Starting phenix.real_space_refine
on Thu Mar 13 03:35:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xcn_38248/03_2025/8xcn_38248.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xcn_38248/03_2025/8xcn_38248.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xcn_38248/03_2025/8xcn_38248.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xcn_38248/03_2025/8xcn_38248.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xcn_38248/03_2025/8xcn_38248.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xcn_38248/03_2025/8xcn_38248.cif"
  }
  resolution = 3.02
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Fe      6      7.16       5
     P       2      5.49       5
     S      46      5.16       5
     C    5420      2.51       5
     N    1489      2.21       5
     O    1638      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8601
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4164
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4164
          Classifications: {'peptide': 540}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 503}
    Chain: "B"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 136, 1080
          Classifications: {'peptide': 136}
          Link IDs: {'PTRANS': 7, 'TRANS': 128}
    Chain: "C"
      Number of atoms: 3130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 413, 3130
          Classifications: {'peptide': 413}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 387}
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 60
          Unusual residues: {'F3S': 1, 'FAD': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 167
          Unusual residues: {'HEC': 3, 'U10': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1}
          Unresolved non-hydrogen planarities: 20

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1767  SG  CYS A 226      52.692  62.655  35.511  1.00 87.42           S
  ATOM   1738  SG  CYS A 222      54.833  67.275  31.351  1.00 83.60           S
  ATOM   1698  SG  CYS A 216      52.906  62.684  28.727  1.00 88.54           S

  Time building chain proxies: 5.41, per 1000 atoms: 0.63
  Number of scatterers: 8601
  At special positions: 0
  Unit cell: (105.78, 107.5, 76.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      6     26.01
     S      46     16.00
     P       2     15.00
     O    1638      8.00
     N    1489      7.00
     C    5420      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=11, symmetry=0
  Number of additional bonds: simple=11, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.65
  Conformation dependent library (CDL) restraints added in 963.3 milliseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" F3S A 602 "
        pdb="FE1  F3S A 602 " - pdb=" SG  CYS A 226 "
        pdb="FE4  F3S A 602 " - pdb=" SG  CYS A 216 "
        pdb="FE3  F3S A 602 " - pdb=" SG  CYS A 222 "
      Number of angles added : 9


  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2012

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      41.8% alpha, 9.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 28
    Processing helix  chain 'A' and resid 43 through 53
    Processing helix  chain 'A' and resid 56 through 61
      removed outlier: 3.587A  pdb=" N   GLN A  61 " --> pdb=" O   ASP A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 97
      removed outlier: 3.591A  pdb=" N   LYS A  97 " --> pdb=" O   THR A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 111
      removed outlier: 3.690A  pdb=" N   TRP A 111 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 123
    Processing helix  chain 'A' and resid 124 through 130
    Processing helix  chain 'A' and resid 138 through 154
      removed outlier: 3.607A  pdb=" N   LEU A 142 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 181 through 194
    Processing helix  chain 'A' and resid 233 through 244
      removed outlier: 4.165A  pdb=" N   ALA A 237 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 301
    Processing helix  chain 'A' and resid 355 through 360
      removed outlier: 3.565A  pdb=" N   SER A 359 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 384
      removed outlier: 4.041A  pdb=" N   MET A 384 " --> pdb=" O   LYS A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 401
      removed outlier: 3.625A  pdb=" N   ASP A 392 " --> pdb=" O   GLY A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 463
      removed outlier: 4.004A  pdb=" N   VAL A 444 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE A 450 " --> pdb=" O   LYS A 446 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   GLN A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   MET A 462 " --> pdb=" O   ILE A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 492
      removed outlier: 3.798A  pdb=" N   SER A 492 " --> pdb=" O   PRO A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 514
      removed outlier: 3.757A  pdb=" N   MET A 514 " --> pdb=" O   GLY A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 542
    Processing helix  chain 'B' and resid 49 through 63
    Processing helix  chain 'B' and resid 68 through 83
    Processing helix  chain 'B' and resid 85 through 100
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 117 through 131
    Processing helix  chain 'B' and resid 147 through 151
      removed outlier: 3.532A  pdb=" N   TYR B 150 " --> pdb=" O   ALA B 147 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLN B 151 " --> pdb=" O   LEU B 148 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 147 through 151'
    Processing helix  chain 'B' and resid 168 through 172
      removed outlier: 3.581A  pdb=" N   VAL B 171 " --> pdb=" O   ASN B 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 41 through 51
    Processing helix  chain 'C' and resid 51 through 56
      removed outlier: 4.212A  pdb=" N   CYS C  55 " --> pdb=" O   ASP C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 105
    Processing helix  chain 'C' and resid 119 through 124
    Processing helix  chain 'C' and resid 127 through 142
      removed outlier: 3.864A  pdb=" N   VAL C 142 " --> pdb=" O   ILE C 138 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 163 through 172
      removed outlier: 3.880A  pdb=" N   TRP C 167 " --> pdb=" O   SER C 163 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ARG C 172 " --> pdb=" O   LYS C 168 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 185 through 197
    Processing helix  chain 'C' and resid 201 through 206
    Processing helix  chain 'C' and resid 245 through 255
    Processing helix  chain 'C' and resid 265 through 274
    Processing helix  chain 'C' and resid 279 through 291
    Processing helix  chain 'C' and resid 316 through 322
      removed outlier: 3.504A  pdb=" N   SER C 322 " --> pdb=" O   ASN C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 334 through 343
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'C' and resid 373 through 383
    Processing helix  chain 'C' and resid 408 through 423
    Processing helix  chain 'C' and resid 431 through 440
    Processing helix  chain 'C' and resid 445 through 451
    Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249
      removed outlier: 3.522A  pdb=" N   LYS A 247 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   ASP A   9 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ALA A 282 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 5.726A  pdb=" N   THR A 266 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   ALA A 267 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   TYR A 271 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 5.518A  pdb=" N   VAL A 254 " --> pdb=" O   TYR A 271 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 249
      removed outlier: 3.522A  pdb=" N   LYS A 247 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   ASP A   9 " --> pdb=" O   ALA A 282 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.527A  pdb=" N   ILE A  87 " --> pdb=" O   VAL A 436 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   HIS A 433 " --> pdb=" O   SER A 422 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200
      removed outlier: 5.215A  pdb=" N   SER A 347 " --> pdb=" O   TYR A 368 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   TYR A 368 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 7.752A  pdb=" N   SER A 330 " --> pdb=" O   ILE A 467 " (cutoff:3.500A)
      removed outlier: 5.322A  pdb=" N   ILE A 467 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 70 through 73
    Processing sheet with id=AA6, first strand: chain 'C' and resid 223 through 224
    Processing sheet with id=AA7, first strand: chain 'C' and resid 384 through 388

    324 hydrogen bonds defined for protein.
    900 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: 2.45

  Time building geometry restraints manager: 2.88 seconds

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

  Histogram of bond lengths:
        0.99 -     1.57: 8733
        1.57 -     2.15: 93
        2.15 -     2.74: 6
        2.74 -     3.32: 0
        3.32 -     3.91: 3
  Bond restraints: 8835
  Sorted by residual:
  bond pdb=" S2  F3S A 602 "
       pdb="FE3  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.300  3.906 -1.606 2.00e-02 2.50e+03 6.44e+03
  bond pdb=" S4  F3S A 602 "
       pdb="FE1  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.233  3.762 -1.529 2.00e-02 2.50e+03 5.84e+03
  bond pdb=" S1  F3S A 602 "
       pdb="FE4  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.258  3.736 -1.478 2.00e-02 2.50e+03 5.46e+03
  bond pdb=" CB  PRO A 144 "
       pdb=" CG  PRO A 144 "
    ideal  model  delta    sigma   weight residual
    1.492  0.987  0.505 5.00e-02 4.00e+02 1.02e+02
  bond pdb=" CG  PRO A 144 "
       pdb=" CD  PRO A 144 "
    ideal  model  delta    sigma   weight residual
    1.503  1.220  0.283 3.40e-02 8.65e+02 6.93e+01
  ... (remaining 8830 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.75: 12061
       14.75 -    29.50: 5
       29.50 -    44.25: 10
       44.25 -    59.00: 1
       59.00 -    73.75: 1
  Bond angle restraints: 12078
  Sorted by residual:
  angle pdb=" CB  PRO A 144 "
        pdb=" CG  PRO A 144 "
        pdb=" CD  PRO A 144 "
      ideal   model   delta    sigma   weight residual
     106.10  179.85  -73.75 3.20e+00 9.77e-02 5.31e+02
  angle pdb=" N   PRO A 144 "
        pdb=" CD  PRO A 144 "
        pdb=" CG  PRO A 144 "
      ideal   model   delta    sigma   weight residual
     103.20   76.60   26.60 1.50e+00 4.44e-01 3.14e+02
  angle pdb=" CA  PRO A 144 "
        pdb=" CB  PRO A 144 "
        pdb=" CG  PRO A 144 "
      ideal   model   delta    sigma   weight residual
     104.50   71.64   32.86 1.90e+00 2.77e-01 2.99e+02
  angle pdb=" S1  F3S A 602 "
        pdb="FE4  F3S A 602 "
        pdb=" S3  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     114.75   68.36   46.39 3.00e+00 1.11e-01 2.39e+02
  angle pdb=" S3  F3S A 602 "
        pdb="FE1  F3S A 602 "
        pdb=" S4  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     112.59   69.90   42.69 3.00e+00 1.11e-01 2.03e+02
  ... (remaining 12073 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.37: 4457
       19.37 -    38.75: 580
       38.75 -    58.12: 146
       58.12 -    77.49: 30
       77.49 -    96.87: 11
  Dihedral angle restraints: 5224
    sinusoidal: 2072
      harmonic: 3152
  Sorted by residual:
  dihedral pdb=" CA  PHE A  80 "
           pdb=" C   PHE A  80 "
           pdb=" N   PRO A  81 "
           pdb=" CA  PRO A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -129.56  -50.44     0      5.00e+00 4.00e-02 1.02e+02
  dihedral pdb=" N   PRO A 144 "
           pdb=" CG  PRO A 144 "
           pdb=" CD  PRO A 144 "
           pdb=" CB  PRO A 144 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.00  126.87  -96.87     1      1.50e+01 4.44e-03 4.78e+01
  dihedral pdb=" CA  TYR A  79 "
           pdb=" C   TYR A  79 "
           pdb=" N   PHE A  80 "
           pdb=" CA  PHE A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.02   31.98     0      5.00e+00 4.00e-02 4.09e+01
  ... (remaining 5221 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    3.449: 1276
       3.449 -    6.898: 0
       6.898 -   10.347: 0
      10.347 -   13.796: 0
      13.796 -   17.245: 1
  Chirality restraints: 1277
  Sorted by residual:
  chirality pdb=" S2  F3S A 602 "
            pdb="FE1  F3S A 602 "
            pdb="FE3  F3S A 602 "
            pdb="FE4  F3S A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     10.77   -6.48   17.24 2.00e-01 2.50e+01 7.43e+03
  chirality pdb=" CB  ILE C 393 "
            pdb=" CA  ILE C 393 "
            pdb=" CG1 ILE C 393 "
            pdb=" CG2 ILE C 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.33 2.00e-01 2.50e+01 2.75e+00
  chirality pdb=" CG  LEU A  35 "
            pdb=" CB  LEU A  35 "
            pdb=" CD1 LEU A  35 "
            pdb=" CD2 LEU A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.90    0.31 2.00e-01 2.50e+01 2.35e+00
  ... (remaining 1274 not shown)

  Planarity restraints: 1568
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1C HEC C 502 "    0.019 2.00e-02 2.50e+03   7.08e-02 1.13e+02
        pdb=" C2C HEC C 502 "   -0.191 2.00e-02 2.50e+03
        pdb=" C3C HEC C 502 "    0.056 2.00e-02 2.50e+03
        pdb=" C4C HEC C 502 "    0.009 2.00e-02 2.50e+03
        pdb=" CAC HEC C 502 "    0.020 2.00e-02 2.50e+03
        pdb=" CHC HEC C 502 "    0.029 2.00e-02 2.50e+03
        pdb=" CHD HEC C 502 "   -0.007 2.00e-02 2.50e+03
        pdb=" CMC HEC C 502 "    0.059 2.00e-02 2.50e+03
        pdb=" NC  HEC C 502 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  66 "   -0.115 5.00e-02 4.00e+02   1.58e-01 4.02e+01
        pdb=" N   PRO A  67 "    0.273 5.00e-02 4.00e+02
        pdb=" CA  PRO A  67 "   -0.077 5.00e-02 4.00e+02
        pdb=" CD  PRO A  67 "   -0.082 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 147 "   -0.111 5.00e-02 4.00e+02   1.55e-01 3.83e+01
        pdb=" N   PRO C 148 "    0.267 5.00e-02 4.00e+02
        pdb=" CA  PRO C 148 "   -0.078 5.00e-02 4.00e+02
        pdb=" CD  PRO C 148 "   -0.077 5.00e-02 4.00e+02
  ... (remaining 1565 not shown)

  Histogram of nonbonded interaction distances:
        1.24 -     1.97: 2
        1.97 -     2.70: 380
        2.70 -     3.44: 13164
        3.44 -     4.17: 22493
        4.17 -     4.90: 39113
  Nonbonded interactions: 75152
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 375 "
            pdb=" O1D HEC C 502 "
     model   vdw
     1.241 3.040
  nonbonded pdb=" CG  ASP C 375 "
            pdb=" O1D HEC C 502 "
     model   vdw
     1.377 3.270
  nonbonded pdb=" NE2 GLN A  46 "
            pdb=" OD1 ASN A  50 "
     model   vdw
     1.988 3.120
  nonbonded pdb=" O   ARG A 358 "
            pdb=" OH  TYR A 443 "
     model   vdw
     2.092 3.040
  nonbonded pdb=" OG1 THR C 234 "
            pdb=" O   PRO C 294 "
     model   vdw
     2.106 3.040
  ... (remaining 75147 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     24.810
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.050
  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:3.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
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      :  0.030   1.606   8835  Z= 1.907
  Angle     :  1.663  73.755  12078  Z= 0.722
  Chirality :  0.485  17.245   1277
  Planarity :  0.011   0.158   1568
  Dihedral  : 18.742  96.866   3212
  Min Nonbonded Distance : 1.241

Molprobity Statistics.
  All-atom Clashscore : 23.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 32.66 %
    Favored  : 65.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.25), residues: 1083
  helix:  0.00 (0.26), residues: 399
  sheet: -1.14 (0.51), residues: 91
  loop : -0.97 (0.25), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A 173 
 HIS   0.021   0.001   HIS C 422 
 PHE   0.018   0.002   PHE B  54 
 TYR   0.040   0.003   TYR A 182 
 ARG   0.021   0.001   ARG A 133 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 304
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.4887 (tpt) cc_final: 0.4682 (tpp)
REVERT: A  330 SER cc_start: 0.8253 (m) cc_final: 0.7989 (t)
REVERT: A  438 TYR cc_start: 0.4133 (t80) cc_final: 0.3841 (t80)
REVERT: A  439 ASP cc_start: 0.7416 (m-30) cc_final: 0.7004 (t0)
REVERT: A  453 GLN cc_start: 0.8496 (tp40) cc_final: 0.8005 (mm-40)
REVERT: A  514 MET cc_start: 0.6719 (mmp) cc_final: 0.6294 (mpp)
REVERT: B   51 ILE cc_start: 0.8267 (mt) cc_final: 0.7989 (tp)
REVERT: B   53 ASP cc_start: 0.8567 (m-30) cc_final: 0.8262 (t0)
REVERT: B   93 LEU cc_start: 0.8556 (mt) cc_final: 0.8343 (tp)
REVERT: B   96 HIS cc_start: 0.8304 (m-70) cc_final: 0.8051 (m90)
REVERT: B  100 ASN cc_start: 0.8856 (m-40) cc_final: 0.8420 (m-40)
REVERT: B  134 GLU cc_start: 0.7744 (mp0) cc_final: 0.7431 (mt-10)
REVERT: C  107 ILE cc_start: 0.8649 (mp) cc_final: 0.8354 (mm)
REVERT: C  284 SER cc_start: 0.8052 (t) cc_final: 0.7712 (p)
  outliers start: 19
  outliers final: 10
  residues processed: 316
  average time/residue: 0.2342
  time to fit residues: 97.5319
Evaluate side-chains
  182 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 172
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  249 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue  115 ASP
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  315 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 51 optimal weight:    5.9990
   chunk 63 optimal weight:    0.4980
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
** A  53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  58 ASN
A 312 ASN
** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 476 ASN
A 539 ASN
** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 326 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.123869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.105774 restraints weight = 16909.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 3.44
r_work: 0.3382 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.4129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.193   8835  Z= 0.341
  Angle     :  1.348  77.889  12078  Z= 0.526
  Chirality :  0.051   0.601   1277
  Planarity :  0.007   0.076   1568
  Dihedral  :  9.927  78.204   1299
  Min Nonbonded Distance : 1.617

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  6.10 %
    Allowed  : 23.50 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.25), residues: 1083
  helix:  0.85 (0.27), residues: 391
  sheet: -1.08 (0.52), residues: 87
  loop : -0.78 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 188 
 HIS   0.009   0.001   HIS A 110 
 PHE   0.019   0.002   PHE C 158 
 TYR   0.017   0.002   TYR C 135 
 ARG   0.005   0.001   ARG C 190 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 219
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.6063 (mt0) cc_final: 0.5854 (mp10)
REVERT: A  211 ASP cc_start: 0.8654 (t0) cc_final: 0.8247 (t0)
REVERT: A  268 ILE cc_start: 0.5175 (OUTLIER) cc_final: 0.4594 (pp)
REVERT: A  312 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.7142 (m-40)
REVERT: A  346 MET cc_start: 0.9022 (mtt) cc_final: 0.8775 (mtp)
REVERT: A  483 THR cc_start: 0.5566 (m) cc_final: 0.4781 (p)
REVERT: A  485 MET cc_start: 0.7667 (mpt) cc_final: 0.6707 (mpt)
REVERT: B   53 ASP cc_start: 0.8679 (m-30) cc_final: 0.8177 (t0)
REVERT: B   93 LEU cc_start: 0.8640 (mt) cc_final: 0.8308 (tp)
REVERT: B   96 HIS cc_start: 0.8580 (m-70) cc_final: 0.8102 (m90)
REVERT: B  100 ASN cc_start: 0.9045 (m-40) cc_final: 0.8574 (m-40)
REVERT: B  102 TYR cc_start: 0.7356 (m-80) cc_final: 0.7117 (m-10)
REVERT: B  140 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7907 (mtpt)
REVERT: C  118 MET cc_start: 0.8183 (tpt) cc_final: 0.7740 (tpt)
REVERT: C  180 PHE cc_start: 0.5847 (OUTLIER) cc_final: 0.5444 (t80)
REVERT: C  210 PHE cc_start: 0.8777 (t80) cc_final: 0.8201 (t80)
REVERT: C  267 MET cc_start: 0.9108 (tpt) cc_final: 0.8250 (tpt)
REVERT: C  374 ASN cc_start: 0.8765 (t0) cc_final: 0.8503 (t0)
REVERT: C  395 MET cc_start: 0.7700 (ttt) cc_final: 0.7019 (ttt)
REVERT: C  410 GLU cc_start: 0.9043 (tp30) cc_final: 0.8803 (tp30)
REVERT: C  425 ASN cc_start: 0.7522 (t0) cc_final: 0.7128 (p0)
REVERT: C  437 GLN cc_start: 0.7971 (tt0) cc_final: 0.7582 (tp40)
  outliers start: 54
  outliers final: 20
  residues processed: 256
  average time/residue: 0.1920
  time to fit residues: 68.0054
Evaluate side-chains
  185 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 ILE
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  312 ASN
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain C residue  180 PHE
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  384 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 24 optimal weight:    0.0670
   chunk 39 optimal weight:    2.9990
   chunk 84 optimal weight:    0.1980
   chunk 4 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0050
   chunk 53 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.4132

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
A  78 ASN
A 312 ASN
** A 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 GLN
A 476 ASN
A 539 ASN
B 118 HIS
C 216 GLN
C 321 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.121332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.102452 restraints weight = 17144.047|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 3.48
r_work: 0.3326 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.4992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.175   8835  Z= 0.301
  Angle     :  1.088  68.308  12078  Z= 0.433
  Chirality :  0.081   2.406   1277
  Planarity :  0.005   0.064   1568
  Dihedral  :  9.490  77.500   1293
  Min Nonbonded Distance : 1.749

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 22.03 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.25), residues: 1083
  helix:  1.25 (0.28), residues: 387
  sheet: -0.01 (0.58), residues: 68
  loop : -0.78 (0.24), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 173 
 HIS   0.005   0.001   HIS A 503 
 PHE   0.026   0.002   PHE C 156 
 TYR   0.023   0.002   TYR B 142 
 ARG   0.004   0.000   ARG C 190 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 180
  time to evaluate  : 0.846 
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: A   61 GLN cc_start: 0.7635 (mp10) cc_final: 0.7377 (mp10)
REVERT: A  211 ASP cc_start: 0.8586 (t0) cc_final: 0.7844 (t0)
REVERT: A  312 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7518 (m-40)
REVERT: A  321 MET cc_start: 0.6210 (tpt) cc_final: 0.5975 (tpt)
REVERT: A  360 GLU cc_start: 0.7969 (pm20) cc_final: 0.7736 (pm20)
REVERT: A  438 TYR cc_start: 0.5359 (t80) cc_final: 0.4263 (t80)
REVERT: A  483 THR cc_start: 0.6220 (m) cc_final: 0.5401 (p)
REVERT: B   53 ASP cc_start: 0.8597 (m-30) cc_final: 0.8205 (t0)
REVERT: B   93 LEU cc_start: 0.8741 (mt) cc_final: 0.8477 (mt)
REVERT: B   96 HIS cc_start: 0.8519 (m-70) cc_final: 0.8197 (m90)
REVERT: B  117 LEU cc_start: 0.8402 (mm) cc_final: 0.8067 (mt)
REVERT: C  159 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.8105 (m)
REVERT: C  180 PHE cc_start: 0.5881 (OUTLIER) cc_final: 0.5326 (t80)
REVERT: C  210 PHE cc_start: 0.8858 (t80) cc_final: 0.8447 (t80)
REVERT: C  374 ASN cc_start: 0.8901 (t0) cc_final: 0.8694 (t0)
REVERT: C  395 MET cc_start: 0.7812 (ttt) cc_final: 0.7609 (ttt)
REVERT: C  410 GLU cc_start: 0.9103 (tp30) cc_final: 0.8819 (tp30)
REVERT: C  425 ASN cc_start: 0.7807 (t0) cc_final: 0.7399 (p0)
  outliers start: 42
  outliers final: 23
  residues processed: 210
  average time/residue: 0.1854
  time to fit residues: 55.2370
Evaluate side-chains
  178 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 152
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  312 ASN
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue  115 ASP
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue   89 HIS
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  180 PHE
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  343 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 78 optimal weight:    0.5980
   chunk 71 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0670
   chunk 0 optimal weight:    7.9990
   chunk 55 optimal weight:    8.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    0.6518

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

Flipped N/Q/H residues before XYZ refinement:
A 503 HIS
A 539 ASN
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.114051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.095316 restraints weight = 17052.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 3.39
r_work: 0.3254 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.5691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098   8835  Z= 0.252
  Angle     :  1.098  85.541  12078  Z= 0.430
  Chirality :  0.058   1.302   1277
  Planarity :  0.006   0.066   1568
  Dihedral  :  9.139  78.425   1293
  Min Nonbonded Distance : 1.820

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 22.60 %
    Favored  : 72.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.26), residues: 1083
  helix:  1.25 (0.28), residues: 392
  sheet: -0.47 (0.57), residues: 76
  loop : -0.69 (0.25), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 173 
 HIS   0.004   0.001   HIS A 110 
 PHE   0.022   0.002   PHE C 156 
 TYR   0.014   0.001   TYR B 142 
 ARG   0.004   0.000   ARG A 490 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 172
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 GLN cc_start: 0.7604 (mp10) cc_final: 0.7238 (mp10)
REVERT: A  211 ASP cc_start: 0.8630 (t0) cc_final: 0.7939 (t0)
REVERT: A  223 MET cc_start: 0.8076 (mmm) cc_final: 0.7550 (mtp)
REVERT: A  259 THR cc_start: 0.6000 (p) cc_final: 0.5596 (t)
REVERT: A  293 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6645 (mm-30)
REVERT: A  312 ASN cc_start: 0.7746 (OUTLIER) cc_final: 0.7242 (m-40)
REVERT: A  327 ILE cc_start: 0.8990 (mt) cc_final: 0.8716 (mp)
REVERT: A  360 GLU cc_start: 0.8057 (pm20) cc_final: 0.7782 (pm20)
REVERT: A  375 SER cc_start: 0.8659 (OUTLIER) cc_final: 0.8407 (m)
REVERT: A  483 THR cc_start: 0.6414 (m) cc_final: 0.5499 (p)
REVERT: B   53 ASP cc_start: 0.8656 (m-30) cc_final: 0.8135 (t0)
REVERT: B   93 LEU cc_start: 0.8893 (mt) cc_final: 0.8640 (mt)
REVERT: B   96 HIS cc_start: 0.8470 (m-70) cc_final: 0.8262 (m90)
REVERT: B  104 ASP cc_start: 0.7642 (t0) cc_final: 0.7337 (t0)
REVERT: B  106 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7909 (mp0)
REVERT: B  117 LEU cc_start: 0.8416 (mm) cc_final: 0.8105 (mt)
REVERT: B  129 TYR cc_start: 0.8483 (m-80) cc_final: 0.8010 (m-80)
REVERT: B  136 GLU cc_start: 0.8301 (pt0) cc_final: 0.7986 (pm20)
REVERT: C   97 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8534 (mp0)
REVERT: C  118 MET cc_start: 0.8302 (tpt) cc_final: 0.7798 (tpt)
REVERT: C  159 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8112 (m)
REVERT: C  161 ARG cc_start: 0.8076 (ptp-170) cc_final: 0.7556 (ptp-110)
REVERT: C  180 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.5404 (t80)
REVERT: C  210 PHE cc_start: 0.8890 (t80) cc_final: 0.8475 (t80)
REVERT: C  395 MET cc_start: 0.8414 (ttt) cc_final: 0.8185 (ttt)
REVERT: C  410 GLU cc_start: 0.9143 (tp30) cc_final: 0.8881 (tp30)
  outliers start: 40
  outliers final: 23
  residues processed: 204
  average time/residue: 0.1947
  time to fit residues: 55.9843
Evaluate side-chains
  173 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  312 ASN
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  115 ASP
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  180 PHE
Chi-restraints excluded: chain C residue  183 THR
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  343 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 77 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A  24 HIS
A  29 ASN
** A  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 HIS
A 539 ASN
B 118 HIS
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  98 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.093757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.074361 restraints weight = 17294.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 3.13
r_work: 0.2883 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.7695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.100   8835  Z= 0.407
  Angle     :  1.150  83.265  12078  Z= 0.467
  Chirality :  0.063   1.438   1277
  Planarity :  0.006   0.068   1568
  Dihedral  :  9.689  82.379   1292
  Min Nonbonded Distance : 1.758

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 22.49 %
    Favored  : 72.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.26), residues: 1083
  helix:  1.13 (0.28), residues: 390
  sheet: -0.51 (0.59), residues: 77
  loop : -0.66 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 173 
 HIS   0.011   0.001   HIS A 110 
 PHE   0.018   0.002   PHE C 156 
 TYR   0.025   0.002   TYR A  96 
 ARG   0.007   0.001   ARG A  52 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 150
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.8189 (p0) cc_final: 0.7684 (p0)
REVERT: A   68 TYR cc_start: 0.9010 (m-80) cc_final: 0.8722 (m-80)
REVERT: A   79 TYR cc_start: 0.8165 (m-80) cc_final: 0.7957 (m-80)
REVERT: A   96 TYR cc_start: 0.7990 (m-80) cc_final: 0.7384 (m-80)
REVERT: A   98 GLN cc_start: 0.6681 (mp10) cc_final: 0.6271 (mm-40)
REVERT: A  211 ASP cc_start: 0.8713 (t0) cc_final: 0.8200 (t0)
REVERT: A  287 ILE cc_start: 0.8770 (mt) cc_final: 0.8498 (tt)
REVERT: A  293 GLU cc_start: 0.8573 (mm-30) cc_final: 0.7975 (mm-30)
REVERT: A  322 MET cc_start: 0.5913 (mmt) cc_final: 0.5593 (mmt)
REVERT: A  356 ASP cc_start: 0.8399 (m-30) cc_final: 0.8093 (m-30)
REVERT: A  375 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8051 (m)
REVERT: A  476 ASN cc_start: 0.8374 (m-40) cc_final: 0.7985 (m-40)
REVERT: A  490 ARG cc_start: 0.8498 (mmm160) cc_final: 0.8210 (mmm160)
REVERT: B   94 ARG cc_start: 0.9392 (mmm-85) cc_final: 0.9182 (mmm-85)
REVERT: B  102 TYR cc_start: 0.7565 (m-80) cc_final: 0.7297 (m-10)
REVERT: B  112 MET cc_start: 0.8492 (mtp) cc_final: 0.7827 (ttp)
REVERT: C   97 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8686 (mp0)
REVERT: C  118 MET cc_start: 0.8718 (tpt) cc_final: 0.7902 (tpt)
REVERT: C  180 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.6018 (t80)
REVERT: C  210 PHE cc_start: 0.9106 (t80) cc_final: 0.8610 (t80)
REVERT: C  410 GLU cc_start: 0.9160 (tp30) cc_final: 0.8830 (tp30)
  outliers start: 46
  outliers final: 22
  residues processed: 184
  average time/residue: 0.1931
  time to fit residues: 50.6156
Evaluate side-chains
  153 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  274 ASP
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue   64 PHE
Chi-restraints excluded: chain C residue  180 PHE
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  343 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 92 optimal weight:    0.3980
   chunk 101 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0050
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 HIS
** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  98 GLN
C 308 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.096295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.077522 restraints weight = 17002.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3076 rms_B_bonded: 3.10
r_work: 0.2944 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.7909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   8835  Z= 0.259
  Angle     :  1.087  83.381  12078  Z= 0.427
  Chirality :  0.062   1.479   1277
  Planarity :  0.005   0.062   1568
  Dihedral  :  9.467  80.724   1290
  Min Nonbonded Distance : 1.785

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 23.95 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.26), residues: 1083
  helix:  1.35 (0.28), residues: 389
  sheet: -0.66 (0.57), residues: 77
  loop : -0.59 (0.25), residues: 617

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 173 
 HIS   0.009   0.001   HIS A 110 
 PHE   0.021   0.001   PHE C 156 
 TYR   0.020   0.001   TYR A 255 
 ARG   0.003   0.000   ARG A  52 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 148
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.7551 (m-30) cc_final: 0.7324 (m-30)
REVERT: A   37 ASP cc_start: 0.8277 (p0) cc_final: 0.7710 (p0)
REVERT: A   68 TYR cc_start: 0.8962 (m-80) cc_final: 0.8600 (m-80)
REVERT: A   79 TYR cc_start: 0.8160 (m-80) cc_final: 0.7942 (m-80)
REVERT: A   96 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7549 (m-80)
REVERT: A   98 GLN cc_start: 0.6991 (mp10) cc_final: 0.6460 (mm-40)
REVERT: A  211 ASP cc_start: 0.8743 (t0) cc_final: 0.8236 (t0)
REVERT: A  293 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8078 (mm-30)
REVERT: A  356 ASP cc_start: 0.8343 (m-30) cc_final: 0.8121 (m-30)
REVERT: A  375 SER cc_start: 0.8522 (OUTLIER) cc_final: 0.7912 (m)
REVERT: A  425 TYR cc_start: 0.8728 (m-80) cc_final: 0.8464 (m-80)
REVERT: A  483 THR cc_start: 0.6932 (m) cc_final: 0.6046 (p)
REVERT: A  490 ARG cc_start: 0.8463 (mmm160) cc_final: 0.8131 (mmm160)
REVERT: B   94 ARG cc_start: 0.9375 (mmm-85) cc_final: 0.9095 (mmm-85)
REVERT: B  112 MET cc_start: 0.8543 (mtp) cc_final: 0.7859 (ttp)
REVERT: B  136 GLU cc_start: 0.8376 (pt0) cc_final: 0.7920 (pm20)
REVERT: C   97 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8688 (mp0)
REVERT: C  118 MET cc_start: 0.8613 (tpt) cc_final: 0.7890 (tpt)
REVERT: C  158 PHE cc_start: 0.7469 (m-10) cc_final: 0.7240 (m-10)
REVERT: C  161 ARG cc_start: 0.7838 (ptp-170) cc_final: 0.7450 (mtp85)
REVERT: C  180 PHE cc_start: 0.6910 (OUTLIER) cc_final: 0.5951 (t80)
REVERT: C  210 PHE cc_start: 0.9067 (t80) cc_final: 0.8633 (t80)
REVERT: C  410 GLU cc_start: 0.9162 (tp30) cc_final: 0.8904 (tp30)
  outliers start: 35
  outliers final: 22
  residues processed: 176
  average time/residue: 0.2071
  time to fit residues: 50.4488
Evaluate side-chains
  165 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 GLU
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   96 TYR
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  274 ASP
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  180 PHE
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  343 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 69 optimal weight:    7.9990
   chunk 13 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 72 optimal weight:    9.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 HIS
A 290 ASN
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.095169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.076496 restraints weight = 17387.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 3.14
r_work: 0.2927 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.8108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   8835  Z= 0.271
  Angle     :  1.089  83.167  12078  Z= 0.427
  Chirality :  0.062   1.484   1277
  Planarity :  0.005   0.065   1568
  Dihedral  :  9.326  81.123   1289
  Min Nonbonded Distance : 1.777

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.25 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 23.62 %
    Favored  : 72.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.26), residues: 1083
  helix:  1.39 (0.28), residues: 391
  sheet: -0.19 (0.60), residues: 71
  loop : -0.54 (0.25), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 173 
 HIS   0.007   0.001   HIS A 110 
 PHE   0.018   0.002   PHE A  80 
 TYR   0.016   0.001   TYR A  96 
 ARG   0.003   0.000   ARG A 418 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 142
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.8255 (p0) cc_final: 0.7643 (p0)
REVERT: A   68 TYR cc_start: 0.8974 (m-80) cc_final: 0.8713 (m-80)
REVERT: A   96 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7537 (m-80)
REVERT: A   98 GLN cc_start: 0.7149 (mp10) cc_final: 0.6593 (mm110)
REVERT: A  211 ASP cc_start: 0.8756 (t0) cc_final: 0.8058 (t0)
REVERT: A  271 TYR cc_start: 0.8127 (m-80) cc_final: 0.7791 (m-80)
REVERT: A  322 MET cc_start: 0.5805 (mmt) cc_final: 0.5464 (mmt)
REVERT: A  356 ASP cc_start: 0.8434 (m-30) cc_final: 0.8036 (m-30)
REVERT: A  360 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8272 (mp0)
REVERT: A  375 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.7918 (m)
REVERT: A  425 TYR cc_start: 0.8736 (m-80) cc_final: 0.8527 (m-80)
REVERT: A  490 ARG cc_start: 0.8434 (mmm160) cc_final: 0.8049 (mmm160)
REVERT: B   94 ARG cc_start: 0.9370 (mmm-85) cc_final: 0.9118 (mmm-85)
REVERT: B  102 TYR cc_start: 0.7749 (m-80) cc_final: 0.7314 (m-10)
REVERT: B  112 MET cc_start: 0.8574 (mtp) cc_final: 0.8063 (ttp)
REVERT: B  115 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.6868 (p0)
REVERT: C   97 GLU cc_start: 0.9087 (mm-30) cc_final: 0.8701 (mp0)
REVERT: C  118 MET cc_start: 0.8631 (tpt) cc_final: 0.7881 (tpt)
REVERT: C  161 ARG cc_start: 0.7773 (ptp-170) cc_final: 0.7339 (mtp85)
REVERT: C  180 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.6005 (t80)
REVERT: C  210 PHE cc_start: 0.9106 (t80) cc_final: 0.8675 (t80)
REVERT: C  410 GLU cc_start: 0.9136 (tp30) cc_final: 0.8862 (tp30)
  outliers start: 36
  outliers final: 21
  residues processed: 171
  average time/residue: 0.2002
  time to fit residues: 47.9817
Evaluate side-chains
  157 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   96 TYR
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  163 ILE
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain B residue  115 ASP
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  180 PHE
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  343 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 81 optimal weight:    7.9990
   chunk 100 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0970
   chunk 72 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 15 optimal weight:    0.2980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 HIS
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.093210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.074689 restraints weight = 17619.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 3.12
r_work: 0.2892 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.8396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.100   8835  Z= 0.304
  Angle     :  1.103  83.254  12078  Z= 0.435
  Chirality :  0.063   1.481   1277
  Planarity :  0.005   0.070   1568
  Dihedral  :  9.300  81.750   1289
  Min Nonbonded Distance : 1.781

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 24.63 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.26), residues: 1083
  helix:  1.41 (0.28), residues: 390
  sheet: -0.52 (0.59), residues: 77
  loop : -0.46 (0.25), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 173 
 HIS   0.008   0.001   HIS A 110 
 PHE   0.017   0.002   PHE C 158 
 TYR   0.032   0.002   TYR A  79 
 ARG   0.004   0.000   ARG A 418 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 143
  time to evaluate  : 0.883 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.8213 (p0) cc_final: 0.7622 (p0)
REVERT: A   68 TYR cc_start: 0.8987 (m-80) cc_final: 0.8717 (m-80)
REVERT: A   96 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.7624 (m-80)
REVERT: A   98 GLN cc_start: 0.7393 (mp10) cc_final: 0.6836 (mm110)
REVERT: A  211 ASP cc_start: 0.8746 (t0) cc_final: 0.8182 (t0)
REVERT: A  271 TYR cc_start: 0.8321 (m-80) cc_final: 0.7992 (m-80)
REVERT: A  356 ASP cc_start: 0.8526 (m-30) cc_final: 0.8107 (m-30)
REVERT: A  360 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8341 (mp0)
REVERT: A  375 SER cc_start: 0.8441 (OUTLIER) cc_final: 0.8009 (m)
REVERT: A  453 GLN cc_start: 0.8680 (tp40) cc_final: 0.8459 (tp-100)
REVERT: B   94 ARG cc_start: 0.9351 (mmm-85) cc_final: 0.9088 (mmm-85)
REVERT: B  112 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8096 (ttp)
REVERT: B  115 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.6859 (p0)
REVERT: C   97 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8708 (mp0)
REVERT: C  118 MET cc_start: 0.8616 (tpt) cc_final: 0.7769 (tpt)
REVERT: C  161 ARG cc_start: 0.7779 (ptp-170) cc_final: 0.7320 (mtp85)
REVERT: C  180 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6240 (t80)
REVERT: C  210 PHE cc_start: 0.9113 (t80) cc_final: 0.8634 (t80)
REVERT: C  395 MET cc_start: 0.8567 (ttt) cc_final: 0.7852 (ttt)
REVERT: C  410 GLU cc_start: 0.9164 (tp30) cc_final: 0.8894 (tp30)
  outliers start: 37
  outliers final: 24
  residues processed: 167
  average time/residue: 0.1902
  time to fit residues: 44.6593
Evaluate side-chains
  163 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 GLU
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue   96 TYR
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  440 VAL
Chi-restraints excluded: chain A residue  477 ASN
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain B residue  112 MET
Chi-restraints excluded: chain B residue  115 ASP
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue  180 PHE
Chi-restraints excluded: chain C residue  182 HIS
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  316 SER
Chi-restraints excluded: chain C residue  343 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0870
   chunk 55 optimal weight:    0.4980
   chunk 27 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0870
   chunk 25 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 49 optimal weight:    0.1980
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.3136

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 HIS
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.098133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.079511 restraints weight = 17431.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 3.18
r_work: 0.2977 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.8452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.103   8835  Z= 0.229
  Angle     :  1.084  83.303  12078  Z= 0.424
  Chirality :  0.062   1.492   1277
  Planarity :  0.005   0.075   1568
  Dihedral  :  9.117  80.852   1289
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 25.08 %
    Favored  : 71.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.26), residues: 1083
  helix:  1.43 (0.28), residues: 391
  sheet:  0.13 (0.66), residues: 61
  loop : -0.55 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 173 
 HIS   0.007   0.001   HIS A 110 
 PHE   0.014   0.001   PHE C 158 
 TYR   0.030   0.001   TYR A  79 
 ARG   0.004   0.000   ARG A 499 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 144
  time to evaluate  : 0.927 
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: A   37 ASP cc_start: 0.8131 (p0) cc_final: 0.7566 (p0)
REVERT: A   54 MET cc_start: 0.8025 (ttp) cc_final: 0.7777 (ttp)
REVERT: A   68 TYR cc_start: 0.8994 (m-80) cc_final: 0.8685 (m-80)
REVERT: A   96 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7623 (m-80)
REVERT: A   98 GLN cc_start: 0.7418 (mp10) cc_final: 0.6829 (mm110)
REVERT: A  211 ASP cc_start: 0.8743 (t0) cc_final: 0.8072 (t0)
REVERT: A  271 TYR cc_start: 0.8343 (m-80) cc_final: 0.7989 (m-80)
REVERT: A  356 ASP cc_start: 0.8509 (m-30) cc_final: 0.8148 (m-30)
REVERT: A  360 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8264 (mp0)
REVERT: A  375 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.8026 (m)
REVERT: A  453 GLN cc_start: 0.8636 (tp40) cc_final: 0.8395 (tp-100)
REVERT: B   94 ARG cc_start: 0.9383 (mmm-85) cc_final: 0.9134 (mmm-85)
REVERT: B  102 TYR cc_start: 0.7684 (m-80) cc_final: 0.7418 (m-80)
REVERT: B  115 ASP cc_start: 0.7544 (OUTLIER) cc_final: 0.6564 (p0)
REVERT: C   97 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8669 (mp0)
REVERT: C  180 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6023 (t80)
REVERT: C  210 PHE cc_start: 0.9054 (t80) cc_final: 0.8562 (t80)
REVERT: C  395 MET cc_start: 0.8242 (ttt) cc_final: 0.7295 (ttt)
REVERT: C  410 GLU cc_start: 0.9159 (tp30) cc_final: 0.8916 (tp30)
  outliers start: 31
  outliers final: 20
  residues processed: 168
  average time/residue: 0.1894
  time to fit residues: 45.2239
Evaluate side-chains
  157 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue   96 TYR
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  253 VAL
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain B residue  115 ASP
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  122 ILE
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  180 PHE
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  343 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 16 optimal weight:    0.0970
   chunk 41 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 77 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 HIS
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.094327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.075480 restraints weight = 17441.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 3.10
r_work: 0.2905 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.8663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   8835  Z= 0.294
  Angle     :  1.098  82.789  12078  Z= 0.432
  Chirality :  0.062   1.494   1277
  Planarity :  0.005   0.073   1568
  Dihedral  :  9.226  82.571   1289
  Min Nonbonded Distance : 1.783

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 25.20 %
    Favored  : 71.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.26), residues: 1083
  helix:  1.50 (0.28), residues: 391
  sheet:  0.27 (0.67), residues: 63
  loop : -0.45 (0.25), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 173 
 HIS   0.009   0.001   HIS A 110 
 PHE   0.017   0.001   PHE C 158 
 TYR   0.032   0.002   TYR A  79 
 ARG   0.004   0.000   ARG C 108 

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

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

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2166 Ramachandran restraints generated.
    1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 133
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ASP cc_start: 0.8241 (p0) cc_final: 0.7634 (p0)
REVERT: A   68 TYR cc_start: 0.8981 (m-80) cc_final: 0.8726 (m-80)
REVERT: A   98 GLN cc_start: 0.7663 (mp10) cc_final: 0.7371 (mp10)
REVERT: A  211 ASP cc_start: 0.8777 (t0) cc_final: 0.8239 (t0)
REVERT: A  271 TYR cc_start: 0.8373 (m-80) cc_final: 0.8040 (m-80)
REVERT: A  330 SER cc_start: 0.8217 (m) cc_final: 0.7915 (t)
REVERT: A  356 ASP cc_start: 0.8556 (m-30) cc_final: 0.8160 (m-30)
REVERT: A  375 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.7973 (m)
REVERT: A  453 GLN cc_start: 0.8710 (tp40) cc_final: 0.8471 (tp-100)
REVERT: B   94 ARG cc_start: 0.9364 (mmm-85) cc_final: 0.9107 (mmm-85)
REVERT: C   97 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8664 (mp0)
REVERT: C  118 MET cc_start: 0.8635 (tpt) cc_final: 0.7813 (tpt)
REVERT: C  180 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6275 (t80)
REVERT: C  210 PHE cc_start: 0.9087 (t80) cc_final: 0.8672 (t80)
REVERT: C  395 MET cc_start: 0.8512 (ttt) cc_final: 0.8137 (ttt)
REVERT: C  410 GLU cc_start: 0.9170 (tp30) cc_final: 0.8899 (tp30)
  outliers start: 29
  outliers final: 19
  residues processed: 157
  average time/residue: 0.1908
  time to fit residues: 42.5429
Evaluate side-chains
  149 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  306 ASN
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  493 VAL
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain B residue  164 HIS
Chi-restraints excluded: chain B residue  177 VAL
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  183 PHE
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  180 PHE
Chi-restraints excluded: chain C residue  239 SER
Chi-restraints excluded: chain C residue  315 TYR
Chi-restraints excluded: chain C residue  343 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0270
   chunk 90 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.9640

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

Flipped N/Q/H residues before XYZ refinement:
** A  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 126 HIS
** B 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.093946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.074873 restraints weight = 17701.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 3.18
r_work: 0.2899 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.8815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   8835  Z= 0.290
  Angle     :  1.101  82.755  12078  Z= 0.436
  Chirality :  0.063   1.499   1277
  Planarity :  0.006   0.075   1568
  Dihedral  :  9.240  82.641   1289
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 25.65 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 1083
  helix:  1.49 (0.28), residues: 392
  sheet:  0.28 (0.68), residues: 63
  loop : -0.48 (0.25), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 173 
 HIS   0.008   0.001   HIS A 110 
 PHE   0.017   0.001   PHE C 158 
 TYR   0.035   0.002   TYR A  79 
 ARG   0.003   0.000   ARG C 108 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4233.91 seconds
wall clock time: 73 minutes 45.65 seconds (4425.65 seconds total)