Starting phenix.real_space_refine
on Fri Jun  6 07:42:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tof_26031/06_2025/7tof_26031.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tof_26031/06_2025/7tof_26031.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tof_26031/06_2025/7tof_26031.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tof_26031/06_2025/7tof_26031.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tof_26031/06_2025/7tof_26031.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tof_26031/06_2025/7tof_26031.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.104
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4838      2.51       5
     N    1318      2.21       5
     O    1392      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7588
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3794
          Classifications: {'peptide': 469}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 3794
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3794
          Classifications: {'peptide': 469}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 445}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   GLU A 504 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  GLU A 504 " occ=0.50
    residue:
      pdb=" N   GLU B 504 " occ=0.50
      ... (3 atoms not shown)
      pdb=" CB  GLU B 504 " occ=0.50
  Time building chain proxies: 5.03, per 1000 atoms: 0.66
  Number of scatterers: 7588
  At special positions: 0
  Unit cell: (73.04, 80.51, 135.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1392      8.00
     N    1318      7.00
     C    4838      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: 1.91
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1760

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 6 sheets defined
      42.3% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 47
    Processing helix  chain 'A' and resid 48 through 58
      removed outlier: 3.822A  pdb=" N   ASP A  58 " --> pdb=" O   TRP A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 89
      Proline residue:  A  86  - end of helix
      removed outlier: 3.856A  pdb=" N   LYS A  89 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 94 through 103
    Processing helix  chain 'A' and resid 114 through 127
      removed outlier: 3.768A  pdb=" N   TYR A 118 " --> pdb=" O   ASP A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 145
      No H-bonds generated for 'chain 'A' and resid 143 through 145'
    Processing helix  chain 'A' and resid 146 through 158
      removed outlier: 3.996A  pdb=" N   LYS A 152 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 191
    Processing helix  chain 'A' and resid 192 through 194
      No H-bonds generated for 'chain 'A' and resid 192 through 194'
    Processing helix  chain 'A' and resid 206 through 217
      removed outlier: 3.745A  pdb=" N   MET A 212 " --> pdb=" O   VAL A 208 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 251
      removed outlier: 4.168A  pdb=" N   PHE A 250 " --> pdb=" O   ARG A 246 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ASP A 251 " --> pdb=" O   GLY A 247 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 246 through 251'
    Processing helix  chain 'A' and resid 253 through 259
      removed outlier: 4.378A  pdb=" N   ARG A 257 " --> pdb=" O   PHE A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 273
    Processing helix  chain 'A' and resid 280 through 294
    Processing helix  chain 'A' and resid 299 through 301
      No H-bonds generated for 'chain 'A' and resid 299 through 301'
    Processing helix  chain 'A' and resid 316 through 320
      removed outlier: 3.621A  pdb=" N   THR A 319 " --> pdb=" O   GLY A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 447
    Processing helix  chain 'A' and resid 454 through 476
      removed outlier: 3.557A  pdb=" N   PHE A 465 " --> pdb=" O   ALA A 461 " (cutoff:3.500A)
      Proline residue:  A 467  - end of helix
    Processing helix  chain 'A' and resid 489 through 500
      removed outlier: 4.037A  pdb=" N   ASP A 493 " --> pdb=" O   PRO A 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 41 through 47
    Processing helix  chain 'B' and resid 47 through 58
      removed outlier: 3.605A  pdb=" N   THR B  51 " --> pdb=" O   LYS B  47 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ASP B  58 " --> pdb=" O   TRP B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 85
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 91 through 93
      No H-bonds generated for 'chain 'B' and resid 91 through 93'
    Processing helix  chain 'B' and resid 94 through 103
      removed outlier: 3.554A  pdb=" N   LEU B  98 " --> pdb=" O   GLU B  94 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   GLU B  99 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 127
      removed outlier: 3.591A  pdb=" N   TYR B 118 " --> pdb=" O   ASP B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 145
      No H-bonds generated for 'chain 'B' and resid 143 through 145'
    Processing helix  chain 'B' and resid 146 through 158
      removed outlier: 3.895A  pdb=" N   LYS B 152 " --> pdb=" O   GLU B 148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 191
    Processing helix  chain 'B' and resid 192 through 194
      No H-bonds generated for 'chain 'B' and resid 192 through 194'
    Processing helix  chain 'B' and resid 206 through 217
      removed outlier: 4.019A  pdb=" N   MET B 212 " --> pdb=" O   VAL B 208 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   VAL B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 259
    Processing helix  chain 'B' and resid 262 through 273
    Processing helix  chain 'B' and resid 280 through 294
    Processing helix  chain 'B' and resid 299 through 301
      No H-bonds generated for 'chain 'B' and resid 299 through 301'
    Processing helix  chain 'B' and resid 316 through 320
    Processing helix  chain 'B' and resid 435 through 447
      removed outlier: 3.571A  pdb=" N   ARG B 439 " --> pdb=" O   ASP B 435 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   VAL B 444 " --> pdb=" O   LEU B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 476
      Proline residue:  B 467  - end of helix
    Processing helix  chain 'B' and resid 489 through 500
      removed outlier: 4.054A  pdb=" N   ASP B 493 " --> pdb=" O   PRO B 489 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 109
      removed outlier: 8.558A  pdb=" N   SER A 106 " --> pdb=" O   THR A  65 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   ILE A  67 " --> pdb=" O   SER A 106 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   VAL A 108 " --> pdb=" O   ILE A  67 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   GLY A  69 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   ILE A  33 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   TYR A 139 " --> pdb=" O   ILE A  33 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   ILE A  35 " --> pdb=" O   TYR A 139 " (cutoff:3.500A)
      removed outlier: 8.097A  pdb=" N   TYR A 197 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE A 167 " --> pdb=" O   TYR A 197 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 421
      removed outlier: 8.494A  pdb=" N   ILE A 355 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   VAL A 233 " --> pdb=" O   ILE A 355 " (cutoff:3.500A)
      removed outlier: 7.328A  pdb=" N   ARG A 357 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   LEU A 235 " --> pdb=" O   ARG A 357 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   GLY A 359 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   PHE A 237 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   CYS A 358 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
      removed outlier: 9.491A  pdb=" N   ILE A 480 " --> pdb=" O   VAL A 303 " (cutoff:3.500A)
      removed outlier: 7.075A  pdb=" N   LEU A 305 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   TYR A 482 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   GLN A 307 " --> pdb=" O   TYR A 482 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 405 through 407
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 109
      removed outlier: 6.221A  pdb=" N   ILE B  33 " --> pdb=" O   LEU B 137 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   TYR B 139 " --> pdb=" O   ILE B  33 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   ILE B  35 " --> pdb=" O   TYR B 139 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARG B 166 " --> pdb=" O   ARG B 136 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   ILE B 168 " --> pdb=" O   PHE B 138 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   TYR B 197 " --> pdb=" O   ASN B 165 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ILE B 167 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 420 through 421
      removed outlier: 3.534A  pdb=" N   LEU B 420 " --> pdb=" O   THR B 402 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ALA B 367 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 8.612A  pdb=" N   ILE B 355 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   VAL B 233 " --> pdb=" O   ILE B 355 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   ARG B 357 " --> pdb=" O   VAL B 233 " (cutoff:3.500A)
      removed outlier: 5.910A  pdb=" N   LEU B 235 " --> pdb=" O   ARG B 357 " (cutoff:3.500A)
      removed outlier: 7.831A  pdb=" N   GLY B 359 " --> pdb=" O   LEU B 235 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   PHE B 237 " --> pdb=" O   GLY B 359 " (cutoff:3.500A)
      removed outlier: 9.297A  pdb=" N   ILE B 480 " --> pdb=" O   VAL B 303 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   LEU B 305 " --> pdb=" O   ILE B 480 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   TYR B 482 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   GLN B 307 " --> pdb=" O   TYR B 482 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 405 through 407

    295 hydrogen bonds defined for protein.
    846 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.22

  Time building geometry restraints manager: 2.27 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: 1498
        1.46 -     1.58: 3684
        1.58 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 7766
  Sorted by residual:
  bond pdb=" CB  TRP B 225 "
       pdb=" CG  TRP B 225 "
    ideal  model  delta    sigma   weight residual
    1.498  1.461  0.037 3.10e-02 1.04e+03 1.44e+00
  bond pdb=" CB  GLU B 156 "
       pdb=" CG  GLU B 156 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.56e-01
  bond pdb=" CA  LYS B 403 "
       pdb=" C   LYS B 403 "
    ideal  model  delta    sigma   weight residual
    1.530  1.520  0.010 1.10e-02 8.26e+03 8.06e-01
  bond pdb=" CG  LEU A 235 "
       pdb=" CD1 LEU A 235 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.01e-01
  bond pdb=" CA  ILE B  36 "
       pdb=" CB  ILE B  36 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.11e-02 8.12e+03 6.37e-01
  ... (remaining 7761 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 10025
        1.26 -     2.52: 387
        2.52 -     3.78: 68
        3.78 -     5.04: 16
        5.04 -     6.30: 6
  Bond angle restraints: 10502
  Sorted by residual:
  angle pdb=" C   TRP A 462 "
        pdb=" N   ARG A 463 "
        pdb=" CA  ARG A 463 "
      ideal   model   delta    sigma   weight residual
     121.14  116.26    4.88 1.75e+00 3.27e-01 7.78e+00
  angle pdb=" N   SER A  29 "
        pdb=" CA  SER A  29 "
        pdb=" C   SER A  29 "
      ideal   model   delta    sigma   weight residual
     113.43  110.35    3.08 1.26e+00 6.30e-01 5.96e+00
  angle pdb=" C   LEU B 214 "
        pdb=" N   ARG B 215 "
        pdb=" CA  ARG B 215 "
      ideal   model   delta    sigma   weight residual
     120.68  124.78   -4.10 1.70e+00 3.46e-01 5.81e+00
  angle pdb=" N   LYS B 205 "
        pdb=" CA  LYS B 205 "
        pdb=" CB  LYS B 205 "
      ideal   model   delta    sigma   weight residual
     113.65  110.11    3.54 1.47e+00 4.63e-01 5.81e+00
  angle pdb=" N   SER B  29 "
        pdb=" CA  SER B  29 "
        pdb=" C   SER B  29 "
      ideal   model   delta    sigma   weight residual
     113.43  110.51    2.92 1.26e+00 6.30e-01 5.35e+00
  ... (remaining 10497 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.83: 4125
       16.83 -    33.66: 421
       33.66 -    50.50: 86
       50.50 -    67.33: 25
       67.33 -    84.16: 17
  Dihedral angle restraints: 4674
    sinusoidal: 1944
      harmonic: 2730
  Sorted by residual:
  dihedral pdb=" CA  ASN A 218 "
           pdb=" C   ASN A 218 "
           pdb=" N   ARG A 219 "
           pdb=" CA  ARG A 219 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.23   18.77     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  ARG B 227 "
           pdb=" C   ARG B 227 "
           pdb=" N   ASP B 228 "
           pdb=" CA  ASP B 228 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.39  -17.61     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  VAL A 259 "
           pdb=" C   VAL A 259 "
           pdb=" N   MET A 260 "
           pdb=" CA  MET A 260 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.72  -17.28     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 4671 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 617
       0.028 -    0.056: 300
       0.056 -    0.084: 117
       0.084 -    0.112: 70
       0.112 -    0.140: 20
  Chirality restraints: 1124
  Sorted by residual:
  chirality pdb=" CA  VAL B 369 "
            pdb=" N   VAL B 369 "
            pdb=" C   VAL B 369 "
            pdb=" CB  VAL B 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality pdb=" CA  VAL B 400 "
            pdb=" N   VAL B 400 "
            pdb=" C   VAL B 400 "
            pdb=" CB  VAL B 400 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.63e-01
  chirality pdb=" CA  VAL A 369 "
            pdb=" N   VAL A 369 "
            pdb=" C   VAL A 369 "
            pdb=" CB  VAL A 369 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 1121 not shown)

  Planarity restraints: 1374
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 480 "   -0.056 5.00e-02 4.00e+02   8.51e-02 1.16e+01
        pdb=" N   PRO A 481 "    0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO A 481 "   -0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A 481 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 222 "   -0.051 5.00e-02 4.00e+02   7.75e-02 9.61e+00
        pdb=" N   PRO A 223 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 223 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 223 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 352 "    0.032 5.00e-02 4.00e+02   4.83e-02 3.73e+00
        pdb=" N   PRO A 353 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 353 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 353 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1371 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 229
        2.71 -     3.26: 7699
        3.26 -     3.81: 12707
        3.81 -     4.35: 15586
        4.35 -     4.90: 26279
  Nonbonded interactions: 62500
  Sorted by model distance:
  nonbonded pdb=" O   TRP B 462 "
            pdb=" OG1 THR B 466 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   ALA A 115 "
            pdb=" NE2 GLN A 119 "
     model   vdw
     2.197 3.120
  nonbonded pdb=" OE1 GLU A 460 "
            pdb=" NH1 ARG A 463 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" NH1 ARG B 175 "
            pdb=" O   GLU B 252 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" OG  SER A 296 "
            pdb=" OE2 GLU A 345 "
     model   vdw
     2.245 3.040
  ... (remaining 62495 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: 0.04
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=0.50 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:             0.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     21.370
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6278
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7766  Z= 0.144
  Angle     :  0.602   6.301  10502  Z= 0.326
  Chirality :  0.044   0.140   1124
  Planarity :  0.005   0.085   1374
  Dihedral  : 15.200  84.160   2914
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 16.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.24 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.28), residues: 930
  helix:  0.31 (0.30), residues: 344
  sheet: -1.18 (0.39), residues: 162
  loop : -0.52 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 164 
 HIS   0.004   0.001   HIS B 155 
 PHE   0.024   0.002   PHE A 102 
 TYR   0.014   0.002   TYR B 484 
 ARG   0.006   0.001   ARG B 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15415 (  295)
  hydrogen bonds       : angle       6.67899 (  846)
  covalent geometry    : bond        0.00319 ( 7766)
  covalent geometry    : angle       0.60152 (10502)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7477 (ptpp) cc_final: 0.7265 (ptpp)
REVERT: B   87 PHE cc_start: 0.7357 (m-10) cc_final: 0.6997 (m-80)
REVERT: B  137 LEU cc_start: 0.7398 (tt) cc_final: 0.7152 (tt)
REVERT: B  345 GLU cc_start: 0.6537 (mm-30) cc_final: 0.6197 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1892
  time to fit residues: 39.9232
Evaluate side-chains
  114 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 83 optimal weight:    2.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 119 GLN
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 261 GLN
** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 GLN
B 153 ASN
** B 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4809 r_free = 0.4809 target = 0.231428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.195980 restraints weight = 10560.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.198946 restraints weight = 7446.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.202092 restraints weight = 5422.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.4529
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4529
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4529 r_free = 0.4529    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4529 r_free = 0.4529    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4529
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6450
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   7766  Z= 0.200
  Angle     :  0.667   8.027  10502  Z= 0.342
  Chirality :  0.047   0.168   1124
  Planarity :  0.005   0.062   1374
  Dihedral  :  4.790  21.237   1032
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 17.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.00 %
    Favored  : 88.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.28), residues: 930
  helix:  0.41 (0.30), residues: 328
  sheet: -1.20 (0.38), residues: 156
  loop : -0.71 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 164 
 HIS   0.005   0.001   HIS B 124 
 PHE   0.028   0.002   PHE A 102 
 TYR   0.017   0.002   TYR A 118 
 ARG   0.006   0.001   ARG B 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04125 (  295)
  hydrogen bonds       : angle       5.68878 (  846)
  covalent geometry    : bond        0.00476 ( 7766)
  covalent geometry    : angle       0.66740 (10502)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ASN cc_start: 0.6661 (m-40) cc_final: 0.6403 (m-40)
REVERT: A  292 LEU cc_start: 0.4639 (mt) cc_final: 0.4319 (mt)
REVERT: B   87 PHE cc_start: 0.7403 (m-10) cc_final: 0.7022 (m-80)
REVERT: B  120 ARG cc_start: 0.7331 (tmm-80) cc_final: 0.7028 (ttp-110)
REVERT: B  170 GLU cc_start: 0.6711 (tp30) cc_final: 0.6393 (tp30)
  outliers start: 12
  outliers final: 7
  residues processed: 148
  average time/residue: 0.1609
  time to fit residues: 33.5947
Evaluate side-chains
  130 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 17 optimal weight:   10.0000
   chunk 45 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0670
   chunk 72 optimal weight:    1.9990
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 90 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   overall best weight:    1.7724

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 165 ASN
B 388 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4829 r_free = 0.4829 target = 0.233153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.197675 restraints weight = 10730.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.201378 restraints weight = 7549.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.203904 restraints weight = 5512.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.4557
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4557
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4557 r_free = 0.4557    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4557 r_free = 0.4557    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4557
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6401
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7766  Z= 0.139
  Angle     :  0.592   7.356  10502  Z= 0.302
  Chirality :  0.045   0.167   1124
  Planarity :  0.004   0.052   1374
  Dihedral  :  4.591  19.572   1032
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 14.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.68 %
    Favored  : 85.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.28), residues: 930
  helix:  0.55 (0.30), residues: 328
  sheet: -1.24 (0.38), residues: 158
  loop : -0.72 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 349 
 HIS   0.005   0.001   HIS A 451 
 PHE   0.022   0.002   PHE A 102 
 TYR   0.015   0.002   TYR B 484 
 ARG   0.005   0.001   ARG B 136 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03554 (  295)
  hydrogen bonds       : angle       5.36724 (  846)
  covalent geometry    : bond        0.00326 ( 7766)
  covalent geometry    : angle       0.59218 (10502)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.839 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  135 ASN cc_start: 0.6667 (m-40) cc_final: 0.6450 (m-40)
REVERT: A  315 GLU cc_start: 0.7996 (mp0) cc_final: 0.6909 (tt0)
REVERT: B   87 PHE cc_start: 0.7395 (m-10) cc_final: 0.7121 (m-80)
REVERT: B  170 GLU cc_start: 0.6777 (tp30) cc_final: 0.6439 (tp30)
  outliers start: 15
  outliers final: 10
  residues processed: 145
  average time/residue: 0.1869
  time to fit residues: 38.0978
Evaluate side-chains
  128 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 62 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9990
   chunk 2 optimal weight:    5.9990
   chunk 4 optimal weight:    0.4980
   chunk 5 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9980
   chunk 50 optimal weight:    7.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.223793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.192632 restraints weight = 10234.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.192675 restraints weight = 8849.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.194734 restraints weight = 7871.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.4421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4420
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4420 r_free = 0.4420    target_work(ls_wunit_k1) = 0.192         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4421 r_free = 0.4421    target_work(ls_wunit_k1) = 0.192         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4421
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6299
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7766  Z= 0.113
  Angle     :  0.564   6.735  10502  Z= 0.288
  Chirality :  0.043   0.142   1124
  Planarity :  0.004   0.051   1374
  Dihedral  :  4.370  18.480   1032
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.73 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.28), residues: 930
  helix:  0.46 (0.30), residues: 340
  sheet: -1.08 (0.39), residues: 158
  loop : -0.61 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 164 
 HIS   0.005   0.001   HIS A 451 
 PHE   0.022   0.001   PHE A 102 
 TYR   0.015   0.001   TYR B 484 
 ARG   0.009   0.000   ARG A 439 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03249 (  295)
  hydrogen bonds       : angle       5.19410 (  846)
  covalent geometry    : bond        0.00260 ( 7766)
  covalent geometry    : angle       0.56441 (10502)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7588 (pttt) cc_final: 0.7327 (pttt)
REVERT: A  236 THR cc_start: 0.7827 (m) cc_final: 0.7584 (m)
REVERT: A  315 GLU cc_start: 0.7641 (mp0) cc_final: 0.6794 (tt0)
  outliers start: 18
  outliers final: 13
  residues processed: 143
  average time/residue: 0.1672
  time to fit residues: 34.0482
Evaluate side-chains
  135 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  356 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  499 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 74 optimal weight:    0.3980
   chunk 9 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 54 optimal weight:   20.0000
   chunk 83 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  64 ASN
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 388 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4814 r_free = 0.4814 target = 0.230965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.197035 restraints weight = 10706.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.199306 restraints weight = 7891.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.201626 restraints weight = 6223.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.4537
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4537 r_free = 0.4537    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4537 r_free = 0.4537    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4537
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6434
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7766  Z= 0.147
  Angle     :  0.593   7.123  10502  Z= 0.303
  Chirality :  0.044   0.151   1124
  Planarity :  0.004   0.052   1374
  Dihedral  :  4.513  19.331   1032
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.59 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.28), residues: 930
  helix:  0.36 (0.29), residues: 342
  sheet: -1.08 (0.37), residues: 174
  loop : -0.62 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 349 
 HIS   0.006   0.001   HIS A 451 
 PHE   0.023   0.002   PHE A 253 
 TYR   0.019   0.002   TYR A 401 
 ARG   0.006   0.000   ARG B  81 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03349 (  295)
  hydrogen bonds       : angle       5.19021 (  846)
  covalent geometry    : bond        0.00348 ( 7766)
  covalent geometry    : angle       0.59272 (10502)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  313 ASP cc_start: 0.7248 (m-30) cc_final: 0.6838 (m-30)
REVERT: A  315 GLU cc_start: 0.7981 (mp0) cc_final: 0.7081 (tt0)
REVERT: B  170 GLU cc_start: 0.6638 (tp30) cc_final: 0.6231 (tp30)
  outliers start: 23
  outliers final: 17
  residues processed: 143
  average time/residue: 0.1849
  time to fit residues: 37.2487
Evaluate side-chains
  137 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  113 ASP
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain B residue   54 TRP
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 49 optimal weight:   10.0000
   chunk 59 optimal weight:    8.9990
   chunk 8 optimal weight:    7.9990
   chunk 91 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 79 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9990
   chunk 87 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 209 GLN
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4790 r_free = 0.4790 target = 0.228179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4489 r_free = 0.4489 target = 0.194115 restraints weight = 10858.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.196036 restraints weight = 7890.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.198349 restraints weight = 6315.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.4506
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4506
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4506 r_free = 0.4506    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4506 r_free = 0.4506    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4506
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6518
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7766  Z= 0.177
  Angle     :  0.635   7.218  10502  Z= 0.322
  Chirality :  0.045   0.151   1124
  Planarity :  0.004   0.055   1374
  Dihedral  :  4.696  22.222   1032
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 18.41 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.28), residues: 930
  helix:  0.24 (0.29), residues: 342
  sheet: -1.44 (0.36), residues: 186
  loop : -0.63 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 349 
 HIS   0.007   0.001   HIS A 451 
 PHE   0.019   0.002   PHE A 102 
 TYR   0.016   0.002   TYR A 401 
 ARG   0.003   0.000   ARG B 370 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03509 (  295)
  hydrogen bonds       : angle       5.30064 (  846)
  covalent geometry    : bond        0.00420 ( 7766)
  covalent geometry    : angle       0.63462 (10502)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 TRP cc_start: 0.7617 (m-10) cc_final: 0.7337 (m-10)
REVERT: A  313 ASP cc_start: 0.7384 (m-30) cc_final: 0.7096 (m-30)
REVERT: A  315 GLU cc_start: 0.8091 (mp0) cc_final: 0.7235 (tt0)
  outliers start: 18
  outliers final: 12
  residues processed: 142
  average time/residue: 0.1863
  time to fit residues: 36.6436
Evaluate side-chains
  128 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  187 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    0.0040
   chunk 43 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 57 optimal weight:    8.9990
   chunk 27 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 47 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 49 optimal weight:    8.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    1.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4808 r_free = 0.4808 target = 0.230225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.196747 restraints weight = 10748.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.199185 restraints weight = 7539.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.201723 restraints weight = 5885.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.4540
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4540
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4540 r_free = 0.4540    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4540 r_free = 0.4540    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4540
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6436
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7766  Z= 0.130
  Angle     :  0.607   9.093  10502  Z= 0.308
  Chirality :  0.045   0.182   1124
  Planarity :  0.004   0.057   1374
  Dihedral  :  4.571  19.605   1032
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 19.27 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.28), residues: 930
  helix:  0.30 (0.29), residues: 342
  sheet: -1.10 (0.38), residues: 174
  loop : -0.67 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 349 
 HIS   0.007   0.001   HIS A 451 
 PHE   0.021   0.002   PHE A 102 
 TYR   0.013   0.002   TYR A 401 
 ARG   0.004   0.000   ARG B 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03280 (  295)
  hydrogen bonds       : angle       5.19999 (  846)
  covalent geometry    : bond        0.00309 ( 7766)
  covalent geometry    : angle       0.60734 (10502)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 TRP cc_start: 0.7554 (m-10) cc_final: 0.7308 (m-10)
REVERT: A  205 LYS cc_start: 0.7629 (tppt) cc_final: 0.7397 (tppt)
REVERT: A  313 ASP cc_start: 0.7342 (m-30) cc_final: 0.7053 (m-30)
REVERT: A  315 GLU cc_start: 0.8066 (mp0) cc_final: 0.7195 (tt0)
REVERT: A  439 ARG cc_start: 0.7525 (mmm160) cc_final: 0.6999 (mmm-85)
REVERT: B  170 GLU cc_start: 0.6696 (tp30) cc_final: 0.6297 (tp30)
REVERT: B  193 GLU cc_start: 0.5507 (tp30) cc_final: 0.5235 (tp30)
  outliers start: 21
  outliers final: 14
  residues processed: 139
  average time/residue: 0.1708
  time to fit residues: 33.2479
Evaluate side-chains
  133 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0070
   chunk 18 optimal weight:    1.9990
   chunk 30 optimal weight:   20.0000
   chunk 89 optimal weight:    9.9990
   chunk 60 optimal weight:    7.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    0.9602

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 388 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4701 r_free = 0.4701 target = 0.221561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.191066 restraints weight = 10439.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.191656 restraints weight = 9818.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.193947 restraints weight = 8446.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.4443
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4442
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4442 r_free = 0.4442    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4442 r_free = 0.4442    target_work(ls_wunit_k1) = 0.194         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4442
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7766  Z= 0.119
  Angle     :  0.595   8.864  10502  Z= 0.303
  Chirality :  0.045   0.180   1124
  Planarity :  0.004   0.057   1374
  Dihedral  :  4.474  18.516   1032
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 21.46 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.28), residues: 930
  helix:  0.32 (0.29), residues: 342
  sheet: -0.99 (0.37), residues: 180
  loop : -0.60 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 349 
 HIS   0.006   0.001   HIS A 451 
 PHE   0.020   0.001   PHE A 102 
 TYR   0.016   0.001   TYR A 401 
 ARG   0.006   0.000   ARG B 120 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03177 (  295)
  hydrogen bonds       : angle       5.13256 (  846)
  covalent geometry    : bond        0.00278 ( 7766)
  covalent geometry    : angle       0.59498 (10502)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 TRP cc_start: 0.7452 (m-10) cc_final: 0.7249 (m-10)
REVERT: A  205 LYS cc_start: 0.7490 (tppt) cc_final: 0.7246 (tppt)
REVERT: A  315 GLU cc_start: 0.7714 (mp0) cc_final: 0.7054 (tt0)
REVERT: A  439 ARG cc_start: 0.7392 (mmm160) cc_final: 0.6853 (mmm160)
REVERT: B  170 GLU cc_start: 0.6653 (tp30) cc_final: 0.6345 (tp30)
REVERT: B  193 GLU cc_start: 0.5401 (tp30) cc_final: 0.5080 (mm-30)
  outliers start: 18
  outliers final: 15
  residues processed: 140
  average time/residue: 0.1769
  time to fit residues: 35.0740
Evaluate side-chains
  138 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 28 optimal weight:   20.0000
   chunk 61 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0870
   chunk 56 optimal weight:   30.0000
   chunk 91 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 14 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    1.4762

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 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 = 0.4820 r_free = 0.4820 target = 0.231443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4533 r_free = 0.4533 target = 0.198009 restraints weight = 10878.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.200390 restraints weight = 7908.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.203135 restraints weight = 6067.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.4559
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4559
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4559 r_free = 0.4559    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.60   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4559 r_free = 0.4559    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4559
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6417
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7766  Z= 0.129
  Angle     :  0.610   8.780  10502  Z= 0.310
  Chirality :  0.044   0.180   1124
  Planarity :  0.004   0.055   1374
  Dihedral  :  4.514  18.753   1032
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 21.59 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.28), residues: 930
  helix:  0.44 (0.30), residues: 334
  sheet: -1.02 (0.37), residues: 180
  loop : -0.67 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 349 
 HIS   0.006   0.001   HIS A 451 
 PHE   0.021   0.001   PHE A 102 
 TYR   0.015   0.002   TYR A 401 
 ARG   0.004   0.000   ARG B 454 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03197 (  295)
  hydrogen bonds       : angle       5.14632 (  846)
  covalent geometry    : bond        0.00306 ( 7766)
  covalent geometry    : angle       0.60978 (10502)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.809 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 TRP cc_start: 0.7524 (m-10) cc_final: 0.7209 (m-10)
REVERT: A  205 LYS cc_start: 0.7600 (tppt) cc_final: 0.7270 (tppt)
REVERT: A  315 GLU cc_start: 0.7997 (mp0) cc_final: 0.7234 (tt0)
REVERT: A  413 PHE cc_start: 0.6368 (t80) cc_final: 0.6066 (m-10)
REVERT: A  439 ARG cc_start: 0.7483 (mmm160) cc_final: 0.6689 (mmm160)
REVERT: B  170 GLU cc_start: 0.6645 (tp30) cc_final: 0.6309 (tp30)
REVERT: B  193 GLU cc_start: 0.5375 (tp30) cc_final: 0.5075 (mm-30)
  outliers start: 18
  outliers final: 15
  residues processed: 138
  average time/residue: 0.1713
  time to fit residues: 33.3361
Evaluate side-chains
  138 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.907 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  352 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 78 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 79 optimal weight:   10.0000
   chunk 54 optimal weight:   20.0000
   chunk 86 optimal weight:    4.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 209 GLN
** B 263 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 = 0.4791 r_free = 0.4791 target = 0.227965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.194362 restraints weight = 10906.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.195886 restraints weight = 7940.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.198902 restraints weight = 6230.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.4523
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4523
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4523 r_free = 0.4523    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4523 r_free = 0.4523    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4523
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6504
moved from start:          0.3703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7766  Z= 0.165
  Angle     :  0.642   8.655  10502  Z= 0.329
  Chirality :  0.047   0.236   1124
  Planarity :  0.004   0.054   1374
  Dihedral  :  4.699  21.270   1032
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 16.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.38 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.59 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.28), residues: 930
  helix:  0.29 (0.30), residues: 334
  sheet: -1.10 (0.38), residues: 180
  loop : -0.73 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 164 
 HIS   0.008   0.001   HIS B 186 
 PHE   0.020   0.002   PHE A 102 
 TYR   0.017   0.002   TYR A 401 
 ARG   0.004   0.001   ARG A 166 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03478 (  295)
  hydrogen bonds       : angle       5.28548 (  846)
  covalent geometry    : bond        0.00395 ( 7766)
  covalent geometry    : angle       0.64229 (10502)

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

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

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1860 Ramachandran restraints generated.
    930 Oldfield, 0 Emsley, 930 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.903 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LYS cc_start: 0.7633 (tppt) cc_final: 0.7356 (tppt)
REVERT: A  315 GLU cc_start: 0.8075 (mp0) cc_final: 0.7302 (tt0)
REVERT: A  404 MET cc_start: 0.6738 (ppp) cc_final: 0.6488 (ppp)
REVERT: A  413 PHE cc_start: 0.6379 (t80) cc_final: 0.5958 (m-10)
REVERT: A  439 ARG cc_start: 0.7548 (mmm160) cc_final: 0.6716 (mmm160)
  outliers start: 21
  outliers final: 18
  residues processed: 137
  average time/residue: 0.1685
  time to fit residues: 33.1717
Evaluate side-chains
  139 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  145 THR
Chi-restraints excluded: chain A residue  167 ILE
Chi-restraints excluded: chain A residue  173 PHE
Chi-restraints excluded: chain A residue  191 PHE
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  292 LEU
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  368 GLU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  371 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 7 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 48 optimal weight:    0.0870
   chunk 33 optimal weight:    4.9990
   chunk 71 optimal weight:    7.9990
   chunk 64 optimal weight:    0.7980
   chunk 3 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 4 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    1.5762

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

Flipped N/Q/H residues before XYZ refinement:
** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 209 GLN
** B 263 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 = 0.4805 r_free = 0.4805 target = 0.229903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.196072 restraints weight = 10752.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.198951 restraints weight = 7747.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.201453 restraints weight = 5671.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.4542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4542 r_free = 0.4542    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4542 r_free = 0.4542    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.55   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7766  Z= 0.134
  Angle     :  0.629   8.571  10502  Z= 0.323
  Chirality :  0.046   0.282   1124
  Planarity :  0.004   0.055   1374
  Dihedral  :  4.638  19.423   1032
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 21.83 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.28), residues: 930
  helix:  0.30 (0.30), residues: 334
  sheet: -1.10 (0.39), residues: 174
  loop : -0.75 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 164 
 HIS   0.010   0.001   HIS B 155 
 PHE   0.021   0.002   PHE A 102 
 TYR   0.015   0.002   TYR A 401 
 ARG   0.007   0.000   ARG B 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03345 (  295)
  hydrogen bonds       : angle       5.25564 (  846)
  covalent geometry    : bond        0.00319 ( 7766)
  covalent geometry    : angle       0.62867 (10502)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2579.39 seconds
wall clock time: 45 minutes 31.49 seconds (2731.49 seconds total)