Starting phenix.real_space_refine
on Wed Aug  5 00:50:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hxd_52464/08_2026/9hxd_52464.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hxd_52464/08_2026/9hxd_52464.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hxd_52464/08_2026/9hxd_52464.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hxd_52464/08_2026/9hxd_52464.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hxd_52464/08_2026/9hxd_52464.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hxd_52464/08_2026/9hxd_52464.cif"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    4988      2.51       5
     N    1348      2.21       5
     O    1348      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7700
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 560, 3850
          Classifications: {'peptide': 560}
          Incomplete info: {'truncation_to_alanine': 217}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 541}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 754
          Unresolved non-hydrogen angles: 928
          Unresolved non-hydrogen dihedrals: 609
          Unresolved non-hydrogen chiralities: 41
          Planarities with less than four sites: {'ARG:plan': 15, 'HIS:plan': 8, 'ASN:plan1': 23, 'GLU:plan': 38, 'GLN:plan1': 14, 'ASP:plan': 14, 'TYR:plan': 3, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 466
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.49, per 1000 atoms: 0.32
  Number of scatterers: 7700
  At special positions: 0
  Unit cell: (124.3, 82.5, 77, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O    1348      8.00
     N    1348      7.00
     C    4988      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=0, symmetry=0
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 475.8 milliseconds
  

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2204

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 2 sheets defined
      71.8% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 14
    Processing helix  chain 'A' and resid 15 through 29
    Processing helix  chain 'A' and resid 34 through 38
    Processing helix  chain 'A' and resid 43 through 61
    Processing helix  chain 'A' and resid 66 through 81
      removed outlier: 4.128A  pdb=" N   HIS A  70 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 89
    Processing helix  chain 'A' and resid 92 through 102
    Processing helix  chain 'A' and resid 107 through 121
      removed outlier: 3.670A  pdb=" N   ILE A 112 " --> pdb=" O   LYS A 108 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   THR A 113 " --> pdb=" O   ASN A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 141
      removed outlier: 3.590A  pdb=" N   GLU A 141 " --> pdb=" O   THR A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 162
      removed outlier: 3.612A  pdb=" N   GLY A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 176
    Processing helix  chain 'A' and resid 187 through 193
      removed outlier: 3.581A  pdb=" N   THR A 191 " --> pdb=" O   GLU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.825A  pdb=" N   TYR A 215 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 223
    Processing helix  chain 'A' and resid 235 through 239
    Processing helix  chain 'A' and resid 258 through 277
      removed outlier: 4.197A  pdb=" N   ALA A 273 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   SER A 274 " --> pdb=" O   LEU A 270 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   THR A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 313
      removed outlier: 3.839A  pdb=" N   HIS A 312 " --> pdb=" O   ASN A 309 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG A 313 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 309 through 313'
    Processing helix  chain 'A' and resid 322 through 329
    Processing helix  chain 'A' and resid 338 through 356
      removed outlier: 4.243A  pdb=" N   LYS A 342 " --> pdb=" O   ASP A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 374
      removed outlier: 4.207A  pdb=" N   ILE A 370 " --> pdb=" O   LEU A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 399
      Proline residue:  A 395  - end of helix
    Processing helix  chain 'A' and resid 400 through 417
    Processing helix  chain 'A' and resid 417 through 426
    Processing helix  chain 'A' and resid 433 through 443
    Processing helix  chain 'A' and resid 446 through 458
      removed outlier: 3.501A  pdb=" N   ILE A 450 " --> pdb=" O   HIS A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 474
    Processing helix  chain 'A' and resid 476 through 507
      removed outlier: 4.082A  pdb=" N   ILE A 498 " --> pdb=" O   GLN A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 538
      removed outlier: 4.118A  pdb=" N   TYR A 525 " --> pdb=" O   HIS A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 565
    Processing helix  chain 'A' and resid 575 through 581
    Processing helix  chain 'B' and resid 11 through 14
    Processing helix  chain 'B' and resid 15 through 29
    Processing helix  chain 'B' and resid 34 through 38
    Processing helix  chain 'B' and resid 43 through 61
    Processing helix  chain 'B' and resid 66 through 81
      removed outlier: 4.128A  pdb=" N   HIS B  70 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 89
    Processing helix  chain 'B' and resid 92 through 102
    Processing helix  chain 'B' and resid 107 through 121
      removed outlier: 3.670A  pdb=" N   ILE B 112 " --> pdb=" O   LYS B 108 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   THR B 113 " --> pdb=" O   ASN B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 141
      removed outlier: 3.590A  pdb=" N   GLU B 141 " --> pdb=" O   THR B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 162
      removed outlier: 3.612A  pdb=" N   GLY B 162 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 176
    Processing helix  chain 'B' and resid 187 through 193
      removed outlier: 3.580A  pdb=" N   THR B 191 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 216
      removed outlier: 3.825A  pdb=" N   TYR B 215 " --> pdb=" O   LYS B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 223
    Processing helix  chain 'B' and resid 235 through 239
    Processing helix  chain 'B' and resid 258 through 277
      removed outlier: 4.197A  pdb=" N   ALA B 273 " --> pdb=" O   ASN B 269 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   SER B 274 " --> pdb=" O   LEU B 270 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   THR B 275 " --> pdb=" O   LYS B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 313
      removed outlier: 3.838A  pdb=" N   HIS B 312 " --> pdb=" O   ASN B 309 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ARG B 313 " --> pdb=" O   PRO B 310 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 309 through 313'
    Processing helix  chain 'B' and resid 322 through 329
    Processing helix  chain 'B' and resid 338 through 356
      removed outlier: 4.243A  pdb=" N   LYS B 342 " --> pdb=" O   ASP B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 374
      removed outlier: 4.208A  pdb=" N   ILE B 370 " --> pdb=" O   LEU B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 399
      Proline residue:  B 395  - end of helix
    Processing helix  chain 'B' and resid 400 through 417
    Processing helix  chain 'B' and resid 417 through 426
    Processing helix  chain 'B' and resid 433 through 443
    Processing helix  chain 'B' and resid 446 through 458
    Processing helix  chain 'B' and resid 460 through 474
    Processing helix  chain 'B' and resid 476 through 507
      removed outlier: 4.082A  pdb=" N   ILE B 498 " --> pdb=" O   GLN B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 517 through 538
      removed outlier: 4.119A  pdb=" N   TYR B 525 " --> pdb=" O   HIS B 521 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 545 through 565
    Processing helix  chain 'B' and resid 575 through 581
    Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227
      removed outlier: 7.330A  pdb=" N   GLU A 202 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL A 295 " --> pdb=" O   GLU A 202 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   SER A 204 " --> pdb=" O   ILE A 293 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ILE A 293 " --> pdb=" O   SER A 204 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   TYR A 206 " --> pdb=" O   GLU A 291 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   GLU A 291 " --> pdb=" O   TYR A 206 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   ASN A 208 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ASN A 292 " --> pdb=" O   ILE A 304 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE A 304 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 225 through 227
      removed outlier: 7.329A  pdb=" N   GLU B 202 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   VAL B 295 " --> pdb=" O   GLU B 202 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   SER B 204 " --> pdb=" O   ILE B 293 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   ILE B 293 " --> pdb=" O   SER B 204 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   TYR B 206 " --> pdb=" O   GLU B 291 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   GLU B 291 " --> pdb=" O   TYR B 206 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   ASN B 208 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ASN B 292 " --> pdb=" O   ILE B 304 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE B 304 " --> pdb=" O   ASN B 292 " (cutoff:3.500A)

    563 hydrogen bonds defined for protein.
    1653 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.91

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2518
        1.34 -     1.46: 1151
        1.46 -     1.57: 4141
        1.57 -     1.69: 0
        1.69 -     1.81: 28
  Bond restraints: 7838
  Sorted by residual:
  bond pdb=" CB  ASN B 472 "
       pdb=" CG  ASN B 472 "
    ideal  model  delta    sigma   weight residual
    1.516  1.553 -0.037 2.50e-02 1.60e+03 2.18e+00
  bond pdb=" CB  ASN A 472 "
       pdb=" CG  ASN A 472 "
    ideal  model  delta    sigma   weight residual
    1.516  1.553 -0.037 2.50e-02 1.60e+03 2.18e+00
  bond pdb=" CA  LYS A 271 "
       pdb=" C   LYS A 271 "
    ideal  model  delta    sigma   weight residual
    1.522  1.506  0.017 1.40e-02 5.10e+03 1.39e+00
  bond pdb=" CA  LYS B 271 "
       pdb=" C   LYS B 271 "
    ideal  model  delta    sigma   weight residual
    1.522  1.507  0.016 1.40e-02 5.10e+03 1.28e+00
  bond pdb=" CB  GLU A 166 "
       pdb=" CG  GLU A 166 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.28e+00
  ... (remaining 7833 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 10338
        1.42 -     2.83: 321
        2.83 -     4.25: 61
        4.25 -     5.66: 30
        5.66 -     7.08: 8
  Bond angle restraints: 10758
  Sorted by residual:
  angle pdb=" CA  ASN B 472 "
        pdb=" CB  ASN B 472 "
        pdb=" CG  ASN B 472 "
      ideal   model   delta    sigma   weight residual
     112.60  115.41   -2.81 1.00e+00 1.00e+00 7.90e+00
  angle pdb=" CA  ASN A 472 "
        pdb=" CB  ASN A 472 "
        pdb=" CG  ASN A 472 "
      ideal   model   delta    sigma   weight residual
     112.60  115.37   -2.77 1.00e+00 1.00e+00 7.69e+00
  angle pdb=" CA  GLU A  27 "
        pdb=" CB  GLU A  27 "
        pdb=" CG  GLU A  27 "
      ideal   model   delta    sigma   weight residual
     114.10  119.43   -5.33 2.00e+00 2.50e-01 7.10e+00
  angle pdb=" CA  GLU B  27 "
        pdb=" CB  GLU B  27 "
        pdb=" CG  GLU B  27 "
      ideal   model   delta    sigma   weight residual
     114.10  119.42   -5.32 2.00e+00 2.50e-01 7.07e+00
  angle pdb=" CB  GLU A 166 "
        pdb=" CG  GLU A 166 "
        pdb=" CD  GLU A 166 "
      ideal   model   delta    sigma   weight residual
     112.60  117.05   -4.45 1.70e+00 3.46e-01 6.84e+00
  ... (remaining 10753 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.19: 4202
       16.19 -    32.39: 318
       32.39 -    48.58: 108
       48.58 -    64.78: 14
       64.78 -    80.97: 2
  Dihedral angle restraints: 4644
    sinusoidal: 1308
      harmonic: 3336
  Sorted by residual:
  dihedral pdb=" CA  GLN B 494 "
           pdb=" C   GLN B 494 "
           pdb=" N   ILE B 495 "
           pdb=" CA  ILE B 495 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.76   25.24     0      5.00e+00 4.00e-02 2.55e+01
  dihedral pdb=" CA  GLN A 494 "
           pdb=" C   GLN A 494 "
           pdb=" N   ILE A 495 "
           pdb=" CA  ILE A 495 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.80   25.20     0      5.00e+00 4.00e-02 2.54e+01
  dihedral pdb=" CA  HIS A  67 "
           pdb=" C   HIS A  67 "
           pdb=" N   ILE A  68 "
           pdb=" CA  ILE A  68 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.25  -18.75     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 4641 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 794
       0.033 -    0.067: 425
       0.067 -    0.100: 95
       0.100 -    0.133: 48
       0.133 -    0.167: 12
  Chirality restraints: 1374
  Sorted by residual:
  chirality pdb=" CG  LEU A   6 "
            pdb=" CB  LEU A   6 "
            pdb=" CD1 LEU A   6 "
            pdb=" CD2 LEU A   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 6.96e-01
  chirality pdb=" CG  LEU B   6 "
            pdb=" CB  LEU B   6 "
            pdb=" CD1 LEU B   6 "
            pdb=" CD2 LEU B   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 6.91e-01
  chirality pdb=" CB  VAL A 506 "
            pdb=" CA  VAL A 506 "
            pdb=" CG1 VAL A 506 "
            pdb=" CG2 VAL A 506 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.85e-01
  ... (remaining 1371 not shown)

  Planarity restraints: 1360
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  74 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.55e+00
        pdb=" C   GLU B  74 "    0.037 2.00e-02 2.50e+03
        pdb=" O   GLU B  74 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU B  75 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  74 "   -0.011 2.00e-02 2.50e+03   2.12e-02 4.50e+00
        pdb=" C   GLU A  74 "    0.037 2.00e-02 2.50e+03
        pdb=" O   GLU A  74 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A  75 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS B 282 "   -0.009 2.00e-02 2.50e+03   1.84e-02 3.40e+00
        pdb=" C   HIS B 282 "    0.032 2.00e-02 2.50e+03
        pdb=" O   HIS B 282 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LYS B 283 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1357 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1664
        2.78 -     3.31: 7517
        3.31 -     3.84: 12705
        3.84 -     4.37: 13307
        4.37 -     4.90: 24069
  Nonbonded interactions: 59262
  Sorted by model distance:
  nonbonded pdb=" O   LYS B 211 "
            pdb=" OG  SER B 214 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   LYS A 211 "
            pdb=" OG  SER A 214 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   ILE A 368 "
            pdb=" OG  SER A 372 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ILE B 368 "
            pdb=" OG  SER B 372 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ALA A 433 "
            pdb=" OG  SER A 436 "
     model   vdw
     2.274 3.040
  ... (remaining 59257 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.030
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6637
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7838  Z= 0.192
  Angle     :  0.669   7.078  10758  Z= 0.357
  Chirality :  0.045   0.167   1374
  Planarity :  0.005   0.038   1360
  Dihedral  : 13.764  80.971   2440
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 20.78 %
    Favored  : 78.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.25), residues: 1088
  helix:  0.89 (0.19), residues: 750
  sheet:  1.31 (0.73), residues: 60
  loop :  0.22 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 496 
 TYR   0.017   0.002   TYR B 499 
 PHE   0.013   0.002   PHE B 467 
 TRP   0.007   0.002   TRP B 416 
 HIS   0.004   0.001   HIS B 523 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00432 /  0.19 ( 7838)
  covalent geometry    : angle       0.66898 /  0.36 (10758)
  hydrogen bonds       : bond        0.14179 /  9.91 (  563)
  hydrogen bonds       : angle       5.22646 /  3.85 ( 1653)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 4
  residues processed: 108
  average time/residue: 0.0655
  time to fit residues: 10.0789
Evaluate side-chains
  103 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  282 HIS
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  282 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0370
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7060

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 494 GLN
** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 494 GLN
** B 523 HIS ** 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 = 0.4732 r_free = 0.4732 target = 0.248924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.213943 restraints weight = 8888.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.217662 restraints weight = 6283.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.220532 restraints weight = 4976.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.221880 restraints weight = 4223.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.223417 restraints weight = 3796.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.4538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6532
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7838  Z= 0.113
  Angle     :  0.480   5.409  10758  Z= 0.251
  Chirality :  0.039   0.139   1374
  Planarity :  0.004   0.027   1360
  Dihedral  :  4.220  34.709   1166
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 20.78 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.25), residues: 1088
  helix:  1.58 (0.19), residues: 756
  sheet:  1.27 (0.71), residues: 60
  loop :  0.22 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 496 
 TYR   0.009   0.001   TYR A 499 
 PHE   0.013   0.001   PHE B 437 
 TRP   0.011   0.002   TRP A 416 
 HIS   0.003   0.001   HIS B 446 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.11 ( 7838)
  covalent geometry    : angle       0.47971 /  0.25 (10758)
  hydrogen bonds       : bond        0.03506 /  2.40 (  563)
  hydrogen bonds       : angle       3.81574 /  2.82 ( 1653)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 ILE cc_start: 0.6076 (mm) cc_final: 0.5717 (mt)
REVERT: B  225 ILE cc_start: 0.6295 (mm) cc_final: 0.5897 (mt)
  outliers start: 11
  outliers final: 7
  residues processed: 110
  average time/residue: 0.0598
  time to fit residues: 9.7710
Evaluate side-chains
  107 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  571 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 20 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 110 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 97 optimal weight:    6.9990
   chunk 28 optimal weight:    8.9990
   chunk 86 optimal weight:    0.0060
   chunk 58 optimal weight:    0.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    0.6798

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 523 HIS
** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 523 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.246432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.209687 restraints weight = 8284.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.214705 restraints weight = 5249.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.218176 restraints weight = 3880.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4450 r_free = 0.4450 target = 0.220120 restraints weight = 3176.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.221559 restraints weight = 2797.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.4455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6405
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   7838  Z= 0.105
  Angle     :  0.453   5.159  10758  Z= 0.237
  Chirality :  0.039   0.139   1374
  Planarity :  0.003   0.028   1360
  Dihedral  :  3.606  17.944   1158
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.29 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.26), residues: 1088
  helix:  1.89 (0.19), residues: 756
  sheet:  1.27 (0.74), residues: 60
  loop :  0.18 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 496 
 TYR   0.015   0.001   TYR A 525 
 PHE   0.011   0.001   PHE A 467 
 TRP   0.026   0.002   TRP B 493 
 HIS   0.006   0.001   HIS B 446 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.11 ( 7838)
  covalent geometry    : angle       0.45328 /  0.24 (10758)
  hydrogen bonds       : bond        0.03253 /  2.23 (  563)
  hydrogen bonds       : angle       3.56189 /  2.63 ( 1653)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.5980 (tp30) cc_final: 0.5553 (tt0)
REVERT: B   74 GLU cc_start: 0.5980 (tp30) cc_final: 0.5543 (tt0)
  outliers start: 14
  outliers final: 12
  residues processed: 116
  average time/residue: 0.0662
  time to fit residues: 11.0118
Evaluate side-chains
  113 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  571 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 85 optimal weight:    9.9990
   chunk 86 optimal weight:    1.9990
   chunk 56 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0970
   chunk 109 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 57 optimal weight:    7.9990
   chunk 76 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 408 ASN
** B 446 HIS ** 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 = 0.4659 r_free = 0.4659 target = 0.245778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.209439 restraints weight = 8427.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.214032 restraints weight = 5372.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.217265 restraints weight = 4012.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.218953 restraints weight = 3310.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.220599 restraints weight = 2934.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.4444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6431
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7838  Z= 0.107
  Angle     :  0.454   5.083  10758  Z= 0.237
  Chirality :  0.040   0.179   1374
  Planarity :  0.003   0.025   1360
  Dihedral  :  3.512  17.333   1158
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 20.78 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.26), residues: 1088
  helix:  2.01 (0.19), residues: 756
  sheet:  1.18 (0.74), residues: 60
  loop :  0.09 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 496 
 TYR   0.018   0.001   TYR B 525 
 PHE   0.011   0.001   PHE A 467 
 TRP   0.029   0.003   TRP A 493 
 HIS   0.005   0.001   HIS B 446 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00231 /  0.11 ( 7838)
  covalent geometry    : angle       0.45433 /  0.24 (10758)
  hydrogen bonds       : bond        0.03079 /  2.10 (  563)
  hydrogen bonds       : angle       3.47476 /  2.56 ( 1653)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  225 ILE cc_start: 0.6051 (mm) cc_final: 0.5644 (mt)
REVERT: B  225 ILE cc_start: 0.6060 (mm) cc_final: 0.5659 (mt)
REVERT: B  345 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6678 (ttt180)
  outliers start: 20
  outliers final: 12
  residues processed: 120
  average time/residue: 0.0684
  time to fit residues: 11.8245
Evaluate side-chains
  115 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  261 THR
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain B residue  261 THR
Chi-restraints excluded: chain B residue  345 ARG
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  571 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 23 optimal weight:    8.9990
   chunk 10 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 83 optimal weight:    0.1980
   chunk 98 optimal weight:    7.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 408 ASN
A 451 ASN
** B 446 HIS ** 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 = 0.4663 r_free = 0.4663 target = 0.245885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.214721 restraints weight = 8446.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.214721 restraints weight = 7448.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.217019 restraints weight = 6086.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.217518 restraints weight = 4710.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.217934 restraints weight = 4318.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.4426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6456
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   7838  Z= 0.101
  Angle     :  0.450   7.479  10758  Z= 0.232
  Chirality :  0.039   0.178   1374
  Planarity :  0.003   0.026   1360
  Dihedral  :  3.406  16.522   1158
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 22.24 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.26), residues: 1088
  helix:  2.15 (0.19), residues: 756
  sheet:  1.20 (0.74), residues: 60
  loop : -0.04 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 496 
 TYR   0.012   0.001   TYR B 525 
 PHE   0.011   0.001   PHE B 467 
 TRP   0.009   0.002   TRP A 493 
 HIS   0.005   0.001   HIS B 446 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00217 /  0.10 ( 7838)
  covalent geometry    : angle       0.44965 /  0.23 (10758)
  hydrogen bonds       : bond        0.02945 /  2.01 (  563)
  hydrogen bonds       : angle       3.38023 /  2.48 ( 1653)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 107
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 MET cc_start: 0.7845 (tpp) cc_final: 0.7132 (tpp)
REVERT: A   74 GLU cc_start: 0.6589 (tp30) cc_final: 0.5871 (tt0)
REVERT: A  225 ILE cc_start: 0.6346 (mm) cc_final: 0.5836 (mt)
REVERT: A  352 MET cc_start: 0.5248 (OUTLIER) cc_final: 0.4408 (tpt)
REVERT: B   25 MET cc_start: 0.7793 (tpp) cc_final: 0.7153 (tpp)
REVERT: B   74 GLU cc_start: 0.6536 (tt0) cc_final: 0.6314 (tt0)
REVERT: B  225 ILE cc_start: 0.6369 (mm) cc_final: 0.5860 (mt)
REVERT: B  282 HIS cc_start: 0.3986 (t70) cc_final: 0.3733 (t70)
REVERT: B  352 MET cc_start: 0.5230 (OUTLIER) cc_final: 0.4456 (tpt)
REVERT: B  525 TYR cc_start: 0.6680 (m-80) cc_final: 0.6455 (m-80)
  outliers start: 20
  outliers final: 14
  residues processed: 119
  average time/residue: 0.0655
  time to fit residues: 11.5053
Evaluate side-chains
  118 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  494 GLN
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  494 GLN
Chi-restraints excluded: chain B residue  571 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   chunk 60 optimal weight:    0.8980
   chunk 62 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 451 ASN
** B 446 HIS ** 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 = 0.4624 r_free = 0.4624 target = 0.241256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.203017 restraints weight = 8550.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.207526 restraints weight = 5600.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.210612 restraints weight = 4250.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.212625 restraints weight = 3568.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.213420 restraints weight = 3174.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6536
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7838  Z= 0.145
  Angle     :  0.509   6.348  10758  Z= 0.264
  Chirality :  0.041   0.191   1374
  Planarity :  0.004   0.027   1360
  Dihedral  :  3.709  18.899   1158
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 23.05 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.26), residues: 1088
  helix:  1.96 (0.19), residues: 758
  sheet:  1.09 (0.74), residues: 60
  loop : -0.06 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 496 
 TYR   0.014   0.001   TYR A 525 
 PHE   0.013   0.001   PHE A 467 
 TRP   0.012   0.002   TRP A   9 
 HIS   0.006   0.001   HIS B 446 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 ( 7838)
  covalent geometry    : angle       0.50879 /  0.26 (10758)
  hydrogen bonds       : bond        0.03446 /  2.36 (  563)
  hydrogen bonds       : angle       3.65468 /  2.68 ( 1653)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 105
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 MET cc_start: 0.7976 (tpp) cc_final: 0.7260 (tpp)
REVERT: A   74 GLU cc_start: 0.6625 (tp30) cc_final: 0.6096 (tt0)
REVERT: A   96 PHE cc_start: 0.5549 (OUTLIER) cc_final: 0.4991 (m-80)
REVERT: A  225 ILE cc_start: 0.6160 (mm) cc_final: 0.5665 (mt)
REVERT: A  352 MET cc_start: 0.4896 (OUTLIER) cc_final: 0.3964 (tpt)
REVERT: B   25 MET cc_start: 0.7975 (tpp) cc_final: 0.7246 (tpp)
REVERT: B   96 PHE cc_start: 0.5548 (OUTLIER) cc_final: 0.4989 (m-80)
REVERT: B  225 ILE cc_start: 0.6169 (mm) cc_final: 0.5675 (mt)
REVERT: B  352 MET cc_start: 0.4870 (OUTLIER) cc_final: 0.4041 (tpt)
REVERT: B  525 TYR cc_start: 0.6900 (m-80) cc_final: 0.6622 (m-80)
  outliers start: 24
  outliers final: 15
  residues processed: 119
  average time/residue: 0.0596
  time to fit residues: 10.6195
Evaluate side-chains
  116 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  449 SER
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  494 GLN
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  494 GLN
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 84 optimal weight:    0.1980
   chunk 98 optimal weight:    6.9990
   chunk 88 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 451 ASN
** B 446 HIS ** 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 = 0.4657 r_free = 0.4657 target = 0.245113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.212647 restraints weight = 8465.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.214951 restraints weight = 7379.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.215451 restraints weight = 5547.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.216327 restraints weight = 5051.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.216878 restraints weight = 4363.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.4415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6488
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7838  Z= 0.103
  Angle     :  0.466   7.857  10758  Z= 0.238
  Chirality :  0.039   0.181   1374
  Planarity :  0.003   0.027   1360
  Dihedral  :  3.437  17.355   1158
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 23.86 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.35 (0.26), residues: 1088
  helix:  2.24 (0.19), residues: 754
  sheet:  1.09 (0.74), residues: 60
  loop : -0.27 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 496 
 TYR   0.015   0.001   TYR A 525 
 PHE   0.011   0.001   PHE B 467 
 TRP   0.006   0.001   TRP A 493 
 HIS   0.007   0.001   HIS B 446 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00225 /  0.10 ( 7838)
  covalent geometry    : angle       0.46556 /  0.24 (10758)
  hydrogen bonds       : bond        0.02943 /  2.00 (  563)
  hydrogen bonds       : angle       3.40052 /  2.50 ( 1653)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 101
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 PHE cc_start: 0.5331 (OUTLIER) cc_final: 0.4798 (m-80)
REVERT: A  225 ILE cc_start: 0.6373 (mm) cc_final: 0.5904 (mt)
REVERT: A  352 MET cc_start: 0.5015 (OUTLIER) cc_final: 0.4145 (tpt)
REVERT: B   96 PHE cc_start: 0.5312 (OUTLIER) cc_final: 0.4759 (m-80)
REVERT: B  225 ILE cc_start: 0.6378 (mm) cc_final: 0.5912 (mt)
REVERT: B  352 MET cc_start: 0.5243 (OUTLIER) cc_final: 0.4456 (tpt)
  outliers start: 22
  outliers final: 16
  residues processed: 114
  average time/residue: 0.0496
  time to fit residues: 8.9024
Evaluate side-chains
  114 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  399 LEU
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  494 GLN
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  399 LEU
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  494 GLN
Chi-restraints excluded: chain B residue  571 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 84 optimal weight:    9.9990
   chunk 98 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 56 optimal weight:   10.0000
   chunk 69 optimal weight:    5.9990
   chunk 76 optimal weight:    9.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.9184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.244353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.212742 restraints weight = 9115.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.211351 restraints weight = 9806.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4443 r_free = 0.4443 target = 0.213494 restraints weight = 9360.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.213915 restraints weight = 7083.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.214198 restraints weight = 5822.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.4448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6741
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   7838  Z= 0.186
  Angle     :  0.572   8.785  10758  Z= 0.294
  Chirality :  0.043   0.222   1374
  Planarity :  0.004   0.033   1360
  Dihedral  :  3.915  19.663   1158
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 24.35 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.26), residues: 1088
  helix:  1.76 (0.19), residues: 762
  sheet:  0.98 (0.75), residues: 60
  loop :  0.01 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 496 
 TYR   0.013   0.002   TYR B 126 
 PHE   0.015   0.002   PHE A 467 
 TRP   0.008   0.002   TRP B 493 
 HIS   0.008   0.001   HIS B 446 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.19 ( 7838)
  covalent geometry    : angle       0.57185 /  0.29 (10758)
  hydrogen bonds       : bond        0.03808 /  2.61 (  563)
  hydrogen bonds       : angle       3.84072 /  2.82 ( 1653)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 PHE cc_start: 0.5032 (OUTLIER) cc_final: 0.4592 (m-80)
REVERT: A  225 ILE cc_start: 0.6567 (mm) cc_final: 0.6069 (mt)
REVERT: A  352 MET cc_start: 0.5146 (OUTLIER) cc_final: 0.4506 (tpt)
REVERT: A  525 TYR cc_start: 0.6988 (m-80) cc_final: 0.6783 (m-80)
REVERT: B   96 PHE cc_start: 0.5061 (OUTLIER) cc_final: 0.4803 (m-80)
REVERT: B  225 ILE cc_start: 0.6528 (mm) cc_final: 0.6035 (mt)
REVERT: B  352 MET cc_start: 0.5206 (OUTLIER) cc_final: 0.4625 (tpt)
  outliers start: 27
  outliers final: 17
  residues processed: 117
  average time/residue: 0.0556
  time to fit residues: 9.9976
Evaluate side-chains
  114 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  359 VAL
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  450 ILE
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  494 GLN
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  288 TRP
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  359 VAL
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  494 GLN
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 92 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 89 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.7580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.248550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.218619 restraints weight = 8959.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.215947 restraints weight = 8515.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.218358 restraints weight = 7456.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.218867 restraints weight = 5726.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.219037 restraints weight = 5316.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.4493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7838  Z= 0.111
  Angle     :  0.512   8.815  10758  Z= 0.253
  Chirality :  0.039   0.194   1374
  Planarity :  0.003   0.030   1360
  Dihedral  :  3.556  18.450   1158
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 25.97 %
    Favored  : 70.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.21 (0.26), residues: 1088
  helix:  2.12 (0.19), residues: 754
  sheet:  1.01 (0.75), residues: 60
  loop : -0.26 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 496 
 TYR   0.017   0.001   TYR B 525 
 PHE   0.011   0.001   PHE B 467 
 TRP   0.005   0.001   TRP A   9 
 HIS   0.007   0.001   HIS B 446 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 ( 7838)
  covalent geometry    : angle       0.51172 /  0.25 (10758)
  hydrogen bonds       : bond        0.03147 /  2.15 (  563)
  hydrogen bonds       : angle       3.50896 /  2.58 ( 1653)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 PHE cc_start: 0.4909 (OUTLIER) cc_final: 0.4652 (m-80)
REVERT: A  225 ILE cc_start: 0.6569 (mm) cc_final: 0.6081 (mt)
REVERT: A  352 MET cc_start: 0.5228 (OUTLIER) cc_final: 0.4334 (tpt)
REVERT: B   96 PHE cc_start: 0.4926 (OUTLIER) cc_final: 0.4527 (m-80)
REVERT: B  225 ILE cc_start: 0.6558 (mm) cc_final: 0.6071 (mt)
REVERT: B  352 MET cc_start: 0.5476 (OUTLIER) cc_final: 0.4727 (tpt)
  outliers start: 19
  outliers final: 14
  residues processed: 109
  average time/residue: 0.0488
  time to fit residues: 8.1914
Evaluate side-chains
  113 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  494 GLN
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  494 GLN
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 88 optimal weight:    0.9980
   chunk 30 optimal weight:   20.0000
   chunk 16 optimal weight:    3.9990
   chunk 69 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 95 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   chunk 93 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.8380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4725 r_free = 0.4725 target = 0.248330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.216664 restraints weight = 8955.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.215001 restraints weight = 9511.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.219323 restraints weight = 8057.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.219300 restraints weight = 5427.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.219818 restraints weight = 5125.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.4501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6648
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7838  Z= 0.114
  Angle     :  0.520   8.971  10758  Z= 0.256
  Chirality :  0.040   0.192   1374
  Planarity :  0.003   0.028   1360
  Dihedral  :  3.457  18.375   1158
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 26.62 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.30 (0.26), residues: 1088
  helix:  2.18 (0.19), residues: 754
  sheet:  1.00 (0.76), residues: 60
  loop : -0.19 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 496 
 TYR   0.015   0.001   TYR B 525 
 PHE   0.011   0.001   PHE B 467 
 TRP   0.005   0.001   TRP A   9 
 HIS   0.006   0.001   HIS B 446 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00256 /  0.11 ( 7838)
  covalent geometry    : angle       0.52000 /  0.26 (10758)
  hydrogen bonds       : bond        0.03146 /  2.13 (  563)
  hydrogen bonds       : angle       3.48376 /  2.56 ( 1653)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 PHE cc_start: 0.4754 (OUTLIER) cc_final: 0.4420 (m-80)
REVERT: A  225 ILE cc_start: 0.6570 (mm) cc_final: 0.6077 (mt)
REVERT: A  352 MET cc_start: 0.5248 (OUTLIER) cc_final: 0.4340 (tpt)
REVERT: B   96 PHE cc_start: 0.5024 (OUTLIER) cc_final: 0.4637 (m-80)
REVERT: B  225 ILE cc_start: 0.6577 (mm) cc_final: 0.6094 (mt)
REVERT: B  352 MET cc_start: 0.5597 (OUTLIER) cc_final: 0.4742 (tpt)
  outliers start: 17
  outliers final: 13
  residues processed: 107
  average time/residue: 0.0607
  time to fit residues: 10.1383
Evaluate side-chains
  112 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 PHE
Chi-restraints excluded: chain A residue  352 MET
Chi-restraints excluded: chain A residue  414 GLN
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  494 GLN
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain B residue   96 PHE
Chi-restraints excluded: chain B residue  257 LEU
Chi-restraints excluded: chain B residue  352 MET
Chi-restraints excluded: chain B residue  368 ILE
Chi-restraints excluded: chain B residue  414 GLN
Chi-restraints excluded: chain B residue  449 SER
Chi-restraints excluded: chain B residue  474 ILE
Chi-restraints excluded: chain B residue  494 GLN
Chi-restraints excluded: chain B residue  571 LEU
Chi-restraints excluded: chain B residue  577 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 57 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 25 optimal weight:    2.9990
   chunk 7 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 50 optimal weight:    0.8980
   overall best weight:    1.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4692 r_free = 0.4692 target = 0.242985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.206319 restraints weight = 8974.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.209355 restraints weight = 6713.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.211667 restraints weight = 5509.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.212611 restraints weight = 4835.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.213574 restraints weight = 4470.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.4461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7838  Z= 0.158
  Angle     :  0.575   8.747  10758  Z= 0.287
  Chirality :  0.042   0.208   1374
  Planarity :  0.004   0.030   1360
  Dihedral  :  3.748  18.844   1158
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 26.62 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.26), residues: 1088
  helix:  1.91 (0.19), residues: 756
  sheet:  0.71 (0.74), residues: 60
  loop : -0.10 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 496 
 TYR   0.012   0.002   TYR A 126 
 PHE   0.013   0.002   PHE A 467 
 TRP   0.006   0.001   TRP B 288 
 HIS   0.007   0.001   HIS B 446 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.16 ( 7838)
  covalent geometry    : angle       0.57480 /  0.29 (10758)
  hydrogen bonds       : bond        0.03559 /  2.43 (  563)
  hydrogen bonds       : angle       3.77018 /  2.77 ( 1653)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1126.27 seconds
wall clock time: 20 minutes 3.47 seconds (1203.47 seconds total)