
  hydrogen bonds       : angle       4.46801 ( 1047)
  link_ALPHA1-3        : bond        0.00953 (    1)
  link_ALPHA1-3        : angle       2.52376 (    3)
  link_BETA1-4         : bond        0.00648 (    4)
  link_BETA1-4         : angle       1.75204 (   12)
  link_BETA1-6         : bond        0.00203 (    1)
  link_BETA1-6         : angle       1.38368 (    3)
  link_NAG-ASN         : bond        0.00490 (    4)
  link_NAG-ASN         : angle       2.02487 (   12)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   46 is missing expected H atoms. Skipping.
Residue VAL  159 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6211 (mm-30)
REVERT: B   59 GLU cc_start: 0.8504 (pm20) cc_final: 0.8196 (pm20)
  outliers start: 12
  outliers final: 8
  residues processed: 112
  average time/residue: 0.1353
  time to fit residues: 21.1747
Evaluate side-chains
  107 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 LYS
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  257 TYR
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 72 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.187816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.159222 restraints weight = 23212.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.166420 restraints weight = 10452.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.170894 restraints weight = 6362.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.173650 restraints weight = 4551.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.175598 restraints weight = 3599.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6097  Z= 0.132
  Angle     :  0.532   6.288   8358  Z= 0.269
  Chirality :  0.038   0.215    990
  Planarity :  0.004   0.050   1016
  Dihedral  :  5.774  55.972   1080
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  :  9.14 %
    Favored  : 88.58 %
  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 aren not related in a simple way.
  whole:  2.18 (0.31), residues: 754
  helix:  2.44 (0.26), residues: 419
  sheet:  0.14 (0.72), residues: 55
  loop :  0.25 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 424 
 TYR   0.017   0.001   TYR B 153 
 PHE   0.011   0.001   PHE A 295 
 TRP   0.007   0.001   TRP B 154 
 HIS   0.004   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6081)
  covalent geometry    : angle       0.52086 ( 8316)
  SS BOND              : bond        0.00535 (    6)
  SS BOND              : angle       1.22488 (   12)
  hydrogen bonds       : bond        0.04114 (  368)
  hydrogen bonds       : angle       4.38042 ( 1047)
  link_ALPHA1-3        : bond        0.00931 (    1)
  link_ALPHA1-3        : angle       2.02950 (    3)
  link_BETA1-4         : bond        0.00691 (    4)
  link_BETA1-4         : angle       1.67408 (   12)
  link_BETA1-6         : bond        0.00229 (    1)
  link_BETA1-6         : angle       1.32144 (    3)
  link_NAG-ASN         : bond        0.00453 (    4)
  link_NAG-ASN         : angle       1.90063 (   12)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   46 is missing expected H atoms. Skipping.
Residue VAL  159 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6283 (mm-30)
REVERT: B   59 GLU cc_start: 0.8493 (pm20) cc_final: 0.8206 (pm20)
  outliers start: 14
  outliers final: 10
  residues processed: 111
  average time/residue: 0.1375
  time to fit residues: 21.2101
Evaluate side-chains
  103 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  184 LYS
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  257 TYR
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 33 optimal weight:    0.3980
   chunk 29 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0670
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.187273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.158561 restraints weight = 23173.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.165769 restraints weight = 10418.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.170298 restraints weight = 6343.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.173141 restraints weight = 4528.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.175080 restraints weight = 3560.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6097  Z= 0.121
  Angle     :  0.527   5.940   8358  Z= 0.266
  Chirality :  0.037   0.216    990
  Planarity :  0.004   0.046   1016
  Dihedral  :  5.484  56.123   1080
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  9.46 %
    Favored  : 88.58 %
  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 aren not related in a simple way.
  whole:  2.32 (0.32), residues: 754
  helix:  2.58 (0.26), residues: 418
  sheet:  0.15 (0.74), residues: 55
  loop :  0.26 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  97 
 TYR   0.016   0.001   TYR B 153 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.006   0.001   TRP A 520 
 HIS   0.004   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6081)
  covalent geometry    : angle       0.51663 ( 8316)
  SS BOND              : bond        0.00268 (    6)
  SS BOND              : angle       1.10854 (   12)
  hydrogen bonds       : bond        0.03964 (  368)
  hydrogen bonds       : angle       4.29534 ( 1047)
  link_ALPHA1-3        : bond        0.00944 (    1)
  link_ALPHA1-3        : angle       1.69816 (    3)
  link_BETA1-4         : bond        0.00702 (    4)
  link_BETA1-4         : angle       1.64972 (   12)
  link_BETA1-6         : bond        0.00222 (    1)
  link_BETA1-6         : angle       1.32914 (    3)
  link_NAG-ASN         : bond        0.00428 (    4)
  link_NAG-ASN         : angle       1.80972 (   12)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   46 is missing expected H atoms. Skipping.
Residue VAL  159 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 MET cc_start: 0.8161 (mtm) cc_final: 0.7368 (mtm)
REVERT: B   59 GLU cc_start: 0.8510 (pm20) cc_final: 0.8211 (pm20)
  outliers start: 12
  outliers final: 11
  residues processed: 109
  average time/residue: 0.1411
  time to fit residues: 21.3281
Evaluate side-chains
  105 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  184 LYS
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  257 TYR
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 28 optimal weight:    0.0870
   chunk 40 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 68 optimal weight:    0.3980
   chunk 57 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.187002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.158263 restraints weight = 23179.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.165475 restraints weight = 10455.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.169934 restraints weight = 6413.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.172788 restraints weight = 4596.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.174640 restraints weight = 3620.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6097  Z= 0.121
  Angle     :  0.521   6.161   8358  Z= 0.262
  Chirality :  0.037   0.217    990
  Planarity :  0.004   0.042   1016
  Dihedral  :  5.295  56.259   1080
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  9.14 %
    Favored  : 88.42 %
  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 aren not related in a simple way.
  whole:  2.33 (0.32), residues: 754
  helix:  2.66 (0.26), residues: 419
  sheet:  0.11 (0.75), residues: 55
  loop :  0.16 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 149 
 TYR   0.016   0.001   TYR B 153 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.007   0.001   TRP A 520 
 HIS   0.003   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6081)
  covalent geometry    : angle       0.51183 ( 8316)
  SS BOND              : bond        0.00250 (    6)
  SS BOND              : angle       1.01125 (   12)
  hydrogen bonds       : bond        0.03918 (  368)
  hydrogen bonds       : angle       4.20187 ( 1047)
  link_ALPHA1-3        : bond        0.00881 (    1)
  link_ALPHA1-3        : angle       1.54039 (    3)
  link_BETA1-4         : bond        0.00689 (    4)
  link_BETA1-4         : angle       1.60282 (   12)
  link_BETA1-6         : bond        0.00231 (    1)
  link_BETA1-6         : angle       1.32085 (    3)
  link_NAG-ASN         : bond        0.00402 (    4)
  link_NAG-ASN         : angle       1.69556 (   12)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   46 is missing expected H atoms. Skipping.
Residue VAL  159 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 VAL cc_start: 0.8925 (m) cc_final: 0.8533 (p)
REVERT: B   59 GLU cc_start: 0.8512 (pm20) cc_final: 0.8190 (pm20)
  outliers start: 15
  outliers final: 12
  residues processed: 104
  average time/residue: 0.1429
  time to fit residues: 20.4679
Evaluate side-chains
  105 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 LEU
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  184 LYS
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  257 TYR
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.186167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.157383 restraints weight = 23251.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.164623 restraints weight = 10470.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.169129 restraints weight = 6387.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.171940 restraints weight = 4570.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.173896 restraints weight = 3606.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.3043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6097  Z= 0.126
  Angle     :  0.524   6.294   8358  Z= 0.263
  Chirality :  0.037   0.217    990
  Planarity :  0.004   0.042   1016
  Dihedral  :  5.245  56.359   1080
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.62 %
    Favored  : 88.25 %
  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 aren not related in a simple way.
  whole:  2.33 (0.32), residues: 754
  helix:  2.68 (0.26), residues: 419
  sheet: -0.02 (0.75), residues: 55
  loop :  0.14 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  85 
 TYR   0.015   0.001   TYR B 153 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.008   0.001   TRP A 520 
 HIS   0.003   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6081)
  covalent geometry    : angle       0.51633 ( 8316)
  SS BOND              : bond        0.00301 (    6)
  SS BOND              : angle       0.83355 (   12)
  hydrogen bonds       : bond        0.03875 (  368)
  hydrogen bonds       : angle       4.18053 ( 1047)
  link_ALPHA1-3        : bond        0.00893 (    1)
  link_ALPHA1-3        : angle       1.48754 (    3)
  link_BETA1-4         : bond        0.00717 (    4)
  link_BETA1-4         : angle       1.58083 (   12)
  link_BETA1-6         : bond        0.00243 (    1)
  link_BETA1-6         : angle       1.32703 (    3)
  link_NAG-ASN         : bond        0.00397 (    4)
  link_NAG-ASN         : angle       1.63091 (   12)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   46 is missing expected H atoms. Skipping.
Residue VAL  159 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Evaluate side-chains
  103 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 GLU cc_start: 0.8520 (pm20) cc_final: 0.8210 (pm20)
  outliers start: 13
  outliers final: 13
  residues processed: 100
  average time/residue: 0.1483
  time to fit residues: 20.1928
Evaluate side-chains
  102 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  184 LYS
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  257 TYR
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0980
   chunk 66 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.173815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.147167 restraints weight = 22535.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.153726 restraints weight = 10283.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.157948 restraints weight = 6285.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.160614 restraints weight = 4486.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.162450 restraints weight = 3518.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6097  Z= 0.122
  Angle     :  0.519   6.085   8358  Z= 0.260
  Chirality :  0.037   0.221    990
  Planarity :  0.004   0.041   1016
  Dihedral  :  5.138  56.282   1080
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.62 %
    Favored  : 88.25 %
  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 aren not related in a simple way.
  whole:  2.39 (0.32), residues: 754
  helix:  2.74 (0.26), residues: 419
  sheet:  0.04 (0.76), residues: 55
  loop :  0.16 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 424 
 TYR   0.015   0.001   TYR B 153 
 PHE   0.010   0.001   PHE A 111 
 TRP   0.009   0.001   TRP A 520 
 HIS   0.003   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6081)
  covalent geometry    : angle       0.51117 ( 8316)
  SS BOND              : bond        0.00240 (    6)
  SS BOND              : angle       0.74035 (   12)
  hydrogen bonds       : bond        0.03832 (  368)
  hydrogen bonds       : angle       4.13332 ( 1047)
  link_ALPHA1-3        : bond        0.00858 (    1)
  link_ALPHA1-3        : angle       1.38383 (    3)
  link_BETA1-4         : bond        0.00715 (    4)
  link_BETA1-4         : angle       1.56155 (   12)
  link_BETA1-6         : bond        0.00248 (    1)
  link_BETA1-6         : angle       1.31980 (    3)
  link_NAG-ASN         : bond        0.00372 (    4)
  link_NAG-ASN         : angle       1.59147 (   12)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   46 is missing expected H atoms. Skipping.
Residue VAL  159 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Evaluate side-chains
  106 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 GLU cc_start: 0.8567 (pm20) cc_final: 0.8263 (pm20)
  outliers start: 13
  outliers final: 11
  residues processed: 102
  average time/residue: 0.1417
  time to fit residues: 19.7180
Evaluate side-chains
  101 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  184 LYS
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  257 TYR
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 18 optimal weight:    0.0670
   chunk 16 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 60 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0980
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.5720

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

Flipped N/Q/H residues before XYZ refinement:
A 228 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.173856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.147334 restraints weight = 22602.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.153892 restraints weight = 10247.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.158086 restraints weight = 6236.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.160686 restraints weight = 4445.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.162550 restraints weight = 3494.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.3350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6097  Z= 0.118
  Angle     :  0.524   6.220   8358  Z= 0.262
  Chirality :  0.037   0.220    990
  Planarity :  0.004   0.041   1016
  Dihedral  :  5.065  56.133   1080
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  9.62 %
    Favored  : 88.25 %
  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 aren not related in a simple way.
  whole:  2.47 (0.32), residues: 754
  helix:  2.77 (0.26), residues: 419
  sheet: -0.01 (0.76), residues: 55
  loop :  0.26 (0.37), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 225 
 TYR   0.015   0.001   TYR B 153 
 PHE   0.009   0.001   PHE A 295 
 TRP   0.008   0.001   TRP A 520 
 HIS   0.003   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6081)
  covalent geometry    : angle       0.51697 ( 8316)
  SS BOND              : bond        0.00290 (    6)
  SS BOND              : angle       0.83607 (   12)
  hydrogen bonds       : bond        0.03792 (  368)
  hydrogen bonds       : angle       4.11749 ( 1047)
  link_ALPHA1-3        : bond        0.00864 (    1)
  link_ALPHA1-3        : angle       1.34178 (    3)
  link_BETA1-4         : bond        0.00724 (    4)
  link_BETA1-4         : angle       1.54909 (   12)
  link_BETA1-6         : bond        0.00238 (    1)
  link_BETA1-6         : angle       1.31976 (    3)
  link_NAG-ASN         : bond        0.00360 (    4)
  link_NAG-ASN         : angle       1.50445 (   12)

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

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

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1508 Ramachandran restraints generated.
    754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LEU   46 is missing expected H atoms. Skipping.
Residue VAL  159 is missing expected H atoms. Skipping.
Residue LYS  273 is missing expected H atoms. Skipping.
Residue LYS  277 is missing expected H atoms. Skipping.
Residue LYS  376 is missing expected H atoms. Skipping.
Residue LYS  467 is missing expected H atoms. Skipping.
Residue LYS  471 is missing expected H atoms. Skipping.
Residue LYS  131 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  233 VAL cc_start: 0.8846 (m) cc_final: 0.8497 (p)
REVERT: B   59 GLU cc_start: 0.8584 (pm20) cc_final: 0.8275 (pm20)
  outliers start: 13
  outliers final: 11
  residues processed: 101
  average time/residue: 0.1469
  time to fit residues: 20.7182
Evaluate side-chains
  103 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  184 LYS
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  204 ILE
Chi-restraints excluded: chain A residue  257 TYR
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain B residue   23 GLU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  152 VAL
Chi-restraints excluded: chain B residue  164 THR
Chi-restraints excluded: chain B residue  213 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 228 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.172941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.147054 restraints weight = 22703.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.153313 restraints weight = 10766.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.157306 restraints weight = 6723.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.159865 restraints weight = 4853.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.161663 restraints weight = 3830.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.3474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6097  Z= 0.128
  Angle     :  0.527   6.207   8358  Z= 0.265
  Chirality :  0.037   0.221    990
  Planarity :  0.004   0.040   1016
  Dihedral  :  5.077  56.059   1080
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 10.11 %
    Favored  : 87.93 %
  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 aren not related in a simple way.
  whole:  2.49 (0.31), residues: 754
  helix:  2.88 (0.26), residues: 411
  sheet: -0.32 (0.71), residues: 61
  loop :  0.28 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 581 
 TYR   0.015   0.001   TYR B 153 
 PHE   0.011   0.001   PHE A 111 
 TRP   0.009   0.001   TRP A 520 
 HIS   0.003   0.001   HIS B  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6081)
  covalent geometry    : angle       0.51960 ( 8316)
  SS BOND              : bond        0.00281 (    6)
  SS BOND              : angle       0.80667 (   12)
  hydrogen bonds       : bond        0.03831 (  368)
  hydrogen bonds       : angle       4.11947 ( 1047)
  link_ALPHA1-3        : bond        0.00794 (    1)
  link_ALPHA1-3        : angle       1.35158 (    3)
  link_BETA1-4         : bond        0.00722 (    4)
  link_BETA1-4         : angle       1.53567 (   12)
  link_BETA1-6         : bond        0.00231 (    1)
  link_BETA1-6         : angle       1.32174 (    3)
  link_NAG-ASN         : bond        0.00354 (    4)
  link_NAG-ASN         : angle       1.49422 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2274.10 seconds
wall clock time: 39 minutes 29.28 seconds (2369.28 seconds total)