Starting phenix.real_space_refine
on Tue Mar  3 17:54:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xji_33228/03_2026/7xji_33228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xji_33228/03_2026/7xji_33228.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xji_33228/03_2026/7xji_33228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xji_33228/03_2026/7xji_33228.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xji_33228/03_2026/7xji_33228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xji_33228/03_2026/7xji_33228.map"
  }
  resolution = 3.9
  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=   0.001 sd=   0.008
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: 5
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     Cl      1      4.86       5
     C    4977      2.51       5
     N    1381      2.21       5
     O    1446      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  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: 7851
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1884
          Classifications: {'peptide': 231}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 30
    Chain: "B"
      Number of atoms: 2543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2543
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
          Unresolved non-hydrogen bonds: 73
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 58
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 6, 'ASP:plan': 3, 'GLU:plan': 4}
          Unresolved non-hydrogen planarities: 63
    Chain: "N"
      Number of atoms: 950
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 950
          Classifications: {'peptide': 128}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 15
    Chain: "R"
      Number of atoms: 2052
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2052
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 16, 'TRANS': 259}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 39
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 4, 'GLU:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 35
    Chain: "G"
      Number of atoms: 393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 393
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "R"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'EI5': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.55, per 1000 atoms: 0.20
  Number of scatterers: 7851
  At special positions: 0
  Unit cell: (101.592, 77.688, 132.667, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      46     16.00
     O    1446      8.00
     N    1381      7.00
     C    4977      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 110 " - pdb=" SG  CYS R 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 189 " - pdb=" SG  CYS R 195 " distance=2.04

  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: 0.72
  Conformation dependent library (CDL) restraints added in 217.5 milliseconds
  

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1926

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 10 sheets defined
      40.5% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 39
      removed outlier: 3.513A  pdb=" N   GLU A  15 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 57
      removed outlier: 3.702A  pdb=" N   ILE A  56 " --> pdb=" O   GLY A  52 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   VAL A  57 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 52 through 57'
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.886A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 297 through 302
      removed outlier: 4.375A  pdb=" N   TYR A 301 " --> pdb=" O   LYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 306
      removed outlier: 3.547A  pdb=" N   ALA A 306 " --> pdb=" O   PRO A 303 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 303 through 306'
    Processing helix  chain 'A' and resid 321 through 341
      removed outlier: 3.553A  pdb=" N   ILE A 331 " --> pdb=" O   ALA A 327 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE A 338 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 381
      removed outlier: 3.899A  pdb=" N   ASP A 368 " --> pdb=" O   ARG A 364 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ASP A 371 " --> pdb=" O   ASN A 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.683A  pdb=" N   GLN B   6 " --> pdb=" O   SER B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.750A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.625A  pdb=" N   ASN N  31 " --> pdb=" O   THR N  28 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 28 through 32'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.640A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 64
      removed outlier: 3.951A  pdb=" N   ALA R  50 " --> pdb=" O   LEU R  46 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 65 through 69
      removed outlier: 3.560A  pdb=" N   GLN R  69 " --> pdb=" O   PRO R  66 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 90
      removed outlier: 3.880A  pdb=" N   VAL R  76 " --> pdb=" O   THR R  72 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 90 through 100
    Processing helix  chain 'R' and resid 106 through 141
    Processing helix  chain 'R' and resid 150 through 170
    Processing helix  chain 'R' and resid 201 through 213
    Processing helix  chain 'R' and resid 213 through 241
    Processing helix  chain 'R' and resid 289 through 318
      removed outlier: 4.493A  pdb=" N   CYS R 304 " --> pdb=" O   THR R 300 " (cutoff:3.500A)
      Proline residue:  R 307  - end of helix
    Processing helix  chain 'R' and resid 324 through 346
      removed outlier: 3.521A  pdb=" N   LEU R 328 " --> pdb=" O   PRO R 324 " (cutoff:3.500A)
      Proline residue:  R 343  - end of helix
    Processing helix  chain 'R' and resid 349 through 360
    Processing helix  chain 'G' and resid 11 through 23
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.510A  pdb=" N   TYR G  40 " --> pdb=" O   ASP G  36 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   CYS G  41 " --> pdb=" O   LEU G  37 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.792A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 3.586A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   HIS A  41 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   PHE A 222 " --> pdb=" O   HIS A  41 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   LEU A  43 " --> pdb=" O   PHE A 222 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 7.590A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 9.496A  pdb=" N   ALA A 243 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.612A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.857A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.222A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.235A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150
      removed outlier: 3.820A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191
      removed outlier: 3.674A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.722A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 4.341A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
      removed outlier: 3.531A  pdb=" N   GLN N   3 " --> pdb=" O   SER N  25 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   SER N  25 " --> pdb=" O   GLN N   3 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.615A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    390 hydrogen bonds defined for protein.
    1122 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: 1.00

  Time building geometry restraints manager: 0.89 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: 2590
        1.34 -     1.46: 1911
        1.46 -     1.58: 3445
        1.58 -     1.70: 0
        1.70 -     1.82: 62
  Bond restraints: 8008
  Sorted by residual:
  bond pdb=" C6  EI5 R 401 "
       pdb=" O1  EI5 R 401 "
    ideal  model  delta    sigma   weight residual
    1.246  1.306 -0.060 2.00e-02 2.50e+03 8.95e+00
  bond pdb=" C4  EI5 R 401 "
       pdb=" C6  EI5 R 401 "
    ideal  model  delta    sigma   weight residual
    1.528  1.488  0.040 2.00e-02 2.50e+03 4.04e+00
  bond pdb=" CB  PRO R 320 "
       pdb=" CG  PRO R 320 "
    ideal  model  delta    sigma   weight residual
    1.492  1.567 -0.075 5.00e-02 4.00e+02 2.26e+00
  bond pdb=" CA  ASN R 192 "
       pdb=" CB  ASN R 192 "
    ideal  model  delta    sigma   weight residual
    1.522  1.530 -0.008 7.00e-03 2.04e+04 1.37e+00
  bond pdb=" C16 EI5 R 401 "
       pdb=" O2  EI5 R 401 "
    ideal  model  delta    sigma   weight residual
    1.401  1.423 -0.022 2.00e-02 2.50e+03 1.25e+00
  ... (remaining 8003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 10638
        1.64 -     3.28: 197
        3.28 -     4.92: 35
        4.92 -     6.56: 14
        6.56 -     8.20: 3
  Bond angle restraints: 10887
  Sorted by residual:
  angle pdb=" N   VAL A 357 "
        pdb=" CA  VAL A 357 "
        pdb=" C   VAL A 357 "
      ideal   model   delta    sigma   weight residual
     112.43  108.30    4.13 9.20e-01 1.18e+00 2.02e+01
  angle pdb=" N   VAL R  37 "
        pdb=" CA  VAL R  37 "
        pdb=" C   VAL R  37 "
      ideal   model   delta    sigma   weight residual
     113.71  110.07    3.64 9.50e-01 1.11e+00 1.47e+01
  angle pdb=" C   LEU R 221 "
        pdb=" N   PHE R 222 "
        pdb=" CA  PHE R 222 "
      ideal   model   delta    sigma   weight residual
     120.68  114.20    6.48 1.70e+00 3.46e-01 1.45e+01
  angle pdb=" CA  CYS R 195 "
        pdb=" CB  CYS R 195 "
        pdb=" SG  CYS R 195 "
      ideal   model   delta    sigma   weight residual
     114.40  122.04   -7.64 2.30e+00 1.89e-01 1.10e+01
  angle pdb=" C   VAL R  90 "
        pdb=" N   VAL R  91 "
        pdb=" CA  VAL R  91 "
      ideal   model   delta    sigma   weight residual
     120.33  122.49   -2.16 8.00e-01 1.56e+00 7.28e+00
  ... (remaining 10882 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.75: 4398
       19.75 -    39.50: 319
       39.50 -    59.25: 38
       59.25 -    79.00: 9
       79.00 -    98.75: 6
  Dihedral angle restraints: 4770
    sinusoidal: 1794
      harmonic: 2976
  Sorted by residual:
  dihedral pdb=" CB  CYS R 110 "
           pdb=" SG  CYS R 110 "
           pdb=" SG  CYS R 196 "
           pdb=" CB  CYS R 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -177.52  -89.48     1      1.00e+01 1.00e-02 9.51e+01
  dihedral pdb=" CB  CYS R 189 "
           pdb=" SG  CYS R 189 "
           pdb=" SG  CYS R 195 "
           pdb=" CB  CYS R 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    4.82   88.18     1      1.00e+01 1.00e-02 9.30e+01
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.93  -54.93     1      1.00e+01 1.00e-02 4.08e+01
  ... (remaining 4767 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 878
       0.039 -    0.078: 281
       0.078 -    0.117: 85
       0.117 -    0.155: 13
       0.155 -    0.194: 1
  Chirality restraints: 1258
  Sorted by residual:
  chirality pdb=" CB  THR A 315 "
            pdb=" CA  THR A 315 "
            pdb=" OG1 THR A 315 "
            pdb=" CG2 THR A 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.44e-01
  chirality pdb=" CA  ILE R 202 "
            pdb=" N   ILE R 202 "
            pdb=" C   ILE R 202 "
            pdb=" CB  ILE R 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.29    0.14 2.00e-01 2.50e+01 4.86e-01
  chirality pdb=" CA  PRO R 320 "
            pdb=" N   PRO R 320 "
            pdb=" C   PRO R 320 "
            pdb=" CB  PRO R 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.66e-01
  ... (remaining 1255 not shown)

  Planarity restraints: 1394
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN R 342 "   -0.031 5.00e-02 4.00e+02   4.78e-02 3.66e+00
        pdb=" N   PRO R 343 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO R 343 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 343 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE R 341 "    0.013 2.00e-02 2.50e+03   1.31e-02 3.02e+00
        pdb=" CG  PHE R 341 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE R 341 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE R 341 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE R 341 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE R 341 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE R 341 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 319 "    0.027 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO R 320 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO R 320 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO R 320 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1391 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 265
        2.71 -     3.26: 7821
        3.26 -     3.81: 12399
        3.81 -     4.35: 15240
        4.35 -     4.90: 26286
  Nonbonded interactions: 62011
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.165 3.040
  nonbonded pdb=" OG1 THR B 128 "
            pdb=" O   ASN B 132 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG  SER B 147 "
            pdb=" O   MET B 188 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   ARG B 314 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OD2 ASP B 258 "
            pdb=" NH1 ARG G  27 "
     model   vdw
     2.289 3.120
  ... (remaining 62006 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.170
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.370
  Find NCS groups from input model:        0.020
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
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   0.075   8012  Z= 0.156
  Angle     :  0.608   8.196  10895  Z= 0.325
  Chirality :  0.042   0.194   1258
  Planarity :  0.004   0.048   1394
  Dihedral  : 13.923  98.747   2832
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.25 (0.27), residues: 1011
  helix:  0.90 (0.27), residues: 391
  sheet: -0.97 (0.35), residues: 221
  loop : -0.61 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 255 
 TYR   0.012   0.001   TYR R 204 
 PHE   0.031   0.002   PHE R 341 
 TRP   0.006   0.001   TRP A 271 
 HIS   0.002   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 8008)
  covalent geometry    : angle       0.60431 (10887)
  SS BOND              : bond        0.00280 (    4)
  SS BOND              : angle       2.40302 (    8)
  hydrogen bonds       : bond        0.19658 (  390)
  hydrogen bonds       : angle       7.35435 ( 1122)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  205 SER cc_start: 0.7508 (p) cc_final: 0.7221 (t)
REVERT: A  252 ASP cc_start: 0.8546 (t0) cc_final: 0.8223 (t0)
REVERT: A  304 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7615 (mm-30)
REVERT: A  344 ASP cc_start: 0.6738 (m-30) cc_final: 0.6388 (p0)
REVERT: B  145 TYR cc_start: 0.8429 (p90) cc_final: 0.8203 (p90)
REVERT: B  156 GLN cc_start: 0.8681 (mm110) cc_final: 0.8090 (mm-40)
REVERT: B  175 GLN cc_start: 0.7788 (pt0) cc_final: 0.7255 (mt0)
REVERT: B  188 MET cc_start: 0.8138 (mmm) cc_final: 0.7211 (mmm)
REVERT: B  262 MET cc_start: 0.7888 (mmm) cc_final: 0.7617 (mmp)
REVERT: N   82 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7857 (tm-30)
REVERT: N   84 ASN cc_start: 0.7227 (m-40) cc_final: 0.7004 (m-40)
REVERT: R  235 LEU cc_start: 0.8159 (tt) cc_final: 0.7909 (tt)
REVERT: G   19 LEU cc_start: 0.7467 (tp) cc_final: 0.6859 (tp)
REVERT: G   21 MET cc_start: 0.6481 (ttm) cc_final: 0.6185 (ttp)
REVERT: G   22 GLU cc_start: 0.5603 (mp0) cc_final: 0.4871 (mp0)
REVERT: G   32 LYS cc_start: 0.8459 (ptpt) cc_final: 0.7588 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.0745
  time to fit residues: 18.0205
Evaluate side-chains
  129 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:   30.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
B 230 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 332 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.128505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.106093 restraints weight = 11388.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.108193 restraints weight = 7685.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.109511 restraints weight = 5934.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.110398 restraints weight = 5028.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.111362 restraints weight = 4489.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   8012  Z= 0.242
  Angle     :  0.676   7.805  10895  Z= 0.352
  Chirality :  0.046   0.227   1258
  Planarity :  0.005   0.044   1394
  Dihedral  :  5.647  84.680   1132
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.15 %
    Favored  : 86.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.24 (0.27), residues: 1011
  helix:  1.05 (0.26), residues: 392
  sheet: -0.97 (0.37), residues: 196
  loop : -0.81 (0.30), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  49 
 TYR   0.018   0.002   TYR N  60 
 PHE   0.039   0.003   PHE R 222 
 TRP   0.012   0.002   TRP B 297 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00566 ( 8008)
  covalent geometry    : angle       0.67349 (10887)
  SS BOND              : bond        0.00294 (    4)
  SS BOND              : angle       2.39790 (    8)
  hydrogen bonds       : bond        0.04797 (  390)
  hydrogen bonds       : angle       5.31595 ( 1122)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  304 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7486 (mm-30)
REVERT: B   57 LYS cc_start: 0.8412 (mtmm) cc_final: 0.7977 (mtmm)
REVERT: B  145 TYR cc_start: 0.8720 (p90) cc_final: 0.8294 (p90)
REVERT: B  175 GLN cc_start: 0.7490 (pt0) cc_final: 0.7248 (mt0)
REVERT: B  188 MET cc_start: 0.8456 (mmm) cc_final: 0.8009 (mmm)
REVERT: B  331 SER cc_start: 0.8725 (t) cc_final: 0.8162 (t)
REVERT: B  333 ASP cc_start: 0.8213 (p0) cc_final: 0.7380 (p0)
REVERT: R  207 LEU cc_start: 0.8973 (tt) cc_final: 0.8766 (tt)
  outliers start: 19
  outliers final: 15
  residues processed: 141
  average time/residue: 0.0685
  time to fit residues: 14.1070
Evaluate side-chains
  130 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   81 THR
Chi-restraints excluded: chain R residue   86 VAL
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  211 VAL
Chi-restraints excluded: chain R residue  312 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 31 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 100 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.130654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.107551 restraints weight = 11108.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.110055 restraints weight = 7122.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.111727 restraints weight = 5269.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.112485 restraints weight = 4311.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.113263 restraints weight = 3863.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8012  Z= 0.121
  Angle     :  0.561   8.501  10895  Z= 0.287
  Chirality :  0.042   0.163   1258
  Planarity :  0.004   0.052   1394
  Dihedral  :  5.167  79.447   1132
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 12.01 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.12 (0.27), residues: 1011
  helix:  1.48 (0.27), residues: 387
  sheet: -0.83 (0.37), residues: 197
  loop : -0.70 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG N  38 
 TYR   0.014   0.001   TYR R 204 
 PHE   0.020   0.002   PHE R 222 
 TRP   0.013   0.001   TRP N  47 
 HIS   0.003   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8008)
  covalent geometry    : angle       0.55936 (10887)
  SS BOND              : bond        0.00246 (    4)
  SS BOND              : angle       1.82761 (    8)
  hydrogen bonds       : bond        0.03984 (  390)
  hydrogen bonds       : angle       4.91060 ( 1122)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 138
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7277 (mm-30)
REVERT: B   57 LYS cc_start: 0.8405 (mtmm) cc_final: 0.8179 (mtmt)
REVERT: B  145 TYR cc_start: 0.8700 (p90) cc_final: 0.8286 (p90)
REVERT: B  175 GLN cc_start: 0.7476 (pt0) cc_final: 0.7222 (mt0)
REVERT: B  188 MET cc_start: 0.8419 (mmm) cc_final: 0.7584 (mmm)
  outliers start: 25
  outliers final: 17
  residues processed: 156
  average time/residue: 0.0705
  time to fit residues: 16.0085
Evaluate side-chains
  138 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  348 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  134 ARG
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  242 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 15 optimal weight:    0.4980
   chunk 5 optimal weight:    4.9990
   chunk 92 optimal weight:    0.0000
   chunk 88 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   chunk 93 optimal weight:   10.0000
   chunk 84 optimal weight:    4.9990
   overall best weight:    2.2990

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 GLN
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.128146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.104745 restraints weight = 11409.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.107125 restraints weight = 7286.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.108798 restraints weight = 5424.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.109877 restraints weight = 4462.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.110644 restraints weight = 3922.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8012  Z= 0.163
  Angle     :  0.586   8.835  10895  Z= 0.299
  Chirality :  0.043   0.234   1258
  Planarity :  0.004   0.053   1394
  Dihedral  :  5.186  76.944   1132
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 13.24 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.15 (0.27), residues: 1011
  helix:  1.46 (0.27), residues: 394
  sheet: -0.63 (0.38), residues: 189
  loop : -0.78 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  42 
 TYR   0.015   0.002   TYR N  80 
 PHE   0.024   0.002   PHE R 222 
 TRP   0.009   0.001   TRP B 297 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8008)
  covalent geometry    : angle       0.58376 (10887)
  SS BOND              : bond        0.00139 (    4)
  SS BOND              : angle       1.80553 (    8)
  hydrogen bonds       : bond        0.03938 (  390)
  hydrogen bonds       : angle       4.79356 ( 1122)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 126
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  304 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7184 (mm-30)
REVERT: B  145 TYR cc_start: 0.8784 (p90) cc_final: 0.8425 (p90)
REVERT: B  175 GLN cc_start: 0.7505 (pt0) cc_final: 0.7232 (mt0)
REVERT: B  188 MET cc_start: 0.8492 (mmm) cc_final: 0.7812 (mmm)
REVERT: B  321 THR cc_start: 0.8073 (p) cc_final: 0.7839 (p)
  outliers start: 35
  outliers final: 21
  residues processed: 151
  average time/residue: 0.0738
  time to fit residues: 16.1611
Evaluate side-chains
  140 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   57 LEU
Chi-restraints excluded: chain R residue   81 THR
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  242 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 19 optimal weight:    0.0270
   chunk 77 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 60 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 93 optimal weight:   10.0000
   chunk 71 optimal weight:    8.9990
   chunk 95 optimal weight:    2.9990
   overall best weight:    2.5844

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.127533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.103973 restraints weight = 11362.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.106323 restraints weight = 7341.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.107902 restraints weight = 5517.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.108631 restraints weight = 4577.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.109545 restraints weight = 4122.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   8012  Z= 0.175
  Angle     :  0.600   8.300  10895  Z= 0.306
  Chirality :  0.043   0.235   1258
  Planarity :  0.004   0.054   1394
  Dihedral  :  5.200  76.028   1132
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 13.60 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.12 (0.27), residues: 1011
  helix:  1.47 (0.27), residues: 394
  sheet: -0.82 (0.37), residues: 200
  loop : -0.73 (0.31), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 379 
 TYR   0.014   0.002   TYR N  80 
 PHE   0.025   0.002   PHE R 222 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 8008)
  covalent geometry    : angle       0.59788 (10887)
  SS BOND              : bond        0.00211 (    4)
  SS BOND              : angle       1.76491 (    8)
  hydrogen bonds       : bond        0.03947 (  390)
  hydrogen bonds       : angle       4.73630 ( 1122)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 125
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7176 (mm-30)
REVERT: B  175 GLN cc_start: 0.7594 (pt0) cc_final: 0.7303 (mt0)
REVERT: B  188 MET cc_start: 0.8458 (mmm) cc_final: 0.7919 (mmm)
  outliers start: 42
  outliers final: 32
  residues processed: 153
  average time/residue: 0.0717
  time to fit residues: 16.0649
Evaluate side-chains
  148 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  348 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  301 LYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   57 LEU
Chi-restraints excluded: chain R residue   81 THR
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  220 MET
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain R residue  303 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   chunk 25 optimal weight:   20.0000
   chunk 83 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.129585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.106207 restraints weight = 11176.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.108594 restraints weight = 7200.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.110230 restraints weight = 5392.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.111191 restraints weight = 4455.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.111662 restraints weight = 3949.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8012  Z= 0.125
  Angle     :  0.566   8.618  10895  Z= 0.285
  Chirality :  0.042   0.210   1258
  Planarity :  0.004   0.055   1394
  Dihedral  :  4.985  73.721   1132
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 15.07 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.26 (0.27), residues: 1011
  helix:  1.62 (0.27), residues: 394
  sheet: -0.73 (0.37), residues: 198
  loop : -0.71 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG N  72 
 TYR   0.016   0.001   TYR N  80 
 PHE   0.016   0.001   PHE R 222 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8008)
  covalent geometry    : angle       0.56431 (10887)
  SS BOND              : bond        0.00148 (    4)
  SS BOND              : angle       1.54370 (    8)
  hydrogen bonds       : bond        0.03635 (  390)
  hydrogen bonds       : angle       4.59829 ( 1122)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 131
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7105 (mm-30)
REVERT: B   57 LYS cc_start: 0.8315 (mtmm) cc_final: 0.8083 (mtmt)
REVERT: B  175 GLN cc_start: 0.7576 (pt0) cc_final: 0.7309 (mt0)
REVERT: B  188 MET cc_start: 0.8451 (mmm) cc_final: 0.8109 (mmm)
  outliers start: 36
  outliers final: 27
  residues processed: 155
  average time/residue: 0.0746
  time to fit residues: 16.8080
Evaluate side-chains
  147 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  348 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  301 LYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  220 MET
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain G residue   50 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 61 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 68 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0010
   chunk 41 optimal weight:    7.9990
   chunk 92 optimal weight:   50.0000
   chunk 70 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.5992

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
N  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.132099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.109652 restraints weight = 11169.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.111909 restraints weight = 7385.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.113469 restraints weight = 5612.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.114192 restraints weight = 4664.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.114907 restraints weight = 4198.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8012  Z= 0.132
  Angle     :  0.570   7.915  10895  Z= 0.287
  Chirality :  0.042   0.206   1258
  Planarity :  0.004   0.055   1394
  Dihedral  :  4.961  72.177   1132
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 15.07 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.30 (0.27), residues: 1011
  helix:  1.67 (0.27), residues: 394
  sheet: -0.74 (0.36), residues: 207
  loop : -0.67 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 314 
 TYR   0.015   0.001   TYR N  80 
 PHE   0.015   0.001   PHE B 235 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 8008)
  covalent geometry    : angle       0.56826 (10887)
  SS BOND              : bond        0.00148 (    4)
  SS BOND              : angle       1.54438 (    8)
  hydrogen bonds       : bond        0.03636 (  390)
  hydrogen bonds       : angle       4.56546 ( 1122)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 129
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.7249 (mm-30) cc_final: 0.7028 (mm-30)
REVERT: B   57 LYS cc_start: 0.8253 (mtmm) cc_final: 0.7991 (mtmt)
REVERT: B  175 GLN cc_start: 0.7516 (pt0) cc_final: 0.7309 (mt0)
REVERT: B  188 MET cc_start: 0.8418 (mmm) cc_final: 0.8087 (mmm)
REVERT: B  226 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8144 (mm-30)
REVERT: B  266 HIS cc_start: 0.6840 (OUTLIER) cc_final: 0.6573 (t-170)
REVERT: N  117 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.6155 (m-80)
REVERT: R   52 VAL cc_start: 0.7725 (t) cc_final: 0.7319 (p)
  outliers start: 43
  outliers final: 30
  residues processed: 160
  average time/residue: 0.0696
  time to fit residues: 16.4938
Evaluate side-chains
  155 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  348 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  301 LYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  220 MET
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain G residue   50 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 87 optimal weight:    1.9990
   chunk 4 optimal weight:    8.9990
   chunk 42 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 63 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0970
   chunk 43 optimal weight:    3.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.131457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.109039 restraints weight = 11194.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.111209 restraints weight = 7474.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.112518 restraints weight = 5725.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.113688 restraints weight = 4822.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.114311 restraints weight = 4258.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8012  Z= 0.150
  Angle     :  0.581   7.770  10895  Z= 0.295
  Chirality :  0.042   0.200   1258
  Planarity :  0.004   0.055   1394
  Dihedral  :  4.992  72.029   1132
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 15.93 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.31 (0.27), residues: 1011
  helix:  1.62 (0.27), residues: 397
  sheet: -0.73 (0.36), residues: 207
  loop : -0.63 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 379 
 TYR   0.014   0.002   TYR N  80 
 PHE   0.015   0.002   PHE B 235 
 TRP   0.008   0.001   TRP A 271 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8008)
  covalent geometry    : angle       0.57866 (10887)
  SS BOND              : bond        0.00173 (    4)
  SS BOND              : angle       2.10549 (    8)
  hydrogen bonds       : bond        0.03709 (  390)
  hydrogen bonds       : angle       4.56060 ( 1122)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 127
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7036 (mm-30)
REVERT: B   57 LYS cc_start: 0.8144 (mtmm) cc_final: 0.7869 (ptpp)
REVERT: B  175 GLN cc_start: 0.7504 (pt0) cc_final: 0.7275 (mt0)
REVERT: B  188 MET cc_start: 0.8425 (mmm) cc_final: 0.8205 (mmm)
REVERT: B  226 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8150 (mm-30)
REVERT: B  266 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6586 (t-170)
REVERT: N  117 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.6243 (m-80)
REVERT: R   52 VAL cc_start: 0.7902 (t) cc_final: 0.7499 (p)
  outliers start: 35
  outliers final: 31
  residues processed: 153
  average time/residue: 0.0670
  time to fit residues: 15.3112
Evaluate side-chains
  157 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 124
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  348 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  301 LYS
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  220 MET
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain R residue  303 LEU
Chi-restraints excluded: chain G residue   50 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 8 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 52 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 23 optimal weight:    4.9990
   chunk 82 optimal weight:    0.3980
   chunk 11 optimal weight:    0.7980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.131536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.108431 restraints weight = 11079.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.110898 restraints weight = 7015.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.112550 restraints weight = 5187.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.113495 restraints weight = 4249.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.114238 restraints weight = 3746.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8012  Z= 0.117
  Angle     :  0.561   7.639  10895  Z= 0.282
  Chirality :  0.042   0.209   1258
  Planarity :  0.004   0.060   1394
  Dihedral  :  4.803  69.911   1132
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 16.30 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.39 (0.27), residues: 1011
  helix:  1.76 (0.27), residues: 394
  sheet: -0.68 (0.36), residues: 207
  loop : -0.65 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G  27 
 TYR   0.016   0.001   TYR N  80 
 PHE   0.014   0.001   PHE B 235 
 TRP   0.009   0.001   TRP B  99 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8008)
  covalent geometry    : angle       0.55965 (10887)
  SS BOND              : bond        0.00173 (    4)
  SS BOND              : angle       1.74396 (    8)
  hydrogen bonds       : bond        0.03483 (  390)
  hydrogen bonds       : angle       4.49800 ( 1122)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.7211 (mm-30) cc_final: 0.7003 (mm-30)
REVERT: B   57 LYS cc_start: 0.8278 (mtmm) cc_final: 0.7981 (mtmm)
REVERT: B  175 GLN cc_start: 0.7568 (pt0) cc_final: 0.7259 (mt0)
REVERT: B  188 MET cc_start: 0.8406 (mmm) cc_final: 0.8121 (mmm)
REVERT: B  226 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8006 (mm-30)
REVERT: B  266 HIS cc_start: 0.6860 (OUTLIER) cc_final: 0.6598 (t-170)
REVERT: B  301 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.6792 (mmmt)
REVERT: N   83 MET cc_start: 0.7339 (OUTLIER) cc_final: 0.6797 (mtm)
REVERT: N  117 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.6174 (m-80)
REVERT: R   52 VAL cc_start: 0.7636 (t) cc_final: 0.7201 (p)
  outliers start: 33
  outliers final: 27
  residues processed: 151
  average time/residue: 0.0700
  time to fit residues: 15.5338
Evaluate side-chains
  161 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  348 TYR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  159 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  301 LYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  220 MET
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain R residue  303 LEU
Chi-restraints excluded: chain G residue   50 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 56 optimal weight:    1.9990
   chunk 68 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 99 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 82 optimal weight:    8.9990
   chunk 87 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.129570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.106321 restraints weight = 11199.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.108672 restraints weight = 7202.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.110263 restraints weight = 5376.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.111377 restraints weight = 4426.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.111898 restraints weight = 3910.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8012  Z= 0.158
  Angle     :  0.588   7.870  10895  Z= 0.299
  Chirality :  0.043   0.263   1258
  Planarity :  0.004   0.057   1394
  Dihedral  :  4.948  71.063   1132
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 17.03 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.36 (0.27), residues: 1011
  helix:  1.71 (0.27), residues: 397
  sheet: -0.70 (0.36), residues: 207
  loop : -0.65 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 379 
 TYR   0.015   0.002   TYR N  80 
 PHE   0.016   0.002   PHE B 235 
 TRP   0.009   0.001   TRP A 271 
 HIS   0.004   0.001   HIS B 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 8008)
  covalent geometry    : angle       0.58598 (10887)
  SS BOND              : bond        0.00180 (    4)
  SS BOND              : angle       1.82199 (    8)
  hydrogen bonds       : bond        0.03691 (  390)
  hydrogen bonds       : angle       4.52650 ( 1122)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: B   57 LYS cc_start: 0.8313 (mtmm) cc_final: 0.8107 (mtmt)
REVERT: B   75 GLN cc_start: 0.7639 (mt0) cc_final: 0.7337 (mt0)
REVERT: B  156 GLN cc_start: 0.8704 (mm-40) cc_final: 0.8311 (mt0)
REVERT: B  175 GLN cc_start: 0.7558 (pt0) cc_final: 0.7190 (mt0)
REVERT: B  188 MET cc_start: 0.8294 (mmm) cc_final: 0.8088 (mmm)
REVERT: B  226 GLU cc_start: 0.8363 (mm-30) cc_final: 0.8057 (mm-30)
REVERT: B  266 HIS cc_start: 0.6971 (OUTLIER) cc_final: 0.6590 (t-170)
REVERT: B  301 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.6904 (mmmt)
REVERT: N  117 TYR cc_start: 0.8113 (OUTLIER) cc_final: 0.6256 (m-80)
REVERT: R   52 VAL cc_start: 0.7777 (t) cc_final: 0.7322 (p)
  outliers start: 31
  outliers final: 27
  residues processed: 150
  average time/residue: 0.0639
  time to fit residues: 14.1367
Evaluate side-chains
  160 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  348 TYR
Chi-restraints excluded: chain B residue   76 ASP
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  266 HIS
Chi-restraints excluded: chain B residue  301 LYS
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   63 SER
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  107 CYS
Chi-restraints excluded: chain N residue  117 TYR
Chi-restraints excluded: chain N residue  122 THR
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue   81 THR
Chi-restraints excluded: chain R residue   89 LEU
Chi-restraints excluded: chain R residue  131 LEU
Chi-restraints excluded: chain R residue  161 VAL
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  165 SER
Chi-restraints excluded: chain R residue  202 ILE
Chi-restraints excluded: chain R residue  220 MET
Chi-restraints excluded: chain R residue  242 LEU
Chi-restraints excluded: chain R residue  303 LEU
Chi-restraints excluded: chain G residue   50 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0060
   chunk 41 optimal weight:    4.9990
   chunk 16 optimal weight:    0.3980
   chunk 61 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 60 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   overall best weight:    1.0598

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

Flipped N/Q/H residues before XYZ refinement:
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.132433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.109401 restraints weight = 11087.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.111882 restraints weight = 6986.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.113571 restraints weight = 5138.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.114550 restraints weight = 4201.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.115347 restraints weight = 3696.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8012  Z= 0.116
  Angle     :  0.565   7.747  10895  Z= 0.284
  Chirality :  0.042   0.249   1258
  Planarity :  0.004   0.057   1394
  Dihedral  :  4.758  69.264   1132
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 17.52 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.42 (0.27), residues: 1011
  helix:  1.79 (0.27), residues: 397
  sheet: -0.66 (0.37), residues: 200
  loop : -0.66 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG G  27 
 TYR   0.015   0.001   TYR N  80 
 PHE   0.014   0.001   PHE B 235 
 TRP   0.010   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 8008)
  covalent geometry    : angle       0.56352 (10887)
  SS BOND              : bond        0.00168 (    4)
  SS BOND              : angle       1.64466 (    8)
  hydrogen bonds       : bond        0.03434 (  390)
  hydrogen bonds       : angle       4.46013 ( 1122)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1157.49 seconds
wall clock time: 20 minutes 46.71 seconds (1246.71 seconds total)