Starting phenix.real_space_refine
on Wed Mar 12 10:57:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xji_33228/03_2025/7xji_33228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xji_33228/03_2025/7xji_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xji_33228/03_2025/7xji_33228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xji_33228/03_2025/7xji_33228.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xji_33228/03_2025/7xji_33228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xji_33228/03_2025/7xji_33228.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 3}
          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: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP: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: 4.89, per 1000 atoms: 0.62
  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: 1.94
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.77
  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: 2.04

  Time building geometry restraints manager: 2.26 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:             0.210
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     20.740
  Find NCS groups from input model:        0.070
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.190
-------------------------------------------------------------------------------
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   8008  Z= 0.224
  Angle     :  0.604   8.196  10887  Z= 0.323
  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 : 9.02
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (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
 TRP   0.006   0.001   TRP A 271 
 HIS   0.002   0.001   HIS B 183 
 PHE   0.031   0.002   PHE R 341 
 TYR   0.012   0.001   TYR R 204 
 ARG   0.008   0.000   ARG A 255 

*********************** 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  : 0.905 
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: 0.8545 (t0) cc_final: 0.8222 (t0)
REVERT: A  304 GLU cc_start: 0.7940 (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: 0.7212 (mmm)
REVERT: B  262 MET cc_start: 0.7889 (mmm) cc_final: 0.7616 (mmp)
REVERT: N   82 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7858 (tm-30)
REVERT: N   84 ASN cc_start: 0.7226 (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: 0.8460 (ptpt) cc_final: 0.7588 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1799
  time to fit residues: 43.5613
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  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 40 optimal weight:    5.9990
   chunk 79 optimal weight:    0.0040
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0980
   chunk 58 optimal weight:    0.9990
   chunk 91 optimal weight:    5.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 338 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.136974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.114923 restraints weight = 10916.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.117260 restraints weight = 7245.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.118656 restraints weight = 5460.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8008  Z= 0.164
  Angle     :  0.582   7.790  10887  Z= 0.299
  Chirality :  0.042   0.220   1258
  Planarity :  0.004   0.045   1394
  Dihedral  :  5.162  84.968   1132
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 10.66 %
    Favored  : 88.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.26), residues: 1011
  helix:  1.46 (0.27), residues: 386
  sheet: -0.67 (0.37), residues: 203
  loop : -0.80 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 297 
 HIS   0.004   0.001   HIS A 347 
 PHE   0.028   0.002   PHE R 222 
 TYR   0.014   0.001   TYR B 264 
 ARG   0.003   0.000   ARG B  49 

*********************** 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
  152 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 142
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A  304 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7270 (mm-30)
REVERT: A  344 ASP cc_start: 0.6547 (m-30) cc_final: 0.6339 (p0)
REVERT: B  145 TYR cc_start: 0.8589 (p90) cc_final: 0.8163 (p90)
REVERT: B  156 GLN cc_start: 0.8665 (mm110) cc_final: 0.8294 (mm-40)
REVERT: B  262 MET cc_start: 0.7618 (mmm) cc_final: 0.7387 (mmm)
REVERT: B  301 LYS cc_start: 0.7936 (mmtt) cc_final: 0.7429 (mmmt)
REVERT: R  235 LEU cc_start: 0.8215 (tt) cc_final: 0.8006 (tt)
  outliers start: 10
  outliers final: 9
  residues processed: 148
  average time/residue: 0.1599
  time to fit residues: 34.8551
Evaluate side-chains
  131 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 122
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  318 LEU
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  165 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 80 optimal weight:    5.9990
   chunk 6 optimal weight:    0.0060
   chunk 23 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 92 optimal weight:    0.3980
   chunk 17 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 36 optimal weight:    8.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
B 156 GLN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 312 ASN
R 338 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.137805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.115639 restraints weight = 10980.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.118079 restraints weight = 7286.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.119425 restraints weight = 5470.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.1788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046   8008  Z= 0.145
  Angle     :  0.537   7.520  10887  Z= 0.274
  Chirality :  0.041   0.162   1258
  Planarity :  0.004   0.048   1394
  Dihedral  :  4.940  78.853   1132
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.75 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.27), residues: 1011
  helix:  1.67 (0.27), residues: 387
  sheet: -0.61 (0.36), residues: 204
  loop : -0.68 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.032   0.001   PHE B 235 
 TYR   0.014   0.001   TYR B  85 
 ARG   0.003   0.000   ARG N  38 

*********************** 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
  158 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 141
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A  304 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7228 (mm-30)
REVERT: B   57 LYS cc_start: 0.8341 (mtmm) cc_final: 0.8112 (mtmt)
REVERT: B  145 TYR cc_start: 0.8654 (p90) cc_final: 0.8265 (p90)
REVERT: R  317 LEU cc_start: 0.7711 (mm) cc_final: 0.7188 (pp)
  outliers start: 17
  outliers final: 8
  residues processed: 152
  average time/residue: 0.1617
  time to fit residues: 35.2011
Evaluate side-chains
  132 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 TYR
Chi-restraints excluded: chain B residue  123 ILE
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain R residue   44 LEU
Chi-restraints excluded: chain R residue  163 VAL
Chi-restraints excluded: chain R residue  164 VAL
Chi-restraints excluded: chain R residue  165 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 69 optimal weight:    0.0970
   chunk 52 optimal weight:    8.9990
   chunk 12 optimal weight:    0.6980
   chunk 71 optimal weight:    7.9990
   overall best weight:    2.3584

-------------------------------------------------------------------------------
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 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.132682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.110583 restraints weight = 11066.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.112880 restraints weight = 7327.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.114141 restraints weight = 5537.790|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.1932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8008  Z= 0.251
  Angle     :  0.593   9.325  10887  Z= 0.300
  Chirality :  0.043   0.233   1258
  Planarity :  0.004   0.051   1394
  Dihedral  :  5.063  76.681   1132
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 13.11 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.27), residues: 1011
  helix:  1.68 (0.27), residues: 388
  sheet: -0.61 (0.38), residues: 191
  loop : -0.68 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.027   0.002   PHE B 235 
 TYR   0.017   0.002   TYR B  85 
 ARG   0.002   0.000   ARG A 379 

*********************** 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: 32
    poor density    : 129
  time to evaluate  : 0.940 
Fit side-chains
REVERT: A  304 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7358 (mm-30)
REVERT: B   57 LYS cc_start: 0.8410 (mtmm) cc_final: 0.8169 (mtmt)
REVERT: B  145 TYR cc_start: 0.8731 (p90) cc_final: 0.8127 (p90)
REVERT: B  188 MET cc_start: 0.8505 (mmm) cc_final: 0.7788 (mmm)
REVERT: N   46 GLU cc_start: 0.7317 (pt0) cc_final: 0.7112 (pt0)
REVERT: R  317 LEU cc_start: 0.7769 (mm) cc_final: 0.7156 (pp)
  outliers start: 32
  outliers final: 20
  residues processed: 151
  average time/residue: 0.1631
  time to fit residues: 35.1834
Evaluate side-chains
  141 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 TYR
Chi-restraints excluded: chain B residue   51 LEU
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 B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 3 optimal weight:    8.9990
   chunk 73 optimal weight:    0.9980
   chunk 76 optimal weight:    6.9990
   chunk 84 optimal weight:    6.9990
   chunk 90 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 26 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  23 ASN
** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.133651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.110352 restraints weight = 10937.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.112893 restraints weight = 6985.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.114572 restraints weight = 5179.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8008  Z= 0.156
  Angle     :  0.541   8.987  10887  Z= 0.274
  Chirality :  0.041   0.236   1258
  Planarity :  0.004   0.053   1394
  Dihedral  :  4.863  73.070   1132
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 13.36 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.47 (0.27), residues: 1011
  helix:  1.83 (0.27), residues: 388
  sheet: -0.60 (0.36), residues: 204
  loop : -0.60 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.021   0.001   PHE B 235 
 TYR   0.016   0.001   TYR N  80 
 ARG   0.001   0.000   ARG N  72 

*********************** 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
  159 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 1.041 
Fit side-chains
REVERT: A  304 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7074 (mm-30)
REVERT: B   57 LYS cc_start: 0.8441 (mtmm) cc_final: 0.8238 (mtmt)
REVERT: B  145 TYR cc_start: 0.8734 (p90) cc_final: 0.8273 (p90)
REVERT: B  188 MET cc_start: 0.8444 (mmm) cc_final: 0.7595 (mmm)
REVERT: R  317 LEU cc_start: 0.7819 (mm) cc_final: 0.7154 (pp)
  outliers start: 27
  outliers final: 19
  residues processed: 150
  average time/residue: 0.2142
  time to fit residues: 46.7064
Evaluate side-chains
  143 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  159 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue    4 LEU
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  131 LEU
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  242 LEU
Chi-restraints excluded: chain G residue   50 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 99 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0770
   chunk 55 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0170
   chunk 86 optimal weight:    4.9990
   chunk 85 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.9780

-------------------------------------------------------------------------------
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
R 312 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.133804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.110761 restraints weight = 10980.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.113278 restraints weight = 7003.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.114751 restraints weight = 5191.910|
|-----------------------------------------------------------------------------|
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8008  Z= 0.156
  Angle     :  0.539   7.811  10887  Z= 0.273
  Chirality :  0.041   0.240   1258
  Planarity :  0.004   0.054   1394
  Dihedral  :  4.765  69.887   1132
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 14.46 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.27), residues: 1011
  helix:  1.85 (0.27), residues: 388
  sheet: -0.62 (0.36), residues: 207
  loop : -0.57 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.020   0.001   PHE B 235 
 TYR   0.015   0.001   TYR N  80 
 ARG   0.001   0.000   ARG N  72 

*********************** 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
  162 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 1.122 
Fit side-chains
REVERT: A  304 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7091 (mm-30)
REVERT: B   57 LYS cc_start: 0.8465 (mtmm) cc_final: 0.8227 (mtmt)
REVERT: B  145 TYR cc_start: 0.8726 (p90) cc_final: 0.8265 (p90)
REVERT: B  188 MET cc_start: 0.8439 (mmm) cc_final: 0.7597 (mmm)
REVERT: R   52 VAL cc_start: 0.7604 (t) cc_final: 0.7200 (p)
REVERT: R  317 LEU cc_start: 0.7718 (mm) cc_final: 0.7112 (pp)
  outliers start: 31
  outliers final: 22
  residues processed: 154
  average time/residue: 0.1803
  time to fit residues: 40.4139
Evaluate side-chains
  146 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  191 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue   70 ILE
Chi-restraints excluded: chain N residue  107 CYS
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  242 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 82 optimal weight:    0.0050
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 69 optimal weight:    0.1980
   chunk 47 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 71 optimal weight:    5.9990
   chunk 61 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.5196

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.138454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.116121 restraints weight = 10858.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.118259 restraints weight = 7178.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.120048 restraints weight = 5468.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8008  Z= 0.137
  Angle     :  0.529   7.432  10887  Z= 0.268
  Chirality :  0.041   0.239   1258
  Planarity :  0.004   0.053   1394
  Dihedral  :  4.621  66.066   1132
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.32 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.27), residues: 1011
  helix:  1.98 (0.27), residues: 388
  sheet: -0.52 (0.36), residues: 214
  loop : -0.50 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.018   0.001   PHE B 235 
 TYR   0.015   0.001   TYR N  80 
 ARG   0.001   0.000   ARG N  38 

*********************** 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
  157 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.819 
Fit side-chains
REVERT: B  145 TYR cc_start: 0.8682 (p90) cc_final: 0.8255 (p90)
REVERT: B  156 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8121 (mt0)
REVERT: B  188 MET cc_start: 0.8421 (mmm) cc_final: 0.7555 (mmm)
REVERT: R   52 VAL cc_start: 0.7763 (t) cc_final: 0.7316 (p)
REVERT: R  317 LEU cc_start: 0.7642 (mm) cc_final: 0.7002 (pp)
  outliers start: 26
  outliers final: 18
  residues processed: 150
  average time/residue: 0.1490
  time to fit residues: 32.4897
Evaluate side-chains
  144 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.815 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  348 TYR
Chi-restraints excluded: chain B residue  100 VAL
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  318 LEU
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue  107 CYS
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  202 ILE
Chi-restraints excluded: chain R residue  220 MET
Chi-restraints excluded: chain R residue  242 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 63 optimal weight:    0.0670
   chunk 20 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   chunk 14 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 91 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 1 optimal weight:    0.4980
   chunk 15 optimal weight:    3.9990
   overall best weight:    0.6118

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.139080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.116832 restraints weight = 10852.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.119113 restraints weight = 7181.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.120773 restraints weight = 5420.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8008  Z= 0.140
  Angle     :  0.526   7.074  10887  Z= 0.265
  Chirality :  0.041   0.237   1258
  Planarity :  0.004   0.055   1394
  Dihedral  :  4.526  64.411   1132
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.30 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.27), residues: 1011
  helix:  2.04 (0.27), residues: 388
  sheet: -0.45 (0.37), residues: 205
  loop : -0.60 (0.30), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 347 
 PHE   0.018   0.001   PHE B 235 
 TYR   0.014   0.001   TYR N  80 
 ARG   0.001   0.000   ARG G  27 

*********************** 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
  148 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.955 
Fit side-chains
REVERT: B  145 TYR cc_start: 0.8661 (p90) cc_final: 0.8253 (p90)
REVERT: B  156 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8125 (mt0)
REVERT: B  188 MET cc_start: 0.8404 (mmm) cc_final: 0.7534 (mmm)
REVERT: R   52 VAL cc_start: 0.7673 (t) cc_final: 0.7221 (p)
REVERT: R  317 LEU cc_start: 0.7612 (mm) cc_final: 0.7027 (pp)
  outliers start: 21
  outliers final: 18
  residues processed: 142
  average time/residue: 0.1727
  time to fit residues: 36.0677
Evaluate side-chains
  141 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 TYR
Chi-restraints excluded: chain B residue  100 VAL
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  318 LEU
Chi-restraints excluded: chain N residue    4 LEU
Chi-restraints excluded: chain N residue  107 CYS
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  202 ILE
Chi-restraints excluded: chain R residue  220 MET
Chi-restraints excluded: chain R residue  242 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0470
   chunk 20 optimal weight:    2.9990
   chunk 4 optimal weight:   20.0000
   chunk 84 optimal weight:    7.9990
   chunk 18 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 69 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0000
   overall best weight:    1.6086

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.135690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.113479 restraints weight = 11100.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.115757 restraints weight = 7377.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.117324 restraints weight = 5589.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8008  Z= 0.196
  Angle     :  0.556   9.082  10887  Z= 0.279
  Chirality :  0.042   0.241   1258
  Planarity :  0.004   0.055   1394
  Dihedral  :  4.673  64.369   1132
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.18 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.27), residues: 1011
  helix:  1.95 (0.27), residues: 394
  sheet: -0.43 (0.37), residues: 201
  loop : -0.62 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.019   0.002   PHE B 235 
 TYR   0.013   0.001   TYR N  80 
 ARG   0.002   0.000   ARG R 135 

*********************** 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
  147 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.900 
Fit side-chains
REVERT: B  145 TYR cc_start: 0.8751 (p90) cc_final: 0.8395 (p90)
REVERT: B  156 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8201 (mt0)
REVERT: B  188 MET cc_start: 0.8483 (mmm) cc_final: 0.7708 (mmm)
REVERT: N   83 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6831 (mtm)
REVERT: R   52 VAL cc_start: 0.7786 (t) cc_final: 0.7326 (p)
REVERT: R  317 LEU cc_start: 0.7588 (mm) cc_final: 0.7012 (pp)
  outliers start: 23
  outliers final: 20
  residues processed: 139
  average time/residue: 0.2050
  time to fit residues: 42.1913
Evaluate side-chains
  142 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  318 LEU
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 N residue  107 CYS
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  202 ILE
Chi-restraints excluded: chain R residue  220 MET
Chi-restraints excluded: chain R residue  242 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 14 optimal weight:    0.0170
   chunk 60 optimal weight:    8.9990
   chunk 16 optimal weight:    0.0030
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   chunk 36 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0970
   overall best weight:    0.8230

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.135684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.112870 restraints weight = 10975.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.115317 restraints weight = 6956.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.116925 restraints weight = 5153.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8008  Z= 0.152
  Angle     :  0.541   8.380  10887  Z= 0.270
  Chirality :  0.041   0.229   1258
  Planarity :  0.004   0.055   1394
  Dihedral  :  4.549  62.536   1132
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.42 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.27), residues: 1011
  helix:  1.96 (0.27), residues: 394
  sheet: -0.38 (0.37), residues: 201
  loop : -0.64 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 347 
 PHE   0.017   0.001   PHE B 235 
 TYR   0.014   0.001   TYR R 204 
 ARG   0.002   0.000   ARG R 135 

********************** 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
  150 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: B  145 TYR cc_start: 0.8726 (p90) cc_final: 0.8374 (p90)
REVERT: B  156 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8191 (mt0)
REVERT: B  188 MET cc_start: 0.8365 (mmm) cc_final: 0.7708 (mmm)
REVERT: N   83 MET cc_start: 0.7272 (OUTLIER) cc_final: 0.6744 (mtm)
REVERT: R   52 VAL cc_start: 0.7595 (t) cc_final: 0.7148 (p)
REVERT: R  317 LEU cc_start: 0.7658 (mm) cc_final: 0.7001 (pp)
  outliers start: 21
  outliers final: 20
  residues processed: 142
  average time/residue: 0.1625
  time to fit residues: 33.4692
Evaluate side-chains
  148 residues out of total 862 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  318 LEU
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 N residue  107 CYS
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  202 ILE
Chi-restraints excluded: chain R residue  220 MET
Chi-restraints excluded: chain R residue  242 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 94 optimal weight:    2.9990
   chunk 28 optimal weight:    5.9990
   chunk 70 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 57 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 100 optimal weight:    0.1980
   chunk 90 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   overall best weight:    1.0184

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.134883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.111749 restraints weight = 11062.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.114256 restraints weight = 7108.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.115951 restraints weight = 5262.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8008  Z= 0.159
  Angle     :  0.541   8.204  10887  Z= 0.271
  Chirality :  0.041   0.229   1258
  Planarity :  0.004   0.055   1394
  Dihedral  :  4.547  62.178   1132
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.18 %
    Favored  : 81.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.27), residues: 1011
  helix:  2.00 (0.27), residues: 394
  sheet: -0.30 (0.38), residues: 196
  loop : -0.64 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.020   0.001   PHE N 103 
 TYR   0.013   0.001   TYR N  80 
 ARG   0.002   0.000   ARG R 135 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2359.54 seconds
wall clock time: 42 minutes 58.31 seconds (2578.31 seconds total)