Starting phenix.real_space_refine
on Mon Jun  9 12:22:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fej_29029/06_2025/8fej_29029.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fej_29029/06_2025/8fej_29029.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fej_29029/06_2025/8fej_29029.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fej_29029/06_2025/8fej_29029.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fej_29029/06_2025/8fej_29029.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fej_29029/06_2025/8fej_29029.cif"
  }
  resolution = 4.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.009 sd=   0.098
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      54      5.16       5
     C    6606      2.51       5
     N    1743      2.21       5
     O    2061      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10464
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 3488
          Classifications: {'peptide': 456}
          Link IDs: {'PTRANS': 15, 'TRANS': 440}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 6.59, per 1000 atoms: 0.63
  Number of scatterers: 10464
  At special positions: 0
  Unit cell: (105.84, 111.24, 123.12, 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      54     16.00
     O    2061      8.00
     N    1743      7.00
     C    6606      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  66 " - pdb=" SG  CYS A 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS A 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 350 " - pdb=" SG  CYS A 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 389 " - pdb=" SG  CYS A 412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  66 " - pdb=" SG  CYS C 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  66 " - pdb=" SG  CYS B 187 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 326 " - pdb=" SG  CYS C 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 326 " - pdb=" SG  CYS B 335 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 350 " - pdb=" SG  CYS C 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 358 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 382 " - pdb=" SG  CYS C 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 387 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 389 " - pdb=" SG  CYS C 412 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 389 " - pdb=" SG  CYS B 412 " distance=2.03

  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: 2.74
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2724 Ramachandran restraints generated.
    1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2556

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 24 sheets defined
      36.8% alpha, 13.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 64 through 66
      No H-bonds generated for 'chain 'A' and resid 64 through 66'
    Processing helix  chain 'A' and resid 67 through 90
      Proline residue:  A  84  - end of helix
    Processing helix  chain 'A' and resid 92 through 94
      No H-bonds generated for 'chain 'A' and resid 92 through 94'
    Processing helix  chain 'A' and resid 119 through 147
      removed outlier: 5.226A  pdb=" N   GLU A 134 " --> pdb=" O   HIS A 130 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   ASN A 135 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   ASN A 144 " --> pdb=" O   ALA A 140 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   ALA A 145 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 178
      removed outlier: 3.946A  pdb=" N   ASN A 175 " --> pdb=" O   GLY A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 209
      removed outlier: 3.652A  pdb=" N   ILE A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 213
      removed outlier: 3.923A  pdb=" N   LEU A 213 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 210 through 213'
    Processing helix  chain 'A' and resid 223 through 230
    Processing helix  chain 'A' and resid 234 through 242
      removed outlier: 3.585A  pdb=" N   LEU A 238 " --> pdb=" O   PHE A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 255
    Processing helix  chain 'A' and resid 344 through 352
    Processing helix  chain 'A' and resid 447 through 473
      removed outlier: 3.540A  pdb=" N   GLN A 463 " --> pdb=" O   ASN A 459 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASN A 464 " --> pdb=" O   GLN A 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 32
    Processing helix  chain 'B' and resid 64 through 66
      No H-bonds generated for 'chain 'B' and resid 64 through 66'
    Processing helix  chain 'B' and resid 67 through 90
      Proline residue:  B  84  - end of helix
    Processing helix  chain 'B' and resid 92 through 94
      No H-bonds generated for 'chain 'B' and resid 92 through 94'
    Processing helix  chain 'B' and resid 119 through 147
      removed outlier: 5.227A  pdb=" N   GLU B 134 " --> pdb=" O   HIS B 130 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   ASN B 135 " --> pdb=" O   ARG B 131 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   ASN B 144 " --> pdb=" O   ALA B 140 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   ALA B 145 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 178
      removed outlier: 3.945A  pdb=" N   ASN B 175 " --> pdb=" O   GLY B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 209
      removed outlier: 3.652A  pdb=" N   ILE B 190 " --> pdb=" O   SER B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 213
      removed outlier: 3.922A  pdb=" N   LEU B 213 " --> pdb=" O   GLY B 210 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 210 through 213'
    Processing helix  chain 'B' and resid 223 through 230
    Processing helix  chain 'B' and resid 234 through 242
      removed outlier: 3.586A  pdb=" N   LEU B 238 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 255
    Processing helix  chain 'B' and resid 344 through 352
    Processing helix  chain 'B' and resid 447 through 473
      removed outlier: 3.541A  pdb=" N   GLN B 463 " --> pdb=" O   ASN B 459 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ASN B 464 " --> pdb=" O   GLN B 460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 32
    Processing helix  chain 'C' and resid 64 through 66
      No H-bonds generated for 'chain 'C' and resid 64 through 66'
    Processing helix  chain 'C' and resid 67 through 90
      Proline residue:  C  84  - end of helix
    Processing helix  chain 'C' and resid 92 through 94
      No H-bonds generated for 'chain 'C' and resid 92 through 94'
    Processing helix  chain 'C' and resid 119 through 147
      removed outlier: 5.226A  pdb=" N   GLU C 134 " --> pdb=" O   HIS C 130 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   ASN C 135 " --> pdb=" O   ARG C 131 " (cutoff:3.500A)
      removed outlier: 4.428A  pdb=" N   ASN C 144 " --> pdb=" O   ALA C 140 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   ALA C 145 " --> pdb=" O   ASN C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 178
      removed outlier: 3.945A  pdb=" N   ASN C 175 " --> pdb=" O   GLY C 172 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 186 through 209
      removed outlier: 3.652A  pdb=" N   ILE C 190 " --> pdb=" O   SER C 186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 210 through 213
      removed outlier: 3.922A  pdb=" N   LEU C 213 " --> pdb=" O   GLY C 210 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 210 through 213'
    Processing helix  chain 'C' and resid 223 through 230
    Processing helix  chain 'C' and resid 234 through 242
      removed outlier: 3.585A  pdb=" N   LEU C 238 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 255
    Processing helix  chain 'C' and resid 344 through 352
    Processing helix  chain 'C' and resid 447 through 473
      removed outlier: 3.540A  pdb=" N   GLN C 463 " --> pdb=" O   ASN C 459 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASN C 464 " --> pdb=" O   GLN C 460 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 39
      removed outlier: 6.135A  pdb=" N   GLU A 290 " --> pdb=" O   GLY A  36 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   THR A  38 " --> pdb=" O   VAL A 288 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL A 288 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 45
    Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55
      removed outlier: 3.700A  pdb=" N   ALA A 272 " --> pdb=" O   ASP A 263 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   ASP A 263 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   GLU A 274 " --> pdb=" O   ILE A 261 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   ILE A 261 " --> pdb=" O   GLU A 274 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97
    Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 156
    Processing sheet with id=AA6, first strand: chain 'A' and resid 221 through 222
      removed outlier: 3.536A  pdb=" N   ILE A 221 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 296 through 297
    Processing sheet with id=AA8, first strand: chain 'A' and resid 405 through 406
      removed outlier: 3.890A  pdb=" N   ALA A 380 " --> pdb=" O   SER A 405 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 415 through 417
      removed outlier: 7.972A  pdb=" N   LEU A 421 " --> pdb=" O   MET B 110 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 34 through 39
      removed outlier: 6.135A  pdb=" N   GLU B 290 " --> pdb=" O   GLY B  36 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   THR B  38 " --> pdb=" O   VAL B 288 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL B 288 " --> pdb=" O   THR B  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 42 through 45
    Processing sheet with id=AB3, first strand: chain 'B' and resid 49 through 55
      removed outlier: 3.700A  pdb=" N   ALA B 272 " --> pdb=" O   ASP B 263 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   ASP B 263 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   GLU B 274 " --> pdb=" O   ILE B 261 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   ILE B 261 " --> pdb=" O   GLU B 274 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 153 through 156
    Processing sheet with id=AB5, first strand: chain 'B' and resid 221 through 222
      removed outlier: 3.536A  pdb=" N   ILE B 221 " --> pdb=" O   GLY B 259 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 296 through 297
    Processing sheet with id=AB7, first strand: chain 'B' and resid 405 through 406
      removed outlier: 3.891A  pdb=" N   ALA B 380 " --> pdb=" O   SER B 405 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 415 through 417
      removed outlier: 7.916A  pdb=" N   LEU B 421 " --> pdb=" O   MET C 110 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 34 through 39
      removed outlier: 6.134A  pdb=" N   GLU C 290 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   THR C  38 " --> pdb=" O   VAL C 288 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL C 288 " --> pdb=" O   THR C  38 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 42 through 45
    Processing sheet with id=AC2, first strand: chain 'C' and resid 49 through 55
      removed outlier: 3.701A  pdb=" N   ALA C 272 " --> pdb=" O   ASP C 263 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   ASP C 263 " --> pdb=" O   ALA C 272 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   GLU C 274 " --> pdb=" O   ILE C 261 " (cutoff:3.500A)
      removed outlier: 7.619A  pdb=" N   ILE C 261 " --> pdb=" O   GLU C 274 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 153 through 156
    Processing sheet with id=AC4, first strand: chain 'C' and resid 221 through 222
      removed outlier: 3.536A  pdb=" N   ILE C 221 " --> pdb=" O   GLY C 259 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 296 through 297
    Processing sheet with id=AC6, first strand: chain 'C' and resid 372 through 374
      removed outlier: 3.890A  pdb=" N   ALA C 380 " --> pdb=" O   SER C 405 " (cutoff:3.500A)

    437 hydrogen bonds defined for protein.
    1158 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: 3.68

  Time building geometry restraints manager: 3.17 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3486
        1.35 -     1.46: 2114
        1.46 -     1.58: 4927
        1.58 -     1.70: 0
        1.70 -     1.81: 78
  Bond restraints: 10605
  Sorted by residual:
  bond pdb=" N   VAL C 181 "
       pdb=" CA  VAL C 181 "
    ideal  model  delta    sigma   weight residual
    1.459  1.467 -0.008 1.25e-02 6.40e+03 4.28e-01
  bond pdb=" N   VAL B 181 "
       pdb=" CA  VAL B 181 "
    ideal  model  delta    sigma   weight residual
    1.459  1.467 -0.008 1.25e-02 6.40e+03 3.68e-01
  bond pdb=" N   VAL A 181 "
       pdb=" CA  VAL A 181 "
    ideal  model  delta    sigma   weight residual
    1.459  1.466 -0.007 1.25e-02 6.40e+03 3.55e-01
  bond pdb=" CG  PRO A 216 "
       pdb=" CD  PRO A 216 "
    ideal  model  delta    sigma   weight residual
    1.503  1.485  0.018 3.40e-02 8.65e+02 2.67e-01
  bond pdb=" CG  PRO B 216 "
       pdb=" CD  PRO B 216 "
    ideal  model  delta    sigma   weight residual
    1.503  1.485  0.018 3.40e-02 8.65e+02 2.66e-01
  ... (remaining 10600 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 14177
        1.04 -     2.08: 169
        2.08 -     3.12: 48
        3.12 -     4.16: 6
        4.16 -     5.20: 18
  Bond angle restraints: 14418
  Sorted by residual:
  angle pdb=" C   PRO B 180 "
        pdb=" N   VAL B 181 "
        pdb=" CA  VAL B 181 "
      ideal   model   delta    sigma   weight residual
     121.97  126.16   -4.19 1.80e+00 3.09e-01 5.42e+00
  angle pdb=" C   PRO C 180 "
        pdb=" N   VAL C 181 "
        pdb=" CA  VAL C 181 "
      ideal   model   delta    sigma   weight residual
     121.97  126.15   -4.18 1.80e+00 3.09e-01 5.39e+00
  angle pdb=" C   PRO A 180 "
        pdb=" N   VAL A 181 "
        pdb=" CA  VAL A 181 "
      ideal   model   delta    sigma   weight residual
     121.97  126.15   -4.18 1.80e+00 3.09e-01 5.38e+00
  angle pdb=" CA  LEU C 455 "
        pdb=" CB  LEU C 455 "
        pdb=" CG  LEU C 455 "
      ideal   model   delta    sigma   weight residual
     116.30  121.50   -5.20 3.50e+00 8.16e-02 2.21e+00
  angle pdb=" CA  LEU B 455 "
        pdb=" CB  LEU B 455 "
        pdb=" CG  LEU B 455 "
      ideal   model   delta    sigma   weight residual
     116.30  121.45   -5.15 3.50e+00 8.16e-02 2.16e+00
  ... (remaining 14413 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.45: 5769
       16.45 -    32.90: 561
       32.90 -    49.35: 159
       49.35 -    65.80: 15
       65.80 -    82.25: 12
  Dihedral angle restraints: 6516
    sinusoidal: 2538
      harmonic: 3978
  Sorted by residual:
  dihedral pdb=" CA  LYS C  79 "
           pdb=" CB  LYS C  79 "
           pdb=" CG  LYS C  79 "
           pdb=" CD  LYS C  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.09   56.09     3      1.50e+01 4.44e-03 9.38e+00
  dihedral pdb=" CA  LYS B  79 "
           pdb=" CB  LYS B  79 "
           pdb=" CG  LYS B  79 "
           pdb=" CD  LYS B  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.08   56.08     3      1.50e+01 4.44e-03 9.38e+00
  dihedral pdb=" CA  LYS A  79 "
           pdb=" CB  LYS A  79 "
           pdb=" CG  LYS A  79 "
           pdb=" CD  LYS A  79 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.06   56.06     3      1.50e+01 4.44e-03 9.38e+00
  ... (remaining 6513 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 1113
       0.025 -    0.050: 359
       0.050 -    0.075: 136
       0.075 -    0.100: 70
       0.100 -    0.125: 77
  Chirality restraints: 1755
  Sorted by residual:
  chirality pdb=" CA  ILE B  57 "
            pdb=" N   ILE B  57 "
            pdb=" C   ILE B  57 "
            pdb=" CB  ILE B  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  ILE B 275 "
            pdb=" N   ILE B 275 "
            pdb=" C   ILE B 275 "
            pdb=" CB  ILE B 275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.91e-01
  chirality pdb=" CA  VAL A 444 "
            pdb=" N   VAL A 444 "
            pdb=" C   VAL A 444 "
            pdb=" CB  VAL A 444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 1752 not shown)

  Planarity restraints: 1854
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL C 368 "   -0.013 5.00e-02 4.00e+02   1.98e-02 6.30e-01
        pdb=" N   PRO C 369 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO C 369 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO C 369 "   -0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 368 "   -0.013 5.00e-02 4.00e+02   1.97e-02 6.22e-01
        pdb=" N   PRO A 369 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO A 369 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO A 369 "   -0.011 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 368 "   -0.013 5.00e-02 4.00e+02   1.96e-02 6.15e-01
        pdb=" N   PRO B 369 "    0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO B 369 "   -0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO B 369 "   -0.011 5.00e-02 4.00e+02
  ... (remaining 1851 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2244
        2.78 -     3.31: 9986
        3.31 -     3.84: 16675
        3.84 -     4.37: 18175
        4.37 -     4.90: 31657
  Nonbonded interactions: 78737
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A  50 "
            pdb=" O   MET A 241 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" NZ  LYS B  50 "
            pdb=" O   MET B 241 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" NZ  LYS C  50 "
            pdb=" O   MET C 241 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" ND2 ASN B 233 "
            pdb=" OE2 GLU B 236 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" ND2 ASN A 233 "
            pdb=" OE2 GLU A 236 "
     model   vdw
     2.289 3.120
  ... (remaining 78732 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.670
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6870
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      :  0.001   0.018  10620  Z= 0.065
  Angle     :  0.367   5.198  14448  Z= 0.189
  Chirality :  0.039   0.125   1755
  Planarity :  0.002   0.020   1854
  Dihedral  : 13.974  82.248   3915
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  2.86 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 14.94 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.24), residues: 1362
  helix:  2.10 (0.26), residues: 444
  sheet:  0.30 (0.38), residues: 165
  loop : -0.81 (0.23), residues: 753

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 303 
 HIS   0.000   0.000   HIS A 130 
 PHE   0.002   0.000   PHE C 371 
 TYR   0.008   0.000   TYR C 270 
 ARG   0.001   0.000   ARG C 104 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15393 (  437)
  hydrogen bonds       : angle       6.22454 ( 1158)
  SS BOND              : bond        0.00064 (   15)
  SS BOND              : angle       0.22342 (   30)
  covalent geometry    : bond        0.00118 (10605)
  covalent geometry    : angle       0.36772 (14418)

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

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

  2724 Ramachandran restraints generated.
    1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2724 Ramachandran restraints generated.
    1362 Oldfield, 0 Emsley, 1362 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 43
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 ASP cc_start: 0.9230 (t70) cc_final: 0.8663 (m-30)
REVERT: A  157 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8298 (mm-40)
REVERT: A  235 ASP cc_start: 0.8292 (m-30) cc_final: 0.8034 (p0)
REVERT: A  292 MET cc_start: 0.6644 (pmm) cc_final: 0.6059 (pmm)
REVERT: A  343 MET cc_start: 0.6173 (ttm) cc_final: 0.5092 (mtt)
REVERT: A  347 LEU cc_start: 0.2258 (OUTLIER) cc_final: 0.1922 (tp)
  outliers start: 17
  outliers final: 2
  residues processed: 58
  average time/residue: 0.1943
  time to fit residues: 14.4241
Evaluate side-chains
  24 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    0.0970
   chunk 102 optimal weight:    0.0870
   chunk 56 optimal weight:    0.6980
   chunk 34 optimal weight:    0.3980
   chunk 69 optimal weight:    0.9990
   chunk 54 optimal weight:   10.0000
   chunk 105 optimal weight:    0.2980
   chunk 40 optimal weight:    0.0060
   chunk 64 optimal weight:   20.0000
   chunk 78 optimal weight:    9.9990
   chunk 122 optimal weight:    0.4980
   overall best weight:    0.1772
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
C 100 ASN
C 453 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.055568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.048083 restraints weight = 55990.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.048282 restraints weight = 51650.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.048360 restraints weight = 48997.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10620  Z= 0.127
  Angle     :  0.560   7.679  14448  Z= 0.284
  Chirality :  0.045   0.229   1755
  Planarity :  0.003   0.044   1854
  Dihedral  :  3.150  17.671   1461
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  2.53 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.24), residues: 1362
  helix:  2.12 (0.25), residues: 441
  sheet:  0.26 (0.38), residues: 165
  loop : -0.83 (0.24), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 303 
 HIS   0.001   0.000   HIS B  24 
 PHE   0.013   0.002   PHE B 105 
 TYR   0.017   0.002   TYR B  74 
 ARG   0.030   0.001   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03661 (  437)
  hydrogen bonds       : angle       5.13922 ( 1158)
  SS BOND              : bond        0.00165 (   15)
  SS BOND              : angle       0.68156 (   30)
  covalent geometry    : bond        0.00254 (10605)
  covalent geometry    : angle       0.55993 (14418)

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

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

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1816 Ramachandran restraints generated.
    908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 27
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   72 ASP cc_start: 0.8781 (t70) cc_final: 0.8085 (m-30)
REVERT: C  151 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6848 (mp0)
REVERT: C  157 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8728 (mm-40)
REVERT: C  230 PHE cc_start: 0.8426 (t80) cc_final: 0.8101 (t80)
REVERT: C  343 MET cc_start: 0.5308 (ttm) cc_final: 0.3558 (mtt)
  outliers start: 2
  outliers final: 1
  residues processed: 29
  average time/residue: 0.2288
  time to fit residues: 8.6898
Evaluate side-chains
  22 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 7 optimal weight:    0.0170
   chunk 51 optimal weight:    0.7980
   chunk 109 optimal weight:    6.9990
   chunk 102 optimal weight:    0.0050
   chunk 131 optimal weight:    0.9990
   chunk 115 optimal weight:   20.0000
   chunk 67 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0970
   chunk 55 optimal weight:    0.3980
   chunk 52 optimal weight:    4.9990
   chunk 75 optimal weight:    6.9990
   overall best weight:    0.2630
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.056047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.048322 restraints weight = 56179.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.048380 restraints weight = 53078.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.048390 restraints weight = 51594.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6987
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  10620  Z= 0.107
  Angle     :  0.504   7.981  14448  Z= 0.256
  Chirality :  0.042   0.151   1755
  Planarity :  0.004   0.064   1854
  Dihedral  :  2.979  11.628   1461
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.23), residues: 1362
  helix:  1.82 (0.25), residues: 441
  sheet:  0.06 (0.39), residues: 165
  loop : -0.93 (0.23), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 303 
 HIS   0.001   0.000   HIS A  24 
 PHE   0.009   0.001   PHE B 105 
 TYR   0.010   0.001   TYR B  74 
 ARG   0.012   0.001   ARG C 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03046 (  437)
  hydrogen bonds       : angle       4.86992 ( 1158)
  SS BOND              : bond        0.00064 (   15)
  SS BOND              : angle       0.39392 (   30)
  covalent geometry    : bond        0.00210 (10605)
  covalent geometry    : angle       0.50409 (14418)

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

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

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 ASP cc_start: 0.8969 (t70) cc_final: 0.8369 (m-30)
REVERT: B  110 MET cc_start: 0.7945 (tpt) cc_final: 0.7192 (pmm)
REVERT: B  157 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8324 (mm-40)
REVERT: B  230 PHE cc_start: 0.8630 (t80) cc_final: 0.8358 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1681
  time to fit residues: 5.6303
Evaluate side-chains
  18 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 105 optimal weight:    1.9990
   chunk 129 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 98 optimal weight:    0.0070
   chunk 93 optimal weight:    0.9990
   chunk 1 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 54 optimal weight:    9.9990
   chunk 103 optimal weight:    0.0870
   overall best weight:    0.5578
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.055470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.047776 restraints weight = 56194.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.047929 restraints weight = 53536.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.048017 restraints weight = 51529.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7002
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10620  Z= 0.084
  Angle     :  0.474   7.654  14448  Z= 0.236
  Chirality :  0.041   0.128   1755
  Planarity :  0.004   0.059   1854
  Dihedral  :  3.061  16.230   1461
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.41 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.22), residues: 1362
  helix:  1.32 (0.24), residues: 441
  sheet: -0.21 (0.38), residues: 165
  loop : -1.05 (0.22), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 303 
 HIS   0.000   0.000   HIS C 130 
 PHE   0.027   0.002   PHE B 277 
 TYR   0.007   0.001   TYR B  74 
 ARG   0.003   0.000   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02469 (  437)
  hydrogen bonds       : angle       4.60911 ( 1158)
  SS BOND              : bond        0.00063 (   15)
  SS BOND              : angle       0.25258 (   30)
  covalent geometry    : bond        0.00170 (10605)
  covalent geometry    : angle       0.47408 (14418)

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

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

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 ASP cc_start: 0.8984 (t70) cc_final: 0.8367 (m-30)
REVERT: B  157 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8321 (mm-40)
REVERT: B  230 PHE cc_start: 0.8805 (t80) cc_final: 0.8481 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1346
  time to fit residues: 4.2303
Evaluate side-chains
  18 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 106 optimal weight:    0.7980
   chunk 77 optimal weight:   20.0000
   chunk 24 optimal weight:    0.2980
   chunk 83 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 120 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0020
   chunk 22 optimal weight:    0.3980
   chunk 134 optimal weight:    8.9990
   chunk 104 optimal weight:    0.2980
   overall best weight:    0.3588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.055366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.047617 restraints weight = 56342.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 16)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.047617 restraints weight = 53530.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.047617 restraints weight = 53530.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10620  Z= 0.085
  Angle     :  0.487   7.259  14448  Z= 0.237
  Chirality :  0.041   0.150   1755
  Planarity :  0.003   0.038   1854
  Dihedral  :  3.028  13.379   1461
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.29 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.22), residues: 1362
  helix:  1.38 (0.24), residues: 441
  sheet: -0.63 (0.37), residues: 165
  loop : -1.21 (0.22), residues: 756

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 303 
 HIS   0.001   0.000   HIS C 130 
 PHE   0.040   0.002   PHE C 277 
 TYR   0.006   0.001   TYR A  74 
 ARG   0.002   0.000   ARG C 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02456 (  437)
  hydrogen bonds       : angle       4.54902 ( 1158)
  SS BOND              : bond        0.00057 (   15)
  SS BOND              : angle       0.24549 (   30)
  covalent geometry    : bond        0.00174 (10605)
  covalent geometry    : angle       0.48699 (14418)

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

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

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 ASP cc_start: 0.9014 (t70) cc_final: 0.8407 (m-30)
REVERT: B  157 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8307 (mm-40)
REVERT: B  230 PHE cc_start: 0.8851 (t80) cc_final: 0.8491 (t80)
REVERT: B  241 MET cc_start: 0.3250 (ptm) cc_final: 0.2530 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1786
  time to fit residues: 5.2114
Evaluate side-chains
  18 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 89 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 116 optimal weight:    4.9990
   chunk 78 optimal weight:   10.0000
   chunk 39 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   chunk 91 optimal weight:    0.4980
   chunk 38 optimal weight:    8.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.3986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 100 ASN
** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.053928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.046355 restraints weight = 55866.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.046528 restraints weight = 53203.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.046528 restraints weight = 50679.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  10620  Z= 0.102
  Angle     :  0.495   6.633  14448  Z= 0.249
  Chirality :  0.042   0.154   1755
  Planarity :  0.006   0.124   1854
  Dihedral  :  3.084  14.704   1461
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.95 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.22), residues: 1362
  helix:  1.39 (0.24), residues: 438
  sheet: -0.83 (0.36), residues: 165
  loop : -1.24 (0.22), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 303 
 HIS   0.001   0.000   HIS B 253 
 PHE   0.015   0.002   PHE B 277 
 TYR   0.007   0.001   TYR A 202 
 ARG   0.001   0.000   ARG C 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02795 (  437)
  hydrogen bonds       : angle       4.58831 ( 1158)
  SS BOND              : bond        0.00113 (   15)
  SS BOND              : angle       0.36335 (   30)
  covalent geometry    : bond        0.00224 (10605)
  covalent geometry    : angle       0.49549 (14418)

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

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

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: B   72 ASP cc_start: 0.9096 (t70) cc_final: 0.8564 (m-30)
REVERT: B  157 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8333 (mm-40)
REVERT: B  230 PHE cc_start: 0.9003 (t80) cc_final: 0.8705 (t80)
REVERT: B  241 MET cc_start: 0.2928 (ptm) cc_final: 0.2682 (ptm)
REVERT: B  343 MET cc_start: 0.5488 (ttm) cc_final: 0.3549 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.1693
  time to fit residues: 5.6519
Evaluate side-chains
  19 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 1 optimal weight:   20.0000
   chunk 66 optimal weight:    0.9980
   chunk 49 optimal weight:    0.0970
   chunk 75 optimal weight:    0.0050
   chunk 132 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0980
   chunk 58 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 127 optimal weight:    0.0770
   chunk 6 optimal weight:    0.0040
   chunk 19 optimal weight:    6.9990
   overall best weight:    0.0562
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.054467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.046906 restraints weight = 56080.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.047099 restraints weight = 52812.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.047099 restraints weight = 50441.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.3615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10620  Z= 0.085
  Angle     :  0.486   8.184  14448  Z= 0.235
  Chirality :  0.041   0.150   1755
  Planarity :  0.003   0.048   1854
  Dihedral  :  2.968  13.080   1461
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.07 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.21), residues: 1362
  helix:  1.16 (0.24), residues: 438
  sheet: -0.84 (0.35), residues: 165
  loop : -1.29 (0.21), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 303 
 HIS   0.000   0.000   HIS B 130 
 PHE   0.007   0.001   PHE B 105 
 TYR   0.008   0.001   TYR C 202 
 ARG   0.003   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02397 (  437)
  hydrogen bonds       : angle       4.45800 ( 1158)
  SS BOND              : bond        0.00065 (   15)
  SS BOND              : angle       0.37153 (   30)
  covalent geometry    : bond        0.00177 (10605)
  covalent geometry    : angle       0.48578 (14418)

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

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

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   72 ASP cc_start: 0.9013 (t70) cc_final: 0.8426 (m-30)
REVERT: B  157 GLN cc_start: 0.8860 (mm-40) cc_final: 0.8439 (mm-40)
REVERT: B  230 PHE cc_start: 0.8920 (t80) cc_final: 0.8604 (t80)
REVERT: B  241 MET cc_start: 0.2727 (ptm) cc_final: 0.2295 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1349
  time to fit residues: 4.2936
Evaluate side-chains
  19 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 15 optimal weight:    0.0370
   chunk 20 optimal weight:    1.9990
   chunk 46 optimal weight:    8.9990
   chunk 65 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 55 optimal weight:    0.0170
   chunk 88 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 38 optimal weight:    6.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0170
   overall best weight:    0.5736
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 218 ASN
B 289 GLN
** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.054210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.046676 restraints weight = 56618.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 18)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.046706 restraints weight = 54230.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.046706 restraints weight = 53072.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  10620  Z= 0.087
  Angle     :  0.513   7.156  14448  Z= 0.254
  Chirality :  0.042   0.149   1755
  Planarity :  0.003   0.052   1854
  Dihedral  :  3.223  24.735   1461
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.17 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.22), residues: 1362
  helix:  1.22 (0.24), residues: 438
  sheet: -0.84 (0.35), residues: 165
  loop : -1.22 (0.22), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 303 
 HIS   0.000   0.000   HIS B 253 
 PHE   0.006   0.001   PHE B 105 
 TYR   0.006   0.001   TYR B 202 
 ARG   0.004   0.000   ARG C 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02560 (  437)
  hydrogen bonds       : angle       4.44051 ( 1158)
  SS BOND              : bond        0.00090 (   15)
  SS BOND              : angle       0.33537 (   30)
  covalent geometry    : bond        0.00181 (10605)
  covalent geometry    : angle       0.51353 (14418)

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

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

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: B   72 ASP cc_start: 0.9130 (t70) cc_final: 0.8598 (m-30)
REVERT: B  157 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8371 (mm-40)
REVERT: B  230 PHE cc_start: 0.9020 (t80) cc_final: 0.8725 (t80)
REVERT: B  241 MET cc_start: 0.2718 (ptm) cc_final: 0.2282 (ptt)
REVERT: B  343 MET cc_start: 0.5133 (ttm) cc_final: 0.3042 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1631
  time to fit residues: 4.8742
Evaluate side-chains
  19 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 95 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0270
   chunk 10 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0000
   chunk 68 optimal weight:    0.4980
   chunk 132 optimal weight:    0.0060
   chunk 128 optimal weight:    8.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.2458
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.054483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.047061 restraints weight = 55103.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.047115 restraints weight = 53032.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.047264 restraints weight = 51690.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019  10620  Z= 0.081
  Angle     :  0.488   7.030  14448  Z= 0.236
  Chirality :  0.041   0.139   1755
  Planarity :  0.003   0.045   1854
  Dihedral  :  3.150  22.230   1461
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.95 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.22), residues: 1362
  helix:  1.12 (0.24), residues: 438
  sheet: -0.83 (0.35), residues: 165
  loop : -1.17 (0.22), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP C 303 
 HIS   0.000   0.000   HIS C 130 
 PHE   0.007   0.001   PHE C 230 
 TYR   0.005   0.001   TYR C 202 
 ARG   0.003   0.000   ARG A 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02234 (  437)
  hydrogen bonds       : angle       4.32489 ( 1158)
  SS BOND              : bond        0.00086 (   15)
  SS BOND              : angle       0.36383 (   30)
  covalent geometry    : bond        0.00166 (10605)
  covalent geometry    : angle       0.48827 (14418)

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

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

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: B   72 ASP cc_start: 0.9030 (t70) cc_final: 0.8445 (m-30)
REVERT: B  157 GLN cc_start: 0.8880 (mm-40) cc_final: 0.8384 (mm-40)
REVERT: B  230 PHE cc_start: 0.9031 (t80) cc_final: 0.8772 (t80)
REVERT: B  343 MET cc_start: 0.5069 (ttm) cc_final: 0.3081 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1243
  time to fit residues: 4.0845
Evaluate side-chains
  20 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 82 optimal weight:    0.0010
   chunk 73 optimal weight:    0.0030
   chunk 4 optimal weight:    3.9990
   chunk 95 optimal weight:    0.5980
   chunk 123 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0670
   chunk 80 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0970
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.1532
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.054396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.046847 restraints weight = 55961.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.047040 restraints weight = 52732.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 11)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.047040 restraints weight = 49878.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.3941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017  10620  Z= 0.085
  Angle     :  0.493   6.922  14448  Z= 0.240
  Chirality :  0.042   0.146   1755
  Planarity :  0.003   0.037   1854
  Dihedral  :  3.001  14.562   1461
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.95 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.21), residues: 1362
  helix:  1.09 (0.24), residues: 438
  sheet: -0.79 (0.36), residues: 162
  loop : -1.20 (0.21), residues: 762

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 303 
 HIS   0.001   0.000   HIS C 130 
 PHE   0.020   0.002   PHE C 277 
 TYR   0.006   0.001   TYR B 202 
 ARG   0.002   0.000   ARG C 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02395 (  437)
  hydrogen bonds       : angle       4.25918 ( 1158)
  SS BOND              : bond        0.00072 (   15)
  SS BOND              : angle       0.34959 (   30)
  covalent geometry    : bond        0.00177 (10605)
  covalent geometry    : angle       0.49309 (14418)

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

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

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  908 Ramachandran restraints generated.
    454 Oldfield, 0 Emsley, 454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: B   72 ASP cc_start: 0.9016 (t70) cc_final: 0.8432 (m-30)
REVERT: B  157 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8393 (mm-40)
REVERT: B  230 PHE cc_start: 0.8948 (t80) cc_final: 0.8742 (t80)
REVERT: B  241 MET cc_start: 0.2683 (ptt) cc_final: 0.2397 (ptt)
REVERT: B  343 MET cc_start: 0.5178 (ttm) cc_final: 0.3153 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1362
  time to fit residues: 4.4703
Evaluate side-chains
  22 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 124 optimal weight:    0.0170
   chunk 41 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9990
   chunk 133 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   chunk 12 optimal weight:   20.0000
   chunk 22 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0570
   overall best weight:    0.6140
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.053340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.045654 restraints weight = 55381.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.045654 restraints weight = 52224.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.045654 restraints weight = 52226.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7090
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018  10620  Z= 0.078
  Angle     :  0.493   8.586  14448  Z= 0.237
  Chirality :  0.042   0.137   1755
  Planarity :  0.003   0.033   1854
  Dihedral  :  3.147  20.608   1461
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.39 %
    Favored  : 93.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.22), residues: 1362
  helix:  1.22 (0.24), residues: 438
  sheet: -0.91 (0.35), residues: 165
  loop : -1.24 (0.21), residues: 759

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B 303 
 HIS   0.000   0.000   HIS C 130 
 PHE   0.012   0.002   PHE C 277 
 TYR   0.007   0.001   TYR A 433 
 ARG   0.002   0.000   ARG C 232 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02256 (  437)
  hydrogen bonds       : angle       4.17568 ( 1158)
  SS BOND              : bond        0.00092 (   15)
  SS BOND              : angle       0.37033 (   30)
  covalent geometry    : bond        0.00165 (10605)
  covalent geometry    : angle       0.49272 (14418)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2551.23 seconds
wall clock time: 46 minutes 47.43 seconds (2807.43 seconds total)