Starting phenix.real_space_refine
on Tue Mar  3 17:07:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tof_26031/03_2026/7tof_26031.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tof_26031/03_2026/7tof_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tof_26031/03_2026/7tof_26031.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tof_26031/03_2026/7tof_26031.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tof_26031/03_2026/7tof_26031.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tof_26031/03_2026/7tof_26031.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.63, per 1000 atoms: 0.21
  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: 0.82
  Conformation dependent library (CDL) restraints added in 318.1 milliseconds
  

  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: 0.24
  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: 1.24

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 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: 0.01
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:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.660
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.080
-------------------------------------------------------------------------------
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 : 16.07
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.006   0.001   ARG B 357 
 TYR   0.014   0.002   TYR B 484 
 PHE   0.024   0.002   PHE A 102 
 TRP   0.022   0.002   TRP B 164 
 HIS   0.004   0.001   HIS B 155 

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

*********************** 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  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LYS cc_start: 0.7476 (ptpp) cc_final: 0.7260 (ptpp)
REVERT: B   87 PHE cc_start: 0.7357 (m-10) cc_final: 0.6999 (m-80)
REVERT: B  137 LEU cc_start: 0.7398 (tt) cc_final: 0.7154 (tt)
REVERT: B  345 GLU cc_start: 0.6537 (mm-30) cc_final: 0.6198 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0823
  time to fit residues: 17.3245
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  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0870
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    7.9990
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:   20.0000
   overall best weight:    2.9764

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4807 r_free = 0.4807 target = 0.231274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.196053 restraints weight = 10710.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.199055 restraints weight = 7718.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.202054 restraints weight = 5591.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.202719 restraints weight = 4398.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.203215 restraints weight = 4101.723|
|-----------------------------------------------------------------------------|
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) = 0.201         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4542 r_free = 0.4542    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6425
moved from start:          0.1688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7766  Z= 0.190
  Angle     :  0.653   7.296  10502  Z= 0.335
  Chirality :  0.046   0.166   1124
  Planarity :  0.005   0.063   1374
  Dihedral  :  4.754  21.006   1032
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 17.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 10.24 %
    Favored  : 88.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.28), residues: 930
  helix:  0.42 (0.30), residues: 328
  sheet: -1.20 (0.38), residues: 156
  loop : -0.68 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 104 
 TYR   0.017   0.002   TYR A 118 
 PHE   0.029   0.002   PHE A 102 
 TRP   0.009   0.002   TRP A 349 
 HIS   0.005   0.001   HIS B 124 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 7766)
  covalent geometry    : angle       0.65325 (10502)
  hydrogen bonds       : bond        0.04174 (  295)
  hydrogen bonds       : angle       5.67214 (  846)

*********************** 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
  153 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ASN cc_start: 0.6590 (m-40) cc_final: 0.6388 (m-40)
REVERT: A  285 ARG cc_start: 0.6604 (mtp180) cc_final: 0.6355 (mtp180)
REVERT: A  292 LEU cc_start: 0.4657 (mt) cc_final: 0.4346 (mt)
REVERT: B   87 PHE cc_start: 0.7343 (m-10) cc_final: 0.6993 (m-80)
REVERT: B  120 ARG cc_start: 0.7238 (tmm-80) cc_final: 0.6958 (ttp-110)
REVERT: B  170 GLU cc_start: 0.6702 (tp30) cc_final: 0.6403 (tp30)
  outliers start: 12
  outliers final: 8
  residues processed: 145
  average time/residue: 0.0746
  time to fit residues: 15.5589
Evaluate side-chains
  127 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
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  167 ILE
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 8 optimal weight:    8.9990
   chunk 57 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 83 optimal weight:    3.9990
   chunk 38 optimal weight:    0.3980
   chunk 81 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 75 optimal weight:   20.0000
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 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 = 0.4747 r_free = 0.4747 target = 0.226367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.195805 restraints weight = 10150.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.197086 restraints weight = 9474.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.199222 restraints weight = 8030.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.200021 restraints weight = 6200.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.201379 restraints weight = 5228.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.4490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4490 r_free = 0.4490    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4490 r_free = 0.4490    target_work(ls_wunit_k1) = 0.200         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4490
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6238
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7766  Z= 0.113
  Angle     :  0.568   7.696  10502  Z= 0.292
  Chirality :  0.044   0.144   1124
  Planarity :  0.004   0.053   1374
  Dihedral  :  4.426  18.449   1032
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.80 %
    Favored  : 85.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.28), residues: 930
  helix:  0.62 (0.30), residues: 328
  sheet: -1.01 (0.38), residues: 156
  loop : -0.66 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 136 
 TYR   0.018   0.002   TYR B 484 
 PHE   0.022   0.001   PHE A 102 
 TRP   0.011   0.001   TRP A 349 
 HIS   0.006   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 7766)
  covalent geometry    : angle       0.56781 (10502)
  hydrogen bonds       : bond        0.03395 (  295)
  hydrogen bonds       : angle       5.32607 (  846)

*********************** 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
  156 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LYS cc_start: 0.7178 (tptp) cc_final: 0.5991 (tptp)
REVERT: A  236 THR cc_start: 0.7886 (m) cc_final: 0.7685 (m)
REVERT: A  292 LEU cc_start: 0.4194 (OUTLIER) cc_final: 0.3301 (mt)
REVERT: A  315 GLU cc_start: 0.7605 (mp0) cc_final: 0.6666 (tt0)
REVERT: A  443 ASP cc_start: 0.5769 (m-30) cc_final: 0.5101 (m-30)
REVERT: A  457 GLU cc_start: 0.7139 (tp30) cc_final: 0.6856 (tp30)
REVERT: B   87 PHE cc_start: 0.7134 (m-10) cc_final: 0.6727 (m-80)
  outliers start: 15
  outliers final: 8
  residues processed: 151
  average time/residue: 0.0719
  time to fit residues: 15.3890
Evaluate side-chains
  139 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
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  292 LEU
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  466 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 37 optimal weight:    9.9990
   chunk 5 optimal weight:   20.0000
   chunk 75 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
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 = 0.4788 r_free = 0.4788 target = 0.228052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.192491 restraints weight = 10806.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.195553 restraints weight = 7912.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.197918 restraints weight = 5969.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.199025 restraints weight = 4541.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.199481 restraints weight = 4199.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.4510
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4510
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4510 r_free = 0.4510    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4510 r_free = 0.4510    target_work(ls_wunit_k1) = 0.197         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4510
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6514
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   7766  Z= 0.202
  Angle     :  0.650   7.557  10502  Z= 0.331
  Chirality :  0.047   0.322   1124
  Planarity :  0.005   0.055   1374
  Dihedral  :  4.787  23.073   1032
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.12 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.28), residues: 930
  helix:  0.18 (0.29), residues: 342
  sheet: -1.48 (0.36), residues: 186
  loop : -0.57 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 136 
 TYR   0.021   0.002   TYR A 401 
 PHE   0.021   0.002   PHE A 253 
 TRP   0.013   0.002   TRP A 349 
 HIS   0.006   0.001   HIS B 263 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 7766)
  covalent geometry    : angle       0.65029 (10502)
  hydrogen bonds       : bond        0.03829 (  295)
  hydrogen bonds       : angle       5.39163 (  846)

*********************** 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
  155 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LYS cc_start: 0.7443 (tptp) cc_final: 0.6256 (tptp)
REVERT: A  313 ASP cc_start: 0.7340 (m-30) cc_final: 0.6903 (m-30)
REVERT: A  315 GLU cc_start: 0.8009 (mp0) cc_final: 0.7013 (tt0)
REVERT: A  443 ASP cc_start: 0.6368 (m-30) cc_final: 0.5610 (m-30)
REVERT: B   99 GLU cc_start: 0.7295 (mp0) cc_final: 0.7076 (pm20)
REVERT: B  170 GLU cc_start: 0.6769 (tp30) cc_final: 0.6471 (tp30)
  outliers start: 21
  outliers final: 14
  residues processed: 148
  average time/residue: 0.0710
  time to fit residues: 15.1527
Evaluate side-chains
  136 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 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  295 ILE
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  371 LEU
Chi-restraints excluded: chain B residue  441 ILE
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 78 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 86 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0570
   chunk 59 optimal weight:    9.9990
   chunk 6 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0670
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.2242

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4824 r_free = 0.4824 target = 0.231844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.197546 restraints weight = 10773.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.200962 restraints weight = 7671.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.203438 restraints weight = 5604.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.204185 restraints weight = 4202.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.204684 restraints weight = 4243.886|
|-----------------------------------------------------------------------------|
r_work (final): 0.4567
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4567
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4567 r_free = 0.4567    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4567 r_free = 0.4567    target_work(ls_wunit_k1) = 0.203         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4567
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6390
moved from start:          0.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7766  Z= 0.123
  Angle     :  0.585   7.799  10502  Z= 0.299
  Chirality :  0.045   0.266   1124
  Planarity :  0.004   0.054   1374
  Dihedral  :  4.553  19.223   1032
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.95 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.72 (0.28), residues: 930
  helix:  0.29 (0.29), residues: 342
  sheet: -1.34 (0.36), residues: 186
  loop : -0.56 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 136 
 TYR   0.014   0.002   TYR A 401 
 PHE   0.021   0.002   PHE A 102 
 TRP   0.011   0.002   TRP A 349 
 HIS   0.007   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 7766)
  covalent geometry    : angle       0.58550 (10502)
  hydrogen bonds       : bond        0.03276 (  295)
  hydrogen bonds       : angle       5.21103 (  846)

*********************** 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
  151 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LYS cc_start: 0.7241 (tptp) cc_final: 0.6017 (tptp)
REVERT: A  236 THR cc_start: 0.8038 (m) cc_final: 0.7802 (m)
REVERT: A  313 ASP cc_start: 0.7189 (m-30) cc_final: 0.6812 (m-30)
REVERT: A  315 GLU cc_start: 0.7967 (mp0) cc_final: 0.7089 (tt0)
REVERT: A  443 ASP cc_start: 0.6048 (m-30) cc_final: 0.5206 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 144
  average time/residue: 0.0682
  time to fit residues: 14.2320
Evaluate side-chains
  137 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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
Chi-restraints excluded: chain B residue  466 THR
Chi-restraints excluded: chain B residue  499 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 27 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 50 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   overall best weight:    1.5990

-------------------------------------------------------------------------------
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 388 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4817 r_free = 0.4817 target = 0.230990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.197220 restraints weight = 10802.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.199205 restraints weight = 7259.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.200935 restraints weight = 5434.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.201866 restraints weight = 4714.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.202275 restraints weight = 4420.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.4547
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4547
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4547 r_free = 0.4547    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4547 r_free = 0.4547    target_work(ls_wunit_k1) = 0.201         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4547
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6431
moved from start:          0.3021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7766  Z= 0.131
  Angle     :  0.595   8.355  10502  Z= 0.302
  Chirality :  0.045   0.324   1124
  Planarity :  0.004   0.054   1374
  Dihedral  :  4.529  19.139   1032
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.27 %
    Favored  : 78.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.28), residues: 930
  helix:  0.37 (0.29), residues: 342
  sheet: -1.31 (0.36), residues: 186
  loop : -0.55 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  81 
 TYR   0.016   0.002   TYR A 401 
 PHE   0.020   0.002   PHE A 102 
 TRP   0.017   0.002   TRP A 349 
 HIS   0.007   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7766)
  covalent geometry    : angle       0.59517 (10502)
  hydrogen bonds       : bond        0.03273 (  295)
  hydrogen bonds       : angle       5.20388 (  846)

*********************** 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
  159 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  205 LYS cc_start: 0.7234 (tptp) cc_final: 0.6079 (tptp)
REVERT: A  236 THR cc_start: 0.8010 (m) cc_final: 0.7779 (m)
REVERT: A  313 ASP cc_start: 0.7280 (m-30) cc_final: 0.7004 (m-30)
REVERT: A  315 GLU cc_start: 0.7994 (mp0) cc_final: 0.7134 (tt0)
REVERT: A  443 ASP cc_start: 0.5906 (m-30) cc_final: 0.5204 (m-30)
REVERT: B  104 ARG cc_start: 0.6570 (mtp180) cc_final: 0.6242 (mtm180)
REVERT: B  170 GLU cc_start: 0.6528 (tp30) cc_final: 0.6156 (tp30)
  outliers start: 22
  outliers final: 15
  residues processed: 151
  average time/residue: 0.0679
  time to fit residues: 14.8458
Evaluate side-chains
  140 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  292 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 61 optimal weight:    8.9990
   chunk 56 optimal weight:    0.0980
   chunk 85 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   chunk 59 optimal weight:    8.9990
   chunk 70 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 52 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.6188

-------------------------------------------------------------------------------
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**
** A 451 HIS ** 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 = 0.231442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.196989 restraints weight = 10820.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4512 r_free = 0.4512 target = 0.199772 restraints weight = 7975.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.202285 restraints weight = 5962.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.203427 restraints weight = 4466.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.203834 restraints weight = 4132.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.4560
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4560 r_free = 0.4560    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4560 r_free = 0.4560    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6416
moved from start:          0.3208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7766  Z= 0.133
  Angle     :  0.601   8.144  10502  Z= 0.306
  Chirality :  0.046   0.319   1124
  Planarity :  0.004   0.055   1374
  Dihedral  :  4.546  18.874   1032
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 20.24 %
    Favored  : 76.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.28), residues: 930
  helix:  0.33 (0.29), residues: 342
  sheet: -1.06 (0.38), residues: 174
  loop : -0.64 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  81 
 TYR   0.015   0.002   TYR A 401 
 PHE   0.019   0.002   PHE A 102 
 TRP   0.014   0.002   TRP A 349 
 HIS   0.006   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7766)
  covalent geometry    : angle       0.60051 (10502)
  hydrogen bonds       : bond        0.03247 (  295)
  hydrogen bonds       : angle       5.17973 (  846)

*********************** 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
  154 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 TRP cc_start: 0.7585 (m-10) cc_final: 0.7324 (m-10)
REVERT: A  205 LYS cc_start: 0.7238 (tptp) cc_final: 0.6001 (tptp)
REVERT: A  236 THR cc_start: 0.8018 (m) cc_final: 0.7798 (m)
REVERT: A  313 ASP cc_start: 0.7267 (m-30) cc_final: 0.7008 (m-30)
REVERT: A  315 GLU cc_start: 0.7998 (mp0) cc_final: 0.7166 (tt0)
REVERT: A  443 ASP cc_start: 0.5902 (m-30) cc_final: 0.5130 (m-30)
REVERT: B  170 GLU cc_start: 0.6658 (tp30) cc_final: 0.6220 (tp30)
  outliers start: 23
  outliers final: 17
  residues processed: 144
  average time/residue: 0.0693
  time to fit residues: 14.1912
Evaluate side-chains
  139 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
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   76 THR
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  298 VAL
Chi-restraints excluded: chain B residue  352 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  466 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 89 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 9 optimal weight:   20.0000
   chunk 61 optimal weight:   10.0000
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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**
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 119 GLN
** B 263 HIS ** 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 = 0.4805 r_free = 0.4805 target = 0.229777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.195967 restraints weight = 10796.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.196962 restraints weight = 7297.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.198207 restraints weight = 6233.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.199701 restraints weight = 5076.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4516 r_free = 0.4516 target = 0.200289 restraints weight = 4685.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.4533
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4533
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4533 r_free = 0.4533    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4533 r_free = 0.4533    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4533
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.3424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7766  Z= 0.153
  Angle     :  0.626   8.775  10502  Z= 0.317
  Chirality :  0.047   0.340   1124
  Planarity :  0.004   0.055   1374
  Dihedral  :  4.666  20.356   1032
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 16.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.10 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.28), residues: 930
  helix:  0.31 (0.29), residues: 342
  sheet: -1.10 (0.37), residues: 180
  loop : -0.64 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  81 
 TYR   0.018   0.002   TYR A 249 
 PHE   0.018   0.002   PHE A 102 
 TRP   0.015   0.002   TRP A 349 
 HIS   0.007   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 7766)
  covalent geometry    : angle       0.62646 (10502)
  hydrogen bonds       : bond        0.03315 (  295)
  hydrogen bonds       : angle       5.21522 (  846)

*********************** 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
  153 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 130
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 TRP cc_start: 0.7615 (m-10) cc_final: 0.7344 (m-10)
REVERT: A  205 LYS cc_start: 0.7208 (tptp) cc_final: 0.5953 (tptp)
REVERT: A  313 ASP cc_start: 0.7367 (m-30) cc_final: 0.7080 (m-30)
REVERT: A  315 GLU cc_start: 0.8099 (mp0) cc_final: 0.7280 (tt0)
REVERT: A  404 MET cc_start: 0.6554 (ppp) cc_final: 0.6326 (ppp)
REVERT: A  412 PHE cc_start: 0.6114 (t80) cc_final: 0.5753 (t80)
REVERT: A  443 ASP cc_start: 0.6058 (m-30) cc_final: 0.5307 (m-30)
REVERT: B   99 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7105 (pm20)
REVERT: B  170 GLU cc_start: 0.6700 (tp30) cc_final: 0.6251 (tp30)
REVERT: B  193 GLU cc_start: 0.5455 (tp30) cc_final: 0.5176 (tp30)
  outliers start: 23
  outliers final: 17
  residues processed: 143
  average time/residue: 0.0747
  time to fit residues: 15.1729
Evaluate side-chains
  138 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
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  368 GLU
Chi-restraints excluded: chain A residue  398 GLU
Chi-restraints excluded: chain B residue   68 VAL
Chi-restraints excluded: chain B residue   76 THR
Chi-restraints excluded: chain B residue   99 GLU
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  207 MET
Chi-restraints excluded: chain B residue  269 CYS
Chi-restraints excluded: chain B residue  292 LEU
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 2 optimal weight:    0.7980
   chunk 9 optimal weight:    9.9990
   chunk 25 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 28 optimal weight:   20.0000
   chunk 59 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 54 optimal weight:   10.0000
   chunk 76 optimal weight:    4.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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**
** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 388 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 = 0.223141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.191485 restraints weight = 10050.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.193782 restraints weight = 8008.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.195795 restraints weight = 6542.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.196685 restraints weight = 4850.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.197285 restraints weight = 4404.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.4464
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4464
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4464 r_free = 0.4464    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4464 r_free = 0.4464    target_work(ls_wunit_k1) = 0.196         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4464
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6328
moved from start:          0.3562

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= 0.121
  Angle     :  0.611   8.831  10502  Z= 0.309
  Chirality :  0.045   0.296   1124
  Planarity :  0.004   0.057   1374
  Dihedral  :  4.514  18.440   1032
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 21.22 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.28), residues: 930
  helix:  0.51 (0.30), residues: 334
  sheet: -0.99 (0.38), residues: 180
  loop : -0.63 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  81 
 TYR   0.018   0.002   TYR A 343 
 PHE   0.020   0.001   PHE A 102 
 TRP   0.011   0.001   TRP A 349 
 HIS   0.006   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7766)
  covalent geometry    : angle       0.61054 (10502)
  hydrogen bonds       : bond        0.03134 (  295)
  hydrogen bonds       : angle       5.13992 (  846)

*********************** 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
  152 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 TRP cc_start: 0.7454 (m-10) cc_final: 0.7247 (m-10)
REVERT: A  205 LYS cc_start: 0.7120 (tptp) cc_final: 0.6319 (tptp)
REVERT: A  315 GLU cc_start: 0.7689 (mp0) cc_final: 0.7061 (tt0)
REVERT: A  413 PHE cc_start: 0.6458 (t80) cc_final: 0.6040 (m-10)
REVERT: A  443 ASP cc_start: 0.5747 (m-30) cc_final: 0.5033 (m-30)
REVERT: B   99 GLU cc_start: 0.7337 (OUTLIER) cc_final: 0.7058 (pm20)
REVERT: B  170 GLU cc_start: 0.6679 (tp30) cc_final: 0.6164 (tp30)
REVERT: B  193 GLU cc_start: 0.5357 (tp30) cc_final: 0.4957 (mm-30)
  outliers start: 20
  outliers final: 16
  residues processed: 143
  average time/residue: 0.0651
  time to fit residues: 13.8887
Evaluate side-chains
  140 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 123
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 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  264 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   76 THR
Chi-restraints excluded: chain B residue   99 GLU
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  292 LEU
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 5 optimal weight:    5.9990
   chunk 47 optimal weight:    7.9990
   chunk 58 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 68 optimal weight:    9.9990
   chunk 56 optimal weight:   30.0000
   chunk 60 optimal weight:    8.9990
   chunk 82 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 129 HIS
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 124 HIS
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.216408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.184699 restraints weight = 10093.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.185997 restraints weight = 7527.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.187898 restraints weight = 6677.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.188681 restraints weight = 4908.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.189689 restraints weight = 4383.573|
|-----------------------------------------------------------------------------|
r_work (final): 0.4374
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4373
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4373 r_free = 0.4373    target_work(ls_wunit_k1) = 0.185         |
| occupancies: max = 1.00  min = 0.61   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4373 r_free = 0.4373    target_work(ls_wunit_k1) = 0.185         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4373
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6563
moved from start:          0.3897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   7766  Z= 0.241
  Angle     :  0.756   9.275  10502  Z= 0.386
  Chirality :  0.052   0.406   1124
  Planarity :  0.005   0.053   1374
  Dihedral  :  5.145  26.704   1032
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 19.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 21.10 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.28), residues: 930
  helix:  0.07 (0.29), residues: 342
  sheet: -1.54 (0.37), residues: 186
  loop : -0.74 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  81 
 TYR   0.023   0.003   TYR A 343 
 PHE   0.039   0.003   PHE A 253 
 TRP   0.027   0.003   TRP A 164 
 HIS   0.010   0.002   HIS B 186 

Details of bonding type rmsd
  covalent geometry    : bond        0.00574 ( 7766)
  covalent geometry    : angle       0.75619 (10502)
  hydrogen bonds       : bond        0.03931 (  295)
  hydrogen bonds       : angle       5.54097 (  846)

********************** 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
  147 residues out of total 822 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 TRP cc_start: 0.7684 (m-10) cc_final: 0.7359 (m-10)
REVERT: A  107 TYR cc_start: 0.7355 (t80) cc_final: 0.7126 (t80)
REVERT: A  205 LYS cc_start: 0.6844 (tptp) cc_final: 0.5830 (tptp)
REVERT: A  315 GLU cc_start: 0.7899 (mp0) cc_final: 0.7354 (tt0)
REVERT: A  443 ASP cc_start: 0.6565 (m-30) cc_final: 0.6038 (m-30)
REVERT: B  170 GLU cc_start: 0.6863 (tp30) cc_final: 0.6272 (tp30)
REVERT: B  193 GLU cc_start: 0.5620 (tp30) cc_final: 0.5326 (tp30)
  outliers start: 21
  outliers final: 15
  residues processed: 139
  average time/residue: 0.0609
  time to fit residues: 12.7849
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  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 ILE
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  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   76 THR
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 26 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   chunk 18 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 60 optimal weight:    4.9990
   chunk 86 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 129 HIS
A 201 HIS
** A 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 449 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 388 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 = 0.4670 r_free = 0.4670 target = 0.216696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4389 r_free = 0.4389 target = 0.184922 restraints weight = 10201.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.186524 restraints weight = 7808.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.188776 restraints weight = 6882.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.189436 restraints weight = 4981.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.190397 restraints weight = 4514.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.4384
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4384 r_free = 0.4384    target_work(ls_wunit_k1) = 0.187         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4384 r_free = 0.4384    target_work(ls_wunit_k1) = 0.187         |
| occupancies: max = 1.00  min = 0.58   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4384
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6532
moved from start:          0.4063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   7766  Z= 0.201
  Angle     :  0.716   9.845  10502  Z= 0.361
  Chirality :  0.050   0.378   1124
  Planarity :  0.005   0.056   1374
  Dihedral  :  5.065  23.923   1032
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 18.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 21.83 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.28), residues: 930
  helix:  0.09 (0.29), residues: 336
  sheet: -1.47 (0.38), residues: 174
  loop : -0.79 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 166 
 TYR   0.020   0.002   TYR A 343 
 PHE   0.031   0.002   PHE A 253 
 TRP   0.017   0.002   TRP A 349 
 HIS   0.007   0.001   HIS A 451 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 7766)
  covalent geometry    : angle       0.71601 (10502)
  hydrogen bonds       : bond        0.03751 (  295)
  hydrogen bonds       : angle       5.52079 (  846)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1260.38 seconds
wall clock time: 22 minutes 30.93 seconds (1350.93 seconds total)