Starting phenix.real_space_refine
on Wed Jan 15 17:10:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xcm_38247/01_2025/8xcm_38247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xcm_38247/01_2025/8xcm_38247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.08
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xcm_38247/01_2025/8xcm_38247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xcm_38247/01_2025/8xcm_38247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xcm_38247/01_2025/8xcm_38247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xcm_38247/01_2025/8xcm_38247.cif"
  }
  resolution = 3.08
  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=   0.014
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    5422      2.51       5
     N    1490      2.21       5
     O    1639      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 33 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8605
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4168
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4168
          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      53.333  64.114  34.976  1.00127.49           S
  ATOM   1738  SG  CYS A 222      53.792  68.828  30.722  1.00131.05           S
  ATOM   1698  SG  CYS A 216      52.555  63.628  28.263  1.00131.75           S

  Time building chain proxies: 5.53, per 1000 atoms: 0.64
  Number of scatterers: 8605
  At special positions: 0
  Unit cell: (104.06, 108.36, 75.68, 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    1639      8.00
     N    1490      7.00
     C    5422      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=12, symmetry=0
  Number of additional bonds: simple=12, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.77
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" F3S A 602 "
        pdb="FE4  F3S A 602 " - pdb=" SG  CYS A 216 "
        pdb="FE1  F3S A 602 " - pdb=" SG  CYS A 226 "
        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:
      41 helices and 8 sheets defined
      40.3% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 29
    Processing helix  chain 'A' and resid 43 through 53
    Processing helix  chain 'A' and resid 55 through 61
      removed outlier: 3.584A  pdb=" N   GLN A  61 " --> pdb=" O   ASP A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 97
      removed outlier: 3.556A  pdb=" N   TYR A  96 " --> pdb=" O   ARG A  93 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LYS A  97 " --> pdb=" O   THR A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 110
    Processing helix  chain 'A' and resid 119 through 123
    Processing helix  chain 'A' and resid 124 through 130
    Processing helix  chain 'A' and resid 138 through 154
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 181 through 194
    Processing helix  chain 'A' and resid 233 through 245
      removed outlier: 4.171A  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: 3.883A  pdb=" N   ARG A 358 " --> pdb=" O   GLY A 355 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER A 359 " --> pdb=" O   ASP A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 384
    Processing helix  chain 'A' and resid 387 through 401
    Processing helix  chain 'A' and resid 441 through 463
      removed outlier: 3.739A  pdb=" N   ILE A 450 " --> pdb=" O   LYS A 446 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   GLN A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 541
    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 111
      removed outlier: 3.791A  pdb=" N   LEU B 108 " --> pdb=" O   ASP B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 131
    Processing helix  chain 'B' and resid 150 through 154
    Processing helix  chain 'B' and resid 168 through 172
      removed outlier: 3.848A  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 52 through 57
      removed outlier: 3.547A  pdb=" N   HIS C  56 " --> pdb=" O   CYS C  52 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   THR C  57 " --> pdb=" O   ALA C  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 52 through 57'
    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 141
    Processing helix  chain 'C' and resid 163 through 172
    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 318 through 322
      removed outlier: 3.746A  pdb=" N   SER C 322 " --> pdb=" O   ASN C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 335 through 343
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'C' and resid 373 through 382
    Processing helix  chain 'C' and resid 408 through 423
    Processing helix  chain 'C' and resid 431 through 441
    Processing helix  chain 'C' and resid 447 through 451
    Processing sheet with id=AA1, first strand: chain 'A' and resid 247 through 249
      removed outlier: 6.464A  pdb=" N   VAL A  10 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 7.533A  pdb=" N   LEU A  36 " --> pdb=" O   VAL A  10 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   ILE A  12 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 89
      removed outlier: 6.618A  pdb=" N   ILE A  87 " --> pdb=" O   VAL A 436 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200
      removed outlier: 5.297A  pdb=" N   SER A 347 " --> pdb=" O   TYR A 368 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   TYR A 368 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   ASP A 404 " --> pdb=" O   ASN A 369 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   SER A 330 " --> pdb=" O   ILE A 467 " (cutoff:3.500A)
      removed outlier: 5.082A  pdb=" N   ILE A 467 " --> pdb=" O   SER A 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 259
      removed outlier: 6.280A  pdb=" N   VAL A 254 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   PHE A 270 " --> pdb=" O   VAL A 254 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   ALA A 256 " --> pdb=" O   ILE A 268 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   ILE A 268 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLU A 258 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE A 270 " --> pdb=" O   HIS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 321 through 322
    Processing sheet with id=AA6, first strand: chain 'C' and resid 70 through 73
    Processing sheet with id=AA7, first strand: chain 'C' and resid 223 through 224
    Processing sheet with id=AA8, first strand: chain 'C' and resid 387 through 388

    304 hydrogen bonds defined for protein.
    849 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: 3.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.76: 8746
        1.76 -     2.30: 90
        2.30 -     2.84: 0
        2.84 -     3.38: 0
        3.38 -     3.92: 3
  Bond restraints: 8839
  Sorted by residual:
  bond pdb=" S2  F3S A 602 "
       pdb="FE3  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.300  3.922 -1.622 2.00e-02 2.50e+03 6.58e+03
  bond pdb=" S1  F3S A 602 "
       pdb="FE4  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.258  3.801 -1.543 2.00e-02 2.50e+03 5.95e+03
  bond pdb=" S4  F3S A 602 "
       pdb="FE1  F3S A 602 "
    ideal  model  delta    sigma   weight residual
    2.233  3.708 -1.475 2.00e-02 2.50e+03 5.44e+03
  bond pdb=" C2D HEC C 502 "
       pdb=" C3D HEC C 502 "
    ideal  model  delta    sigma   weight residual
    1.544  1.325  0.219 2.00e-02 2.50e+03 1.20e+02
  bond pdb=" C2D HEC C 503 "
       pdb=" C3D HEC C 503 "
    ideal  model  delta    sigma   weight residual
    1.544  1.333  0.211 2.00e-02 2.50e+03 1.12e+02
  ... (remaining 8834 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.38: 12065
        9.38 -    18.75: 8
       18.75 -    28.13: 0
       28.13 -    37.51: 8
       37.51 -    46.89: 2
  Bond angle restraints: 12083
  Sorted by residual:
  angle pdb=" S1  F3S A 602 "
        pdb="FE4  F3S A 602 "
        pdb=" S3  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     114.75   67.86   46.89 3.00e+00 1.11e-01 2.44e+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   71.35   41.24 3.00e+00 1.11e-01 1.89e+02
  angle pdb=" S2  F3S A 602 "
        pdb="FE3  F3S A 602 "
        pdb=" S4  F3S A 602 "
      ideal   model   delta    sigma   weight residual
     103.26   67.65   35.61 3.00e+00 1.11e-01 1.41e+02
  angle pdb="FE3  F3S A 602 "
        pdb=" S2  F3S A 602 "
        pdb="FE4  F3S A 602 "
      ideal   model   delta    sigma   weight residual
      71.75   38.28   33.47 3.00e+00 1.11e-01 1.24e+02
  angle pdb="FE1  F3S A 602 "
        pdb=" S2  F3S A 602 "
        pdb="FE3  F3S A 602 "
      ideal   model   delta    sigma   weight residual
      72.09   38.78   33.31 3.00e+00 1.11e-01 1.23e+02
  ... (remaining 12078 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4442
       17.92 -    35.84: 588
       35.84 -    53.76: 160
       53.76 -    71.68: 24
       71.68 -    89.60: 13
  Dihedral angle restraints: 5227
    sinusoidal: 2075
      harmonic: 3152
  Sorted by residual:
  dihedral pdb=" CA  ALA C 117 "
           pdb=" C   ALA C 117 "
           pdb=" N   MET C 118 "
           pdb=" CA  MET C 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.36   29.64     0      5.00e+00 4.00e-02 3.51e+01
  dihedral pdb=" CA  MET C 395 "
           pdb=" C   MET C 395 "
           pdb=" N   PRO C 396 "
           pdb=" CA  PRO C 396 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.54   28.46     0      5.00e+00 4.00e-02 3.24e+01
  dihedral pdb=" C2C HEC C 503 "
           pdb=" C3C HEC C 503 "
           pdb=" CAC HEC C 503 "
           pdb=" CBC HEC C 503 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00   11.00   49.00     2      1.00e+01 1.00e-02 2.73e+01
  ... (remaining 5224 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    3.271: 1276
       3.271 -    6.543: 0
       6.543 -    9.814: 0
       9.814 -   13.085: 0
      13.085 -   16.356: 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   -5.59   16.36 2.00e-01 2.50e+01 6.69e+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    2.42    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  PRO B 160 "
            pdb=" N   PRO B 160 "
            pdb=" C   PRO B 160 "
            pdb=" CB  PRO B 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.44e-01
  ... (remaining 1274 not shown)

  Planarity restraints: 1569
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 118 "   -0.083 5.00e-02 4.00e+02   1.20e-01 2.31e+01
        pdb=" N   PRO B 119 "    0.208 5.00e-02 4.00e+02
        pdb=" CA  PRO B 119 "   -0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO B 119 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CBD HEC C 501 "   -0.022 2.00e-02 2.50e+03   4.77e-02 2.28e+01
        pdb=" CGD HEC C 501 "    0.082 2.00e-02 2.50e+03
        pdb=" O1D HEC C 501 "   -0.030 2.00e-02 2.50e+03
        pdb=" O2D HEC C 501 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG C 311 "    0.070 5.00e-02 4.00e+02   1.03e-01 1.69e+01
        pdb=" N   PRO C 312 "   -0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO C 312 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO C 312 "    0.055 5.00e-02 4.00e+02
  ... (remaining 1566 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 252
        2.67 -     3.23: 8905
        3.23 -     3.79: 14843
        3.79 -     4.34: 19937
        4.34 -     4.90: 31824
  Nonbonded interactions: 75761
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  79 "
            pdb=" O   GLN A  98 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" OH  TYR A 118 "
            pdb=" OG  SER A 522 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" OH  TYR A 145 "
            pdb=" OD2 ASP A 535 "
     model   vdw
     2.132 3.040
  nonbonded pdb=" OH  TYR A 118 "
            pdb=" O   SER A 517 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OD1 ASN A 369 "
            pdb=" OG1 THR A 371 "
     model   vdw
     2.187 3.040
  ... (remaining 75756 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:             1.350
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     24.660
  Find NCS groups from input model:        0.090
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
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   1.622   8839  Z= 1.402
  Angle     :  1.333  46.886  12083  Z= 0.534
  Chirality :  0.460  16.356   1277
  Planarity :  0.007   0.120   1569
  Dihedral  : 17.720  89.597   3215
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 18.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 29.23 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.26), residues: 1083
  helix:  1.25 (0.28), residues: 375
  sheet: -1.91 (0.65), residues: 58
  loop : -0.59 (0.25), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  51 
 HIS   0.006   0.001   HIS A 110 
 PHE   0.012   0.001   PHE A 270 
 TYR   0.023   0.002   TYR A 271 
 ARG   0.008   0.001   ARG C 172 

*********************** 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
  145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 139
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASP cc_start: 0.8366 (t0) cc_final: 0.7955 (m-30)
REVERT: A  146 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7607 (t80)
REVERT: A  262 LYS cc_start: 0.9159 (tptp) cc_final: 0.8807 (tppt)
REVERT: A  490 ARG cc_start: 0.8281 (ptt-90) cc_final: 0.7776 (pmt-80)
REVERT: B  141 VAL cc_start: 0.8530 (t) cc_final: 0.8256 (p)
REVERT: B  169 TYR cc_start: 0.9015 (p90) cc_final: 0.8719 (p90)
REVERT: C  120 TYR cc_start: 0.8736 (p90) cc_final: 0.8387 (p90)
REVERT: C  172 ARG cc_start: 0.8618 (ttp-110) cc_final: 0.7719 (mmt-90)
  outliers start: 6
  outliers final: 2
  residues processed: 144
  average time/residue: 0.2223
  time to fit residues: 44.2491
Evaluate side-chains
  127 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 124
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain C residue  343 CYS
Chi-restraints excluded: chain C residue  384 VAL
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:    7.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 98 optimal weight:    0.4980
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  53 ASN
** A  98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 198 ASN
A 332 GLN
** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 453 GLN
** A 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 118 HIS
B 168 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.085728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.067922 restraints weight = 18081.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 3.20
r_work: 0.2784 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.100   8839  Z= 0.393
  Angle     :  1.149  86.326  12083  Z= 0.456
  Chirality :  0.068   1.731   1277
  Planarity :  0.006   0.066   1569
  Dihedral  :  9.262  79.591   1288
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 23.93 %
    Favored  : 72.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.26), residues: 1083
  helix:  1.27 (0.28), residues: 381
  sheet: -1.30 (0.59), residues: 70
  loop : -0.63 (0.25), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  51 
 HIS   0.004   0.001   HIS A 503 
 PHE   0.023   0.002   PHE A  80 
 TYR   0.016   0.002   TYR A 271 
 ARG   0.006   0.001   ARG A 452 

*********************** 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
  167 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 134
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 MET cc_start: 0.8917 (mtp) cc_final: 0.8547 (mtp)
REVERT: A  221 ASN cc_start: 0.8540 (t0) cc_final: 0.7978 (t0)
REVERT: A  262 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8901 (tppp)
REVERT: A  266 THR cc_start: 0.8597 (m) cc_final: 0.8341 (p)
REVERT: A  305 ARG cc_start: 0.8425 (tpt90) cc_final: 0.7286 (ttm110)
REVERT: A  456 MET cc_start: 0.8759 (mmm) cc_final: 0.8552 (tpp)
REVERT: A  478 HIS cc_start: 0.7817 (m170) cc_final: 0.7617 (m170)
REVERT: A  535 ASP cc_start: 0.8593 (t0) cc_final: 0.8013 (m-30)
REVERT: B   49 ASP cc_start: 0.8470 (m-30) cc_final: 0.8075 (t0)
REVERT: B  100 ASN cc_start: 0.8389 (t0) cc_final: 0.8101 (t0)
REVERT: B  141 VAL cc_start: 0.8816 (t) cc_final: 0.8606 (p)
REVERT: B  173 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8510 (mm-30)
REVERT: B  180 MET cc_start: 0.8957 (mmm) cc_final: 0.8612 (mmm)
REVERT: C  118 MET cc_start: 0.8824 (tpt) cc_final: 0.8267 (tpt)
REVERT: C  395 MET cc_start: 0.8576 (tpt) cc_final: 0.8239 (tpt)
REVERT: C  410 GLU cc_start: 0.8757 (tp30) cc_final: 0.8544 (tp30)
  outliers start: 33
  outliers final: 21
  residues processed: 157
  average time/residue: 0.2011
  time to fit residues: 44.1715
Evaluate side-chains
  139 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  262 LYS
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   83 LYS
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue  152 THR
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  393 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 53 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0670
   chunk 42 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 13 optimal weight:    0.8980
   chunk 80 optimal weight:    8.9990
   chunk 37 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.7118

-------------------------------------------------------------------------------
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 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 168 ASN
** C 124 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 = 0.3279 r_free = 0.3279 target = 0.089110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.071457 restraints weight = 17972.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 3.20
r_work: 0.2845 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.104   8839  Z= 0.246
  Angle     :  1.060  83.330  12083  Z= 0.412
  Chirality :  0.061   1.497   1277
  Planarity :  0.005   0.057   1569
  Dihedral  :  8.722  82.172   1287
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 22.12 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.26), residues: 1083
  helix:  1.48 (0.28), residues: 380
  sheet: -1.40 (0.59), residues: 74
  loop : -0.56 (0.25), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  51 
 HIS   0.004   0.001   HIS A 503 
 PHE   0.012   0.001   PHE B  60 
 TYR   0.016   0.001   TYR A 271 
 ARG   0.005   0.000   ARG A 452 

*********************** 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
  173 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 131
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLN cc_start: 0.8713 (tp40) cc_final: 0.8349 (tp-100)
REVERT: A   57 ASP cc_start: 0.8479 (t0) cc_final: 0.7947 (m-30)
REVERT: A  156 MET cc_start: 0.8670 (mtp) cc_final: 0.8236 (mtp)
REVERT: A  175 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.6950 (mmt)
REVERT: A  221 ASN cc_start: 0.8530 (t0) cc_final: 0.7813 (t0)
REVERT: A  266 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8441 (p)
REVERT: A  305 ARG cc_start: 0.8486 (tpt90) cc_final: 0.7421 (ttm110)
REVERT: A  535 ASP cc_start: 0.8566 (t0) cc_final: 0.8033 (m-30)
REVERT: B   49 ASP cc_start: 0.8421 (m-30) cc_final: 0.8072 (t0)
REVERT: B  100 ASN cc_start: 0.8417 (t0) cc_final: 0.8200 (t0)
REVERT: B  141 VAL cc_start: 0.8649 (t) cc_final: 0.8426 (p)
REVERT: B  173 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8492 (mm-30)
REVERT: B  180 MET cc_start: 0.8896 (mmm) cc_final: 0.8691 (mmm)
REVERT: C  118 MET cc_start: 0.8708 (tpt) cc_final: 0.7739 (tpt)
REVERT: C  211 LEU cc_start: 0.9392 (tp) cc_final: 0.9125 (tt)
REVERT: C  395 MET cc_start: 0.8273 (tpt) cc_final: 0.7735 (tpt)
  outliers start: 42
  outliers final: 24
  residues processed: 162
  average time/residue: 0.1968
  time to fit residues: 45.0584
Evaluate side-chains
  143 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  175 MET
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   83 LYS
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  393 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 68 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9980
   overall best weight:    1.3782

-------------------------------------------------------------------------------
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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN
B 168 ASN
** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.088200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.070315 restraints weight = 17920.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 3.13
r_work: 0.2824 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.101   8839  Z= 0.315
  Angle     :  1.078  83.792  12083  Z= 0.420
  Chirality :  0.062   1.491   1277
  Planarity :  0.005   0.056   1569
  Dihedral  :  8.804  83.357   1287
  Min Nonbonded Distance : 1.802

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 21.78 %
    Favored  : 72.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.26), residues: 1083
  helix:  1.59 (0.28), residues: 380
  sheet: -1.25 (0.61), residues: 72
  loop : -0.57 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  51 
 HIS   0.004   0.001   HIS A 503 
 PHE   0.018   0.001   PHE A  80 
 TYR   0.015   0.002   TYR A 271 
 ARG   0.011   0.001   ARG C  60 

*********************** 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
  169 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 120
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8175 (m-30)
REVERT: A   84 ASN cc_start: 0.9132 (t0) cc_final: 0.8901 (t0)
REVERT: A  156 MET cc_start: 0.8794 (mtp) cc_final: 0.8375 (mtp)
REVERT: A  175 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.6846 (mmt)
REVERT: A  221 ASN cc_start: 0.8536 (t0) cc_final: 0.7869 (t0)
REVERT: A  247 LYS cc_start: 0.8061 (mmmm) cc_final: 0.7738 (tttm)
REVERT: A  266 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8292 (p)
REVERT: A  305 ARG cc_start: 0.8555 (tpt90) cc_final: 0.7467 (ttm110)
REVERT: A  505 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8485 (p0)
REVERT: A  535 ASP cc_start: 0.8595 (t0) cc_final: 0.8086 (m-30)
REVERT: B   49 ASP cc_start: 0.8391 (m-30) cc_final: 0.8066 (t0)
REVERT: B  100 ASN cc_start: 0.8435 (t0) cc_final: 0.8183 (t0)
REVERT: B  136 GLU cc_start: 0.8971 (pm20) cc_final: 0.8600 (pm20)
REVERT: B  141 VAL cc_start: 0.8732 (t) cc_final: 0.8502 (p)
REVERT: B  173 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8547 (mm-30)
REVERT: C  118 MET cc_start: 0.8755 (tpt) cc_final: 0.7939 (tpt)
REVERT: C  161 ARG cc_start: 0.8564 (ptp-110) cc_final: 0.8095 (ptp-110)
REVERT: C  211 LEU cc_start: 0.9397 (tp) cc_final: 0.9008 (tt)
REVERT: C  395 MET cc_start: 0.8333 (tpt) cc_final: 0.7773 (tpt)
  outliers start: 49
  outliers final: 29
  residues processed: 158
  average time/residue: 0.2009
  time to fit residues: 45.2218
Evaluate side-chains
  145 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 0.995 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  175 MET
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue   83 LYS
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  280 ASP
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  393 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 92 optimal weight:    0.4980
   chunk 26 optimal weight:    0.5980
   chunk 51 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
B 123 GLN
B 168 ASN
** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.087415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.070058 restraints weight = 17645.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 3.15
r_work: 0.2826 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   8839  Z= 0.247
  Angle     :  1.054  83.660  12083  Z= 0.407
  Chirality :  0.060   1.478   1277
  Planarity :  0.005   0.055   1569
  Dihedral  :  8.667  84.418   1287
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 21.90 %
    Favored  : 73.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.26), residues: 1083
  helix:  1.65 (0.28), residues: 380
  sheet: -1.19 (0.63), residues: 72
  loop : -0.55 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  51 
 HIS   0.004   0.001   HIS A 110 
 PHE   0.015   0.001   PHE B  60 
 TYR   0.015   0.001   TYR A 271 
 ARG   0.004   0.000   ARG A 264 

*********************** 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
  163 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 120
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ASN cc_start: 0.9069 (t0) cc_final: 0.8785 (t0)
REVERT: A  156 MET cc_start: 0.8678 (mtp) cc_final: 0.8256 (mtp)
REVERT: A  175 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7031 (mmt)
REVERT: A  221 ASN cc_start: 0.8552 (t0) cc_final: 0.7704 (t0)
REVERT: A  247 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7753 (tttm)
REVERT: A  266 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8338 (p)
REVERT: A  305 ARG cc_start: 0.8614 (tpt90) cc_final: 0.7574 (ttm110)
REVERT: A  308 HIS cc_start: 0.8061 (OUTLIER) cc_final: 0.7603 (t-170)
REVERT: A  535 ASP cc_start: 0.8606 (t0) cc_final: 0.8136 (m-30)
REVERT: B   49 ASP cc_start: 0.8374 (m-30) cc_final: 0.8065 (t0)
REVERT: B  100 ASN cc_start: 0.8432 (t0) cc_final: 0.8211 (t0)
REVERT: B  141 VAL cc_start: 0.8680 (t) cc_final: 0.8445 (p)
REVERT: B  173 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8551 (mm-30)
REVERT: B  177 VAL cc_start: 0.8837 (m) cc_final: 0.8548 (t)
REVERT: C  118 MET cc_start: 0.8736 (tpt) cc_final: 0.7884 (tpt)
REVERT: C  211 LEU cc_start: 0.9391 (tp) cc_final: 0.8989 (tt)
REVERT: C  395 MET cc_start: 0.8263 (tpt) cc_final: 0.7746 (tpt)
  outliers start: 43
  outliers final: 31
  residues processed: 149
  average time/residue: 0.1896
  time to fit residues: 40.3914
Evaluate side-chains
  146 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  175 MET
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  308 HIS
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  280 ASP
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  393 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 104 optimal weight:    0.8980
   chunk 99 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 24 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0870
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
B 168 ASN
** C 124 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 = 0.3309 r_free = 0.3309 target = 0.090742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.073518 restraints weight = 17566.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3019 rms_B_bonded: 2.97
r_work: 0.2893 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   8839  Z= 0.229
  Angle     :  1.047  83.675  12083  Z= 0.403
  Chirality :  0.060   1.478   1277
  Planarity :  0.005   0.055   1569
  Dihedral  :  8.517  85.239   1287
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 21.90 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.26), residues: 1083
  helix:  1.69 (0.28), residues: 380
  sheet: -1.32 (0.63), residues: 74
  loop : -0.50 (0.25), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  51 
 HIS   0.004   0.001   HIS A 110 
 PHE   0.016   0.001   PHE B  60 
 TYR   0.014   0.001   TYR A 271 
 ARG   0.003   0.000   ARG A 264 

*********************** 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
  174 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 129
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 GLN cc_start: 0.8719 (tp40) cc_final: 0.8403 (tp-100)
REVERT: A   84 ASN cc_start: 0.9008 (t0) cc_final: 0.8685 (t0)
REVERT: A  156 MET cc_start: 0.8678 (mtp) cc_final: 0.8287 (mtp)
REVERT: A  175 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7132 (mmt)
REVERT: A  221 ASN cc_start: 0.8593 (t0) cc_final: 0.7708 (t0)
REVERT: A  247 LYS cc_start: 0.7973 (mmmm) cc_final: 0.7666 (tttm)
REVERT: A  305 ARG cc_start: 0.8643 (tpt90) cc_final: 0.7550 (ttm110)
REVERT: A  320 ASN cc_start: 0.7529 (t0) cc_final: 0.6943 (t0)
REVERT: A  535 ASP cc_start: 0.8547 (t0) cc_final: 0.8124 (m-30)
REVERT: B   49 ASP cc_start: 0.8394 (m-30) cc_final: 0.8058 (t0)
REVERT: B  136 GLU cc_start: 0.9093 (pm20) cc_final: 0.8811 (pm20)
REVERT: B  141 VAL cc_start: 0.8648 (t) cc_final: 0.8414 (p)
REVERT: B  173 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8615 (mm-30)
REVERT: B  177 VAL cc_start: 0.8844 (m) cc_final: 0.8585 (t)
REVERT: B  180 MET cc_start: 0.8812 (mmm) cc_final: 0.8596 (mmm)
REVERT: C  118 MET cc_start: 0.8713 (tpt) cc_final: 0.7853 (tpt)
REVERT: C  315 TYR cc_start: 0.7782 (p90) cc_final: 0.7552 (p90)
REVERT: C  328 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8371 (p)
REVERT: C  395 MET cc_start: 0.8191 (tpt) cc_final: 0.7815 (tpt)
  outliers start: 45
  outliers final: 37
  residues processed: 160
  average time/residue: 0.1899
  time to fit residues: 43.6080
Evaluate side-chains
  155 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  175 MET
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  280 ASP
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain C residue  411 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 64 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
B 123 GLN
B 168 ASN
** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.090754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.072980 restraints weight = 17814.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3012 rms_B_bonded: 3.05
r_work: 0.2881 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   8839  Z= 0.243
  Angle     :  1.049  83.666  12083  Z= 0.404
  Chirality :  0.060   1.476   1277
  Planarity :  0.005   0.054   1569
  Dihedral  :  8.526  85.835   1287
  Min Nonbonded Distance : 1.805

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 21.78 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.26), residues: 1083
  helix:  1.79 (0.28), residues: 376
  sheet: -1.28 (0.63), residues: 73
  loop : -0.46 (0.25), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  51 
 HIS   0.004   0.001   HIS A 110 
 PHE   0.018   0.001   PHE C 210 
 TYR   0.025   0.001   TYR A  79 
 ARG   0.004   0.000   ARG C 161 

*********************** 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
  170 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 125
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 ASN cc_start: 0.8986 (t0) cc_final: 0.8656 (t0)
REVERT: A  156 MET cc_start: 0.8669 (mtp) cc_final: 0.8321 (mtp)
REVERT: A  175 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.7169 (mmt)
REVERT: A  221 ASN cc_start: 0.8608 (t0) cc_final: 0.7695 (t0)
REVERT: A  247 LYS cc_start: 0.8048 (mmmm) cc_final: 0.7759 (tttm)
REVERT: A  305 ARG cc_start: 0.8682 (tpt90) cc_final: 0.7482 (ttm110)
REVERT: A  320 ASN cc_start: 0.7514 (t0) cc_final: 0.6931 (t0)
REVERT: A  535 ASP cc_start: 0.8555 (t0) cc_final: 0.8130 (m-30)
REVERT: B   49 ASP cc_start: 0.8386 (m-30) cc_final: 0.8051 (t0)
REVERT: B  104 ASP cc_start: 0.8430 (m-30) cc_final: 0.7467 (p0)
REVERT: B  136 GLU cc_start: 0.9100 (pm20) cc_final: 0.8840 (pm20)
REVERT: B  141 VAL cc_start: 0.8634 (t) cc_final: 0.8403 (p)
REVERT: B  173 GLU cc_start: 0.8960 (mm-30) cc_final: 0.8721 (mm-30)
REVERT: B  177 VAL cc_start: 0.8845 (m) cc_final: 0.8594 (t)
REVERT: C  115 TYR cc_start: 0.7677 (m-80) cc_final: 0.7476 (m-80)
REVERT: C  118 MET cc_start: 0.8717 (tpt) cc_final: 0.7846 (tpt)
REVERT: C  328 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8382 (p)
REVERT: C  395 MET cc_start: 0.8139 (tpt) cc_final: 0.7652 (tpt)
  outliers start: 45
  outliers final: 39
  residues processed: 159
  average time/residue: 0.2019
  time to fit residues: 45.3549
Evaluate side-chains
  156 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 115
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  175 MET
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain B residue  168 ASN
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   73 SER
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  280 ASP
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain C residue  411 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0270
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 80 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.7442

-------------------------------------------------------------------------------
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 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
B 123 GLN
** C 124 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 = 0.3311 r_free = 0.3311 target = 0.090812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.073155 restraints weight = 17868.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 3.07
r_work: 0.2882 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   8839  Z= 0.240
  Angle     :  1.056  83.666  12083  Z= 0.408
  Chirality :  0.060   1.473   1277
  Planarity :  0.005   0.063   1569
  Dihedral  :  8.457  86.342   1287
  Min Nonbonded Distance : 1.804

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 22.80 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.27), residues: 1083
  helix:  1.79 (0.28), residues: 376
  sheet: -1.46 (0.58), residues: 83
  loop : -0.41 (0.26), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  51 
 HIS   0.004   0.001   HIS A 503 
 PHE   0.019   0.001   PHE B  60 
 TYR   0.022   0.001   TYR A  79 
 ARG   0.004   0.000   ARG C 161 

*********************** 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
  164 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 119
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8076 (m-30)
REVERT: A   84 ASN cc_start: 0.8989 (t0) cc_final: 0.8641 (t0)
REVERT: A  156 MET cc_start: 0.8660 (mtp) cc_final: 0.8347 (mtp)
REVERT: A  175 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7226 (mmt)
REVERT: A  221 ASN cc_start: 0.8621 (t0) cc_final: 0.7699 (t0)
REVERT: A  247 LYS cc_start: 0.8074 (mmmm) cc_final: 0.7787 (tttm)
REVERT: A  305 ARG cc_start: 0.8665 (tpt90) cc_final: 0.7570 (ttm110)
REVERT: A  535 ASP cc_start: 0.8559 (t0) cc_final: 0.8154 (m-30)
REVERT: B   49 ASP cc_start: 0.8391 (m-30) cc_final: 0.8083 (t70)
REVERT: B  104 ASP cc_start: 0.8409 (m-30) cc_final: 0.7482 (p0)
REVERT: B  136 GLU cc_start: 0.9098 (pm20) cc_final: 0.8811 (pm20)
REVERT: B  141 VAL cc_start: 0.8638 (t) cc_final: 0.8405 (p)
REVERT: B  173 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8686 (mm-30)
REVERT: B  177 VAL cc_start: 0.8872 (m) cc_final: 0.8627 (t)
REVERT: C  115 TYR cc_start: 0.7666 (m-80) cc_final: 0.7434 (m-80)
REVERT: C  118 MET cc_start: 0.8757 (tpt) cc_final: 0.7914 (tpt)
REVERT: C  182 HIS cc_start: 0.9208 (m90) cc_final: 0.8980 (m-70)
REVERT: C  328 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8379 (p)
REVERT: C  395 MET cc_start: 0.8030 (tpt) cc_final: 0.7516 (tpt)
  outliers start: 45
  outliers final: 37
  residues processed: 155
  average time/residue: 0.1873
  time to fit residues: 41.6897
Evaluate side-chains
  156 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 116
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue   54 MET
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  175 MET
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   73 SER
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  280 ASP
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain C residue  411 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 95 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0970
   chunk 13 optimal weight:    1.9990
   chunk 84 optimal weight:    0.3980
   chunk 47 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 99 optimal weight:    0.6980
   chunk 80 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
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 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN
** C 124 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 = 0.3318 r_free = 0.3318 target = 0.091000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.074096 restraints weight = 17968.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 3.08
r_work: 0.2904 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.103   8839  Z= 0.230
  Angle     :  1.052  83.615  12083  Z= 0.406
  Chirality :  0.060   1.470   1277
  Planarity :  0.005   0.055   1569
  Dihedral  :  8.291  86.946   1285
  Min Nonbonded Distance : 1.803

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 22.80 %
    Favored  : 72.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.27), residues: 1083
  helix:  1.84 (0.28), residues: 370
  sheet: -1.15 (0.62), residues: 73
  loop : -0.44 (0.25), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  51 
 HIS   0.005   0.001   HIS A 503 
 PHE   0.020   0.001   PHE B  60 
 TYR   0.020   0.001   TYR A  79 
 ARG   0.003   0.000   ARG A 264 

*********************** 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
  162 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 120
  time to evaluate  : 0.742 
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   57 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8040 (m-30)
REVERT: A   84 ASN cc_start: 0.8884 (t0) cc_final: 0.8534 (t0)
REVERT: A  156 MET cc_start: 0.8656 (mtp) cc_final: 0.8355 (mtp)
REVERT: A  175 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7199 (mmt)
REVERT: A  221 ASN cc_start: 0.8611 (t0) cc_final: 0.7584 (t0)
REVERT: A  247 LYS cc_start: 0.8064 (mmmm) cc_final: 0.7778 (tttm)
REVERT: A  305 ARG cc_start: 0.8689 (tpt90) cc_final: 0.7572 (ttm110)
REVERT: A  320 ASN cc_start: 0.6830 (t0) cc_final: 0.6544 (t0)
REVERT: A  526 MET cc_start: 0.8253 (mtm) cc_final: 0.7827 (mtt)
REVERT: A  535 ASP cc_start: 0.8540 (t0) cc_final: 0.8146 (m-30)
REVERT: B   49 ASP cc_start: 0.8378 (m-30) cc_final: 0.8078 (t70)
REVERT: B  104 ASP cc_start: 0.8489 (m-30) cc_final: 0.7554 (p0)
REVERT: B  123 GLN cc_start: 0.8538 (tt0) cc_final: 0.8291 (tt0)
REVERT: B  136 GLU cc_start: 0.9101 (pm20) cc_final: 0.8813 (pm20)
REVERT: B  141 VAL cc_start: 0.8623 (t) cc_final: 0.8385 (p)
REVERT: B  173 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8736 (mm-30)
REVERT: B  177 VAL cc_start: 0.8903 (m) cc_final: 0.8680 (t)
REVERT: C  118 MET cc_start: 0.8653 (tpt) cc_final: 0.7843 (tpt)
REVERT: C  182 HIS cc_start: 0.9207 (m90) cc_final: 0.8967 (m-70)
REVERT: C  328 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8354 (p)
  outliers start: 42
  outliers final: 36
  residues processed: 152
  average time/residue: 0.1881
  time to fit residues: 41.0695
Evaluate side-chains
  156 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 117
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  175 MET
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  283 LYS
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   73 SER
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  100 SER
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain C residue  411 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 46 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 505 ASN
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 124 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 = 0.3277 r_free = 0.3277 target = 0.088742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.071261 restraints weight = 17936.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.2978 rms_B_bonded: 3.05
r_work: 0.2850 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.101   8839  Z= 0.284
  Angle     :  1.072  83.972  12083  Z= 0.417
  Chirality :  0.061   1.474   1277
  Planarity :  0.005   0.054   1569
  Dihedral  :  8.458  88.030   1285
  Min Nonbonded Distance : 1.808

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 23.59 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.27), residues: 1083
  helix:  1.86 (0.28), residues: 369
  sheet: -1.36 (0.58), residues: 83
  loop : -0.44 (0.26), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  51 
 HIS   0.006   0.001   HIS A 503 
 PHE   0.023   0.001   PHE B  60 
 TYR   0.023   0.001   TYR A  79 
 ARG   0.004   0.000   ARG A 490 

********************** 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 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 122
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASP cc_start: 0.8609 (OUTLIER) cc_final: 0.8128 (m-30)
REVERT: A   84 ASN cc_start: 0.8924 (t0) cc_final: 0.8562 (t0)
REVERT: A  156 MET cc_start: 0.8745 (mtp) cc_final: 0.8443 (mtp)
REVERT: A  175 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7087 (mmt)
REVERT: A  221 ASN cc_start: 0.8584 (t0) cc_final: 0.7703 (t0)
REVERT: A  247 LYS cc_start: 0.8105 (mmmm) cc_final: 0.7817 (tttm)
REVERT: A  305 ARG cc_start: 0.8691 (tpt90) cc_final: 0.7509 (ttm110)
REVERT: A  320 ASN cc_start: 0.6996 (t0) cc_final: 0.6645 (t0)
REVERT: A  477 GLN cc_start: 0.8749 (mp10) cc_final: 0.8368 (mp10)
REVERT: A  535 ASP cc_start: 0.8551 (t0) cc_final: 0.8153 (m-30)
REVERT: B   49 ASP cc_start: 0.8410 (m-30) cc_final: 0.8102 (t70)
REVERT: B  104 ASP cc_start: 0.8521 (m-30) cc_final: 0.7554 (p0)
REVERT: B  123 GLN cc_start: 0.8595 (tt0) cc_final: 0.8349 (tt0)
REVERT: B  136 GLU cc_start: 0.9114 (pm20) cc_final: 0.8835 (pm20)
REVERT: B  141 VAL cc_start: 0.8723 (t) cc_final: 0.8496 (p)
REVERT: B  173 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8709 (mm-30)
REVERT: B  177 VAL cc_start: 0.8918 (m) cc_final: 0.8685 (t)
REVERT: C  118 MET cc_start: 0.8787 (tpt) cc_final: 0.8175 (tpt)
REVERT: C  182 HIS cc_start: 0.9210 (m90) cc_final: 0.8974 (m-70)
REVERT: C  328 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8391 (p)
  outliers start: 40
  outliers final: 34
  residues processed: 154
  average time/residue: 0.1893
  time to fit residues: 41.7927
Evaluate side-chains
  154 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 117
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  164 THR
Chi-restraints excluded: chain A residue  175 MET
Chi-restraints excluded: chain A residue  281 VAL
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  332 GLN
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  375 SER
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  404 ASP
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  437 THR
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain A residue  494 VAL
Chi-restraints excluded: chain A residue  505 ASN
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain B residue   73 SER
Chi-restraints excluded: chain B residue   76 LEU
Chi-restraints excluded: chain B residue  120 THR
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  140 LYS
Chi-restraints excluded: chain C residue   55 CYS
Chi-restraints excluded: chain C residue   73 SER
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  127 THR
Chi-restraints excluded: chain C residue  179 VAL
Chi-restraints excluded: chain C residue  272 GLU
Chi-restraints excluded: chain C residue  276 GLN
Chi-restraints excluded: chain C residue  328 THR
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  384 VAL
Chi-restraints excluded: chain C residue  393 ILE
Chi-restraints excluded: chain C residue  411 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 74 optimal weight:    0.2980
   chunk 77 optimal weight:    0.0470
   chunk 103 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9980
   chunk 69 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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 433 HIS
A 505 ASN
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 124 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 = 0.3322 r_free = 0.3322 target = 0.091269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.074138 restraints weight = 17963.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 3.11
r_work: 0.2907 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.103   8839  Z= 0.221
  Angle     :  1.051  83.530  12083  Z= 0.407
  Chirality :  0.060   1.474   1277
  Planarity :  0.005   0.057   1569
  Dihedral  :  8.273  88.418   1285
  Min Nonbonded Distance : 1.803

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 24.49 %
    Favored  : 71.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.99 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.27), residues: 1083
  helix:  1.82 (0.28), residues: 371
  sheet: -1.45 (0.59), residues: 83
  loop : -0.44 (0.26), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  51 
 HIS   0.007   0.001   HIS A 503 
 PHE   0.022   0.001   PHE B  60 
 TYR   0.018   0.001   TYR A  79 
 ARG   0.004   0.000   ARG A 490 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3622.68 seconds
wall clock time: 65 minutes 35.12 seconds (3935.12 seconds total)