Starting phenix.real_space_refine
on Fri Jun 13 20:15:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vww_43604/06_2025/8vww_43604.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vww_43604/06_2025/8vww_43604.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/8vww_43604/06_2025/8vww_43604.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vww_43604/06_2025/8vww_43604.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vww_43604/06_2025/8vww_43604.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vww_43604/06_2025/8vww_43604.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=   0.000 sd=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1936 atoms to isotropic.
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      28      5.16       5
     C    4411      2.51       5
     N    1158      2.21       5
     O    1349      1.98       5
     H    6855      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13801
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4013
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 4013
          Classifications: {'peptide': 247}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 239}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1866
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 1866
          Classifications: {'peptide': 122}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "C"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 1595
          Classifications: {'peptide': 107}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 3199
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 3199
          Classifications: {'peptide': 217}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 201}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 3128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 3128
          Classifications: {'peptide': 206}
          Modifications used: {'NH3': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 194}
          Chain breaks: 1
  Time building chain proxies: 8.68, per 1000 atoms: 0.63
  Number of scatterers: 13801
  At special positions: 0
  Unit cell: (73.3216, 94.1516, 153.309, 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)
     S      28     16.00
     O    1349      8.00
     N    1158      7.00
     C    4411      6.00
     H    6855      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 287 " - pdb=" SG  CYS A 295 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 439 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 400 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 479 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 140 " - pdb=" SG  CYS H 196 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 216 " - pdb=" SG  CYS L 214 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " 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: 3.37
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1660

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 19 sheets defined
      10.6% alpha, 37.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 256 through 272
    Processing helix  chain 'A' and resid 282 through 291
    Processing helix  chain 'A' and resid 296 through 309
    Processing helix  chain 'A' and resid 394 through 398
      removed outlier: 4.103A  pdb=" N   ILE A 398 " --> pdb=" O   LEU A 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.505A  pdb=" N   ASN B  32 " --> pdb=" O   VAL B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 87
    Processing helix  chain 'C' and resid 79 through 83
    Processing helix  chain 'H' and resid 61 through 64
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.794A  pdb=" N   THR H  87 " --> pdb=" O   ALA H  84 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 156 through 158
      No H-bonds generated for 'chain 'H' and resid 156 through 158'
    Processing helix  chain 'H' and resid 185 through 189
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.596A  pdb=" N   PHE L  83 " --> pdb=" O   SER L  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 121 through 127
    Processing helix  chain 'L' and resid 183 through 187
    Processing sheet with id=AA1, first strand: chain 'A' and resid 314 through 315
    Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 355
      removed outlier: 6.941A  pdb=" N   SER A 360 " --> pdb=" O   SER A 442 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   SER A 442 " --> pdb=" O   SER A 360 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   CYS A 439 " --> pdb=" O   SER A 436 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER A 436 " --> pdb=" O   CYS A 439 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 376
      removed outlier: 3.583A  pdb=" N   ILE A 375 " --> pdb=" O   ILE A 461 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 385 through 386
      removed outlier: 6.199A  pdb=" N   VAL A 385 " --> pdb=" O   GLN A 501 " (cutoff:3.500A)
      removed outlier: 8.091A  pdb=" N   LYS A 503 " --> pdb=" O   VAL A 385 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 5 through 7
      removed outlier: 3.595A  pdb=" N   SER B   7 " --> pdb=" O   SER B  21 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   SER B  21 " --> pdb=" O   SER B   7 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LEU B  18 " --> pdb=" O   MET B  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.937A  pdb=" N   MET B  34 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   VAL B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.642A  pdb=" N   ALA B 100E" --> pdb=" O   ARG B  96 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.302A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
      removed outlier: 5.347A  pdb=" N   LEU C  33 " --> pdb=" O   TYR C  49 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   TYR C  49 " --> pdb=" O   LEU C  33 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ASP C  50 " --> pdb=" O   SER C  53 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.302A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   GLN C  90 " --> pdb=" O   THR C  97 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   THR C  97 " --> pdb=" O   GLN C  90 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.650A  pdb=" N   GLN H   5 " --> pdb=" O   THR H  23 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   THR H  23 " --> pdb=" O   GLN H   5 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.770A  pdb=" N   THR H 107 " --> pdb=" O   TYR H  90 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   TRP H  35A" --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   SER H  50 " --> pdb=" O   TRP H  35A" (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.770A  pdb=" N   THR H 107 " --> pdb=" O   TYR H  90 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 120 through 124
      removed outlier: 6.156A  pdb=" N   TYR H 176 " --> pdb=" O   ASP H 144 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   SER H 177 " --> pdb=" O   ALA H 168 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ALA H 168 " --> pdb=" O   SER H 177 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   SER H 179 " --> pdb=" O   PHE H 166 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 151 through 154
      removed outlier: 4.396A  pdb=" N   TYR H 194 " --> pdb=" O   VAL H 211 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 4 through 6
      removed outlier: 3.892A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   SER L  67 " --> pdb=" O   ASP L  70 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 14
      removed outlier: 3.563A  pdb=" N   ALA L  84 " --> pdb=" O   VAL L 104 " (cutoff:3.500A)
      removed outlier: 6.020A  pdb=" N   LEU L  33 " --> pdb=" O   ALA L  50 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ILE L  48 " --> pdb=" O   TRP L  35 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   ALA L  50 " --> pdb=" O   THR L  53 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 116 through 118
      removed outlier: 3.557A  pdb=" N   VAL L 133 " --> pdb=" O   PHE L 118 " (cutoff:3.500A)
      removed outlier: 6.019A  pdb=" N   TYR L 173 " --> pdb=" O   ASN L 138 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 145 through 149
      removed outlier: 3.702A  pdb=" N   LYS L 145 " --> pdb=" O   THR L 197 " (cutoff:3.500A)

    265 hydrogen bonds defined for protein.
    660 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: 5.35

  Time building geometry restraints manager: 4.19 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 6855
        1.03 -     1.23: 6
        1.23 -     1.42: 3002
        1.42 -     1.62: 4058
        1.62 -     1.81: 34
  Bond restraints: 13955
  Sorted by residual:
  bond pdb=" CB  TRP H  47 "
       pdb=" CG  TRP H  47 "
    ideal  model  delta    sigma   weight residual
    1.498  1.473  0.025 3.10e-02 1.04e+03 6.64e-01
  bond pdb=" CB  CYS A 287 "
       pdb=" SG  CYS A 287 "
    ideal  model  delta    sigma   weight residual
    1.808  1.783  0.025 3.30e-02 9.18e+02 5.61e-01
  bond pdb=" CB  CYS B  92 "
       pdb=" SG  CYS B  92 "
    ideal  model  delta    sigma   weight residual
    1.808  1.784  0.024 3.30e-02 9.18e+02 5.34e-01
  bond pdb=" CB  GLN A 373 "
       pdb=" CG  GLN A 373 "
    ideal  model  delta    sigma   weight residual
    1.520  1.499  0.021 3.00e-02 1.11e+03 4.88e-01
  bond pdb=" ND2 ASN A 402 "
       pdb="HD22 ASN A 402 "
    ideal  model  delta    sigma   weight residual
    0.860  0.846  0.014 2.00e-02 2.50e+03 4.88e-01
  ... (remaining 13950 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 24534
        1.49 -     2.98: 573
        2.98 -     4.47: 59
        4.47 -     5.96: 5
        5.96 -     7.45: 2
  Bond angle restraints: 25173
  Sorted by residual:
  angle pdb=" N   PRO H 149 "
        pdb=" CA  PRO H 149 "
        pdb=" C   PRO H 149 "
      ideal   model   delta    sigma   weight residual
     110.21  113.99   -3.78 1.64e+00 3.72e-01 5.31e+00
  angle pdb=" N   TYR A 359 "
        pdb=" CA  TYR A 359 "
        pdb=" C   TYR A 359 "
      ideal   model   delta    sigma   weight residual
     108.79  105.26    3.53 1.53e+00 4.27e-01 5.31e+00
  angle pdb=" N   HIS A 431 "
        pdb=" CA  HIS A 431 "
        pdb=" C   HIS A 431 "
      ideal   model   delta    sigma   weight residual
     108.02  104.04    3.98 1.78e+00 3.16e-01 4.99e+00
  angle pdb=" N   LYS H 201 "
        pdb=" CA  LYS H 201 "
        pdb=" C   LYS H 201 "
      ideal   model   delta    sigma   weight residual
     109.81  114.67   -4.86 2.21e+00 2.05e-01 4.84e+00
  angle pdb=" N   ILE A 309 "
        pdb=" CA  ILE A 309 "
        pdb=" C   ILE A 309 "
      ideal   model   delta    sigma   weight residual
     109.34  113.84   -4.50 2.08e+00 2.31e-01 4.68e+00
  ... (remaining 25168 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 5997
       17.82 -    35.63: 425
       35.63 -    53.45: 141
       53.45 -    71.27: 98
       71.27 -    89.08: 7
  Dihedral angle restraints: 6668
    sinusoidal: 3593
      harmonic: 3075
  Sorted by residual:
  dihedral pdb=" CA  ALA B  88 "
           pdb=" C   ALA B  88 "
           pdb=" N   VAL B  89 "
           pdb=" CA  VAL B  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.45   26.55     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CA  PRO H  98 "
           pdb=" C   PRO H  98 "
           pdb=" N   ASP H  99 "
           pdb=" CA  ASP H  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.74  -26.26     0      5.00e+00 4.00e-02 2.76e+01
  dihedral pdb=" CA  ILE H  69 "
           pdb=" C   ILE H  69 "
           pdb=" N   SER H  70 "
           pdb=" CA  SER H  70 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.71   25.29     0      5.00e+00 4.00e-02 2.56e+01
  ... (remaining 6665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 674
       0.032 -    0.065: 260
       0.065 -    0.097: 91
       0.097 -    0.130: 57
       0.130 -    0.162: 9
  Chirality restraints: 1091
  Sorted by residual:
  chirality pdb=" CA  ILE A 254 "
            pdb=" N   ILE A 254 "
            pdb=" C   ILE A 254 "
            pdb=" CB  ILE A 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.58e-01
  chirality pdb=" CA  ILE C  48 "
            pdb=" N   ILE C  48 "
            pdb=" C   ILE C  48 "
            pdb=" CB  ILE C  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.38e-01
  chirality pdb=" CA  VAL A 433 "
            pdb=" N   VAL A 433 "
            pdb=" C   VAL A 433 "
            pdb=" CB  VAL A 433 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.99e-01
  ... (remaining 1088 not shown)

  Planarity restraints: 2068
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 496 "    0.029 2.00e-02 2.50e+03   4.99e-02 3.74e+01
        pdb=" CD  GLN A 496 "   -0.057 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 496 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 496 "    0.086 2.00e-02 2.50e+03
        pdb="HE21 GLN A 496 "    0.005 2.00e-02 2.50e+03
        pdb="HE22 GLN A 496 "   -0.058 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 402 "   -0.040 2.00e-02 2.50e+03   4.83e-02 3.49e+01
        pdb=" CG  ASN A 402 "    0.037 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 402 "   -0.001 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 402 "    0.075 2.00e-02 2.50e+03
        pdb="HD21 ASN A 402 "    0.002 2.00e-02 2.50e+03
        pdb="HD22 ASN A 402 "   -0.073 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 248 "    0.024 2.00e-02 2.50e+03   2.95e-02 1.31e+01
        pdb=" CG  ASN A 248 "   -0.022 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 248 "   -0.000 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 248 "   -0.047 2.00e-02 2.50e+03
        pdb="HD21 ASN A 248 "   -0.000 2.00e-02 2.50e+03
        pdb="HD22 ASN A 248 "    0.045 2.00e-02 2.50e+03
  ... (remaining 2065 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 509
        2.15 -     2.76: 26284
        2.76 -     3.37: 37766
        3.37 -     3.99: 49393
        3.99 -     4.60: 76250
  Nonbonded interactions: 190202
  Sorted by model distance:
  nonbonded pdb=" HG1 THR A 367 "
            pdb=" OG  SER A 370 "
     model   vdw
     1.533 2.450
  nonbonded pdb=" O   GLY A 350 "
            pdb=" H   SER A 365 "
     model   vdw
     1.562 2.450
  nonbonded pdb=" OE1 GLN L   6 "
            pdb=" H   GLY L 101 "
     model   vdw
     1.587 2.450
  nonbonded pdb=" O   GLN L 124 "
            pdb=" HG  SER L 127 "
     model   vdw
     1.595 2.450
  nonbonded pdb=" H   GLN L  79 "
            pdb=" OD2 ASP L  82 "
     model   vdw
     1.600 2.450
  ... (remaining 190197 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:             5.160
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.090
  Construct map_model_manager:             0.240
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     34.580
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
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   0.031   7111  Z= 0.150
  Angle     :  0.637   7.449   9659  Z= 0.343
  Chirality :  0.045   0.162   1091
  Planarity :  0.006   0.063   1219
  Dihedral  : 13.699  89.083   2558
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.53 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  7.67 %
    Favored  : 90.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.82 (0.27), residues: 883
  helix: -1.07 (0.56), residues: 57
  sheet: -0.13 (0.28), residues: 340
  loop : -0.72 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.005   TRP B 100A
 HIS   0.009   0.003   HIS A 453 
 PHE   0.015   0.002   PHE A 408 
 TYR   0.035   0.005   TYR C  87 
 ARG   0.014   0.002   ARG L 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.25068 (  254)
  hydrogen bonds       : angle       9.84470 (  660)
  SS BOND              : bond        0.00382 (   11)
  SS BOND              : angle       1.32899 (   22)
  covalent geometry    : bond        0.00342 ( 7100)
  covalent geometry    : angle       0.63428 ( 9637)

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

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

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 222
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  286 TRP cc_start: 0.8376 (t60) cc_final: 0.7900 (t60)
REVERT: A  480 THR cc_start: 0.8008 (m) cc_final: 0.7795 (p)
REVERT: B   13 GLN cc_start: 0.8050 (mp10) cc_final: 0.7681 (mp10)
REVERT: B   33 TYR cc_start: 0.8155 (m-10) cc_final: 0.7904 (m-10)
REVERT: B   75 LYS cc_start: 0.8772 (mmtm) cc_final: 0.8565 (mmtt)
REVERT: B  101 ASP cc_start: 0.7671 (p0) cc_final: 0.7431 (p0)
REVERT: C  106 ILE cc_start: 0.6146 (mm) cc_final: 0.5819 (mm)
REVERT: H  194 TYR cc_start: 0.8112 (m-80) cc_final: 0.7898 (m-80)
REVERT: H  199 ASN cc_start: 0.8846 (t0) cc_final: 0.8636 (t0)
REVERT: L   70 ASP cc_start: 0.8145 (t70) cc_final: 0.7817 (t0)
REVERT: L   92 TYR cc_start: 0.8689 (t80) cc_final: 0.8377 (t80)
REVERT: L  145 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7939 (mtmm)
REVERT: L  167 ASP cc_start: 0.8535 (t70) cc_final: 0.7189 (m-30)
  outliers start: 16
  outliers final: 3
  residues processed: 233
  average time/residue: 0.5431
  time to fit residues: 160.8249
Evaluate side-chains
  151 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 148
  time to evaluate  : 2.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 MET
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain L residue  135 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
A 422 GLN
H  60 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.144578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.118963 restraints weight = 28312.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.123462 restraints weight = 15516.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.126508 restraints weight = 10198.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   7111  Z= 0.251
  Angle     :  0.720   8.159   9659  Z= 0.383
  Chirality :  0.046   0.161   1091
  Planarity :  0.004   0.035   1219
  Dihedral  :  6.387  49.610    979
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.17 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.51 (0.28), residues: 883
  helix:  0.35 (0.68), residues: 53
  sheet: -0.09 (0.28), residues: 342
  loop : -0.52 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP H 154 
 HIS   0.006   0.002   HIS A 456 
 PHE   0.016   0.002   PHE A 321 
 TYR   0.019   0.002   TYR A 465 
 ARG   0.007   0.001   ARG A 289 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05036 (  254)
  hydrogen bonds       : angle       7.40223 (  660)
  SS BOND              : bond        0.00571 (   11)
  SS BOND              : angle       1.21762 (   22)
  covalent geometry    : bond        0.00576 ( 7100)
  covalent geometry    : angle       0.71839 ( 9637)

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

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

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 155
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.7001 (OUTLIER) cc_final: 0.6673 (pmm)
REVERT: A  286 TRP cc_start: 0.8546 (t60) cc_final: 0.8115 (t60)
REVERT: B   13 GLN cc_start: 0.8269 (mp10) cc_final: 0.7878 (mp10)
REVERT: C   18 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.5530 (ttt-90)
REVERT: C   39 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6765 (mtpt)
REVERT: H    6 GLU cc_start: 0.8585 (mp0) cc_final: 0.8259 (mp0)
REVERT: H  199 ASN cc_start: 0.8910 (t0) cc_final: 0.8701 (t0)
REVERT: L   92 TYR cc_start: 0.8679 (t80) cc_final: 0.8466 (t80)
  outliers start: 21
  outliers final: 9
  residues processed: 165
  average time/residue: 0.4535
  time to fit residues: 99.3816
Evaluate side-chains
  139 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain B residue   85 GLU
Chi-restraints excluded: chain B residue   99 SER
Chi-restraints excluded: chain C residue   18 ARG
Chi-restraints excluded: chain C residue   39 LYS
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain H residue  205 THR
Chi-restraints excluded: chain L residue  135 LEU
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain L residue  178 THR
Chi-restraints excluded: chain L residue  180 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0670
   chunk 44 optimal weight:    0.9980
   chunk 75 optimal weight:    0.5980
   chunk 69 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
H 164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.144778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.118559 restraints weight = 28617.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.123304 restraints weight = 15058.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.126426 restraints weight = 9623.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7111  Z= 0.144
  Angle     :  0.607   7.982   9659  Z= 0.315
  Chirality :  0.043   0.156   1091
  Planarity :  0.004   0.038   1219
  Dihedral  :  5.724  48.031    976
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.22 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.24 (0.28), residues: 883
  helix:  0.96 (0.69), residues: 55
  sheet:  0.01 (0.28), residues: 348
  loop : -0.33 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 100A
 HIS   0.004   0.001   HIS L 198 
 PHE   0.008   0.001   PHE H 100B
 TYR   0.013   0.002   TYR L  87 
 ARG   0.005   0.000   ARG L 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04283 (  254)
  hydrogen bonds       : angle       6.81265 (  660)
  SS BOND              : bond        0.00330 (   11)
  SS BOND              : angle       0.79801 (   22)
  covalent geometry    : bond        0.00333 ( 7100)
  covalent geometry    : angle       0.60605 ( 9637)

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

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

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 1.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6734 (pmm)
REVERT: A  286 TRP cc_start: 0.8373 (t60) cc_final: 0.7937 (t60)
REVERT: A  475 LEU cc_start: 0.8714 (mt) cc_final: 0.8491 (mt)
REVERT: H    6 GLU cc_start: 0.8588 (mp0) cc_final: 0.8167 (mp0)
REVERT: H  199 ASN cc_start: 0.8872 (t0) cc_final: 0.8650 (t0)
REVERT: L  167 ASP cc_start: 0.7630 (t70) cc_final: 0.6688 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 147
  average time/residue: 0.4193
  time to fit residues: 82.3820
Evaluate side-chains
  141 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue   99 SER
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain L residue  115 VAL
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain L residue  180 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 66 optimal weight:    0.2980
   chunk 83 optimal weight:    0.0000
   chunk 18 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 75 optimal weight:    0.3980
   overall best weight:    0.5384

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

Flipped N/Q/H residues before XYZ refinement:
L  55 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.144333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.117529 restraints weight = 28480.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.122453 restraints weight = 14641.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.125683 restraints weight = 9276.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.4545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7111  Z= 0.137
  Angle     :  0.582   8.281   9659  Z= 0.302
  Chirality :  0.043   0.154   1091
  Planarity :  0.004   0.049   1219
  Dihedral  :  5.144  21.006    970
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 15.73 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.19 (0.29), residues: 883
  helix:  1.27 (0.71), residues: 55
  sheet: -0.01 (0.27), residues: 359
  loop : -0.30 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H 154 
 HIS   0.004   0.001   HIS L 198 
 PHE   0.015   0.001   PHE L 209 
 TYR   0.011   0.001   TYR L  49 
 ARG   0.005   0.000   ARG C  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03688 (  254)
  hydrogen bonds       : angle       6.43253 (  660)
  SS BOND              : bond        0.00313 (   11)
  SS BOND              : angle       0.85544 (   22)
  covalent geometry    : bond        0.00319 ( 7100)
  covalent geometry    : angle       0.58133 ( 9637)

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

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

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6758 (pmm)
REVERT: A  286 TRP cc_start: 0.8393 (t60) cc_final: 0.7942 (t60)
REVERT: B   13 GLN cc_start: 0.8069 (mp10) cc_final: 0.7730 (mp10)
REVERT: C   70 ASP cc_start: 0.7353 (t70) cc_final: 0.7122 (m-30)
REVERT: C   92 ASN cc_start: 0.8569 (OUTLIER) cc_final: 0.8190 (t0)
REVERT: H    6 GLU cc_start: 0.8563 (mp0) cc_final: 0.8127 (mp0)
REVERT: L  167 ASP cc_start: 0.7627 (t70) cc_final: 0.6468 (m-30)
REVERT: L  170 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7355 (m-30)
  outliers start: 14
  outliers final: 9
  residues processed: 139
  average time/residue: 0.3843
  time to fit residues: 73.0487
Evaluate side-chains
  140 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue   99 SER
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   92 ASN
Chi-restraints excluded: chain H residue   96 ASP
Chi-restraints excluded: chain H residue  112 SER
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain L residue  180 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 83 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0050
   chunk 80 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
A 248 ASN
B 105 GLN
L  55 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.145015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.118582 restraints weight = 29138.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.123062 restraints weight = 15788.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.125978 restraints weight = 10380.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.4771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7111  Z= 0.130
  Angle     :  0.562   7.589   9659  Z= 0.291
  Chirality :  0.043   0.152   1091
  Planarity :  0.003   0.037   1219
  Dihedral  :  4.924  20.332    970
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 17.01 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.07 (0.29), residues: 883
  helix:  1.45 (0.71), residues: 55
  sheet:  0.02 (0.28), residues: 343
  loop : -0.17 (0.29), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 154 
 HIS   0.007   0.001   HIS L 198 
 PHE   0.013   0.001   PHE L 209 
 TYR   0.011   0.001   TYR L  49 
 ARG   0.003   0.000   ARG A 490 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03467 (  254)
  hydrogen bonds       : angle       6.21989 (  660)
  SS BOND              : bond        0.00324 (   11)
  SS BOND              : angle       0.77229 (   22)
  covalent geometry    : bond        0.00304 ( 7100)
  covalent geometry    : angle       0.56131 ( 9637)

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

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

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6699 (pmm)
REVERT: A  286 TRP cc_start: 0.8397 (t60) cc_final: 0.7962 (t60)
REVERT: B   13 GLN cc_start: 0.8093 (mp10) cc_final: 0.7738 (mp10)
REVERT: H    6 GLU cc_start: 0.8548 (mp0) cc_final: 0.8139 (mp0)
REVERT: L  167 ASP cc_start: 0.7595 (t70) cc_final: 0.6309 (m-30)
REVERT: L  170 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7316 (m-30)
  outliers start: 11
  outliers final: 7
  residues processed: 141
  average time/residue: 0.3813
  time to fit residues: 73.4132
Evaluate side-chains
  133 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue   85 GLU
Chi-restraints excluded: chain C residue   20 THR
Chi-restraints excluded: chain H residue   96 ASP
Chi-restraints excluded: chain H residue  178 LEU
Chi-restraints excluded: chain L residue  170 ASP
Chi-restraints excluded: chain L residue  180 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 19 optimal weight:    0.4980
   chunk 63 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 105 GLN
C  92 ASN
L  55 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.143581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.116505 restraints weight = 29570.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.121092 restraints weight = 16046.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.124155 restraints weight = 10590.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.5066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7111  Z= 0.160
  Angle     :  0.584   7.753   9659  Z= 0.300
  Chirality :  0.043   0.147   1091
  Planarity :  0.003   0.037   1219
  Dihedral  :  4.911  20.754    970
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.65 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.12 (0.29), residues: 883
  helix:  1.38 (0.72), residues: 55
  sheet: -0.01 (0.28), residues: 334
  loop : -0.20 (0.29), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 100A
 HIS   0.004   0.001   HIS L 198 
 PHE   0.011   0.001   PHE L 209 
 TYR   0.015   0.002   TYR L  49 
 ARG   0.002   0.000   ARG B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03519 (  254)
  hydrogen bonds       : angle       6.11712 (  660)
  SS BOND              : bond        0.00371 (   11)
  SS BOND              : angle       0.89165 (   22)
  covalent geometry    : bond        0.00373 ( 7100)
  covalent geometry    : angle       0.58277 ( 9637)

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

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

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 1.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6803 (pmm)
REVERT: A  286 TRP cc_start: 0.8457 (t60) cc_final: 0.8022 (t60)
REVERT: H    6 GLU cc_start: 0.8513 (mp0) cc_final: 0.8060 (mp0)
REVERT: H  142 VAL cc_start: 0.9220 (m) cc_final: 0.8849 (p)
REVERT: L  167 ASP cc_start: 0.7686 (t70) cc_final: 0.6234 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 139
  average time/residue: 0.4082
  time to fit residues: 75.9321
Evaluate side-chains
  133 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  380 HIS
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue   99 SER
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   96 ASP
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  187 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 72 optimal weight:    0.0570
   chunk 49 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 86 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.6098

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

Flipped N/Q/H residues before XYZ refinement:
B 105 GLN
L  55 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.144270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.117623 restraints weight = 29453.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.122099 restraints weight = 16087.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.125074 restraints weight = 10675.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.5247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7111  Z= 0.135
  Angle     :  0.562   7.756   9659  Z= 0.288
  Chirality :  0.043   0.154   1091
  Planarity :  0.003   0.033   1219
  Dihedral  :  4.815  19.834    970
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 17.26 %
    Favored  : 81.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.09 (0.29), residues: 883
  helix:  1.55 (0.73), residues: 55
  sheet: -0.02 (0.28), residues: 341
  loop : -0.18 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 100A
 HIS   0.003   0.001   HIS L 198 
 PHE   0.011   0.001   PHE H 122 
 TYR   0.012   0.001   TYR L  49 
 ARG   0.005   0.000   ARG C  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03317 (  254)
  hydrogen bonds       : angle       5.98583 (  660)
  SS BOND              : bond        0.00323 (   11)
  SS BOND              : angle       0.73861 (   22)
  covalent geometry    : bond        0.00316 ( 7100)
  covalent geometry    : angle       0.56137 ( 9637)

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

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

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 127
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6844 (pmm)
REVERT: B   13 GLN cc_start: 0.8046 (mp10) cc_final: 0.7801 (mp10)
REVERT: H    6 GLU cc_start: 0.8474 (mp0) cc_final: 0.8041 (mp0)
REVERT: H  142 VAL cc_start: 0.9215 (m) cc_final: 0.8847 (p)
REVERT: L  167 ASP cc_start: 0.7596 (t70) cc_final: 0.6159 (m-30)
  outliers start: 12
  outliers final: 9
  residues processed: 136
  average time/residue: 0.3967
  time to fit residues: 72.3779
Evaluate side-chains
  133 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 123
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  380 HIS
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue   99 SER
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   96 ASP
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  187 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 72 optimal weight:    0.2980
   chunk 42 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 83 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 373 GLN
A 496 GLN
B 105 GLN
L  55 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.142875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.116334 restraints weight = 29361.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.120828 restraints weight = 15836.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123814 restraints weight = 10389.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.5433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7111  Z= 0.149
  Angle     :  0.566   7.834   9659  Z= 0.291
  Chirality :  0.043   0.152   1091
  Planarity :  0.003   0.034   1219
  Dihedral  :  4.774  20.093    970
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.62 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.15 (0.29), residues: 883
  helix:  1.58 (0.73), residues: 55
  sheet: -0.03 (0.29), residues: 333
  loop : -0.25 (0.29), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 100A
 HIS   0.003   0.001   HIS L 198 
 PHE   0.010   0.001   PHE L 209 
 TYR   0.014   0.001   TYR L  49 
 ARG   0.005   0.000   ARG C  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03297 (  254)
  hydrogen bonds       : angle       5.93384 (  660)
  SS BOND              : bond        0.00320 (   11)
  SS BOND              : angle       0.77137 (   22)
  covalent geometry    : bond        0.00349 ( 7100)
  covalent geometry    : angle       0.56554 ( 9637)

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

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

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 1.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 GLN cc_start: 0.8038 (mp10) cc_final: 0.7700 (mp10)
REVERT: B   31 SER cc_start: 0.7922 (p) cc_final: 0.7590 (t)
REVERT: H    6 GLU cc_start: 0.8469 (mp0) cc_final: 0.8027 (mp0)
REVERT: H  142 VAL cc_start: 0.9211 (m) cc_final: 0.8842 (p)
REVERT: L  167 ASP cc_start: 0.7624 (t70) cc_final: 0.6058 (m-30)
  outliers start: 15
  outliers final: 12
  residues processed: 138
  average time/residue: 0.3977
  time to fit residues: 74.1972
Evaluate side-chains
  136 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  380 HIS
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue   99 SER
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue   96 ASP
Chi-restraints excluded: chain H residue  112 SER
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  187 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 64 optimal weight:    0.0010
   chunk 19 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 61 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.6386

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

Flipped N/Q/H residues before XYZ refinement:
B 105 GLN
L   3 GLN
L  55 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.143503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.116960 restraints weight = 29387.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.121436 restraints weight = 16016.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.124379 restraints weight = 10623.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.5554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7111  Z= 0.137
  Angle     :  0.560   7.836   9659  Z= 0.287
  Chirality :  0.043   0.157   1091
  Planarity :  0.003   0.033   1219
  Dihedral  :  4.736  19.775    970
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 16.75 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.15 (0.29), residues: 883
  helix:  1.66 (0.73), residues: 55
  sheet: -0.06 (0.29), residues: 340
  loop : -0.24 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 100A
 HIS   0.004   0.001   HIS L 198 
 PHE   0.012   0.001   PHE H 122 
 TYR   0.012   0.001   TYR L  49 
 ARG   0.006   0.000   ARG C  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  254)
  hydrogen bonds       : angle       5.89824 (  660)
  SS BOND              : bond        0.00312 (   11)
  SS BOND              : angle       0.75005 (   22)
  covalent geometry    : bond        0.00322 ( 7100)
  covalent geometry    : angle       0.55984 ( 9637)

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

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

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 125
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 GLU cc_start: 0.8161 (tt0) cc_final: 0.7910 (mt-10)
REVERT: B   13 GLN cc_start: 0.8058 (mp10) cc_final: 0.7729 (mp10)
REVERT: B   31 SER cc_start: 0.7854 (p) cc_final: 0.7629 (t)
REVERT: H    6 GLU cc_start: 0.8474 (mp0) cc_final: 0.8022 (mp0)
  outliers start: 13
  outliers final: 12
  residues processed: 134
  average time/residue: 0.4602
  time to fit residues: 82.7415
Evaluate side-chains
  135 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  380 HIS
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue   99 SER
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue   96 ASP
Chi-restraints excluded: chain H residue  112 SER
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  187 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 60 optimal weight:    0.8980
   chunk 57 optimal weight:    0.5980
   chunk 59 optimal weight:    0.8980
   chunk 86 optimal weight:    0.4980
   chunk 5 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 476 ASN
B  32 ASN
B 105 GLN
L  55 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.143687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.117472 restraints weight = 29575.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.121981 restraints weight = 15996.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.124986 restraints weight = 10521.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.5674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7111  Z= 0.126
  Angle     :  0.559   7.863   9659  Z= 0.286
  Chirality :  0.043   0.164   1091
  Planarity :  0.003   0.033   1219
  Dihedral  :  4.678  19.271    970
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.01 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.16 (0.29), residues: 883
  helix:  1.69 (0.73), residues: 55
  sheet: -0.08 (0.29), residues: 340
  loop : -0.24 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 100A
 HIS   0.004   0.001   HIS L 198 
 PHE   0.010   0.001   PHE L 209 
 TYR   0.011   0.001   TYR L  49 
 ARG   0.005   0.000   ARG C  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03119 (  254)
  hydrogen bonds       : angle       5.85431 (  660)
  SS BOND              : bond        0.00297 (   11)
  SS BOND              : angle       0.64498 (   22)
  covalent geometry    : bond        0.00297 ( 7100)
  covalent geometry    : angle       0.55923 ( 9637)

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

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

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1766 Ramachandran restraints generated.
    883 Oldfield, 0 Emsley, 883 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 129
  time to evaluate  : 2.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  306 GLU cc_start: 0.8147 (tt0) cc_final: 0.7910 (mt-10)
REVERT: B   31 SER cc_start: 0.7775 (p) cc_final: 0.7514 (t)
REVERT: B  105 GLN cc_start: 0.8478 (mm-40) cc_final: 0.7487 (pp30)
REVERT: C   42 ARG cc_start: 0.7710 (tpp80) cc_final: 0.7281 (tpp80)
REVERT: H    6 GLU cc_start: 0.8478 (mp0) cc_final: 0.8042 (mp0)
REVERT: H  210 LYS cc_start: 0.8614 (pptt) cc_final: 0.8198 (tttt)
REVERT: L  167 ASP cc_start: 0.8107 (t0) cc_final: 0.6425 (m-30)
  outliers start: 13
  outliers final: 12
  residues processed: 138
  average time/residue: 0.5548
  time to fit residues: 105.2306
Evaluate side-chains
  138 residues out of total 782 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 LYS
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  380 HIS
Chi-restraints excluded: chain A residue  484 ASP
Chi-restraints excluded: chain B residue   99 SER
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   92 CYS
Chi-restraints excluded: chain H residue   96 ASP
Chi-restraints excluded: chain H residue  112 SER
Chi-restraints excluded: chain H residue  138 LEU
Chi-restraints excluded: chain L residue  180 THR
Chi-restraints excluded: chain L residue  187 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 476 ASN
L  55 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.141809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.115181 restraints weight = 29577.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.119697 restraints weight = 15996.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.122692 restraints weight = 10577.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.5752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7111  Z= 0.166
  Angle     :  0.580   7.845   9659  Z= 0.298
  Chirality :  0.043   0.158   1091
  Planarity :  0.003   0.033   1219
  Dihedral  :  4.765  20.720    970
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 16.88 %
    Favored  : 81.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.28 (0.29), residues: 883
  helix:  1.66 (0.74), residues: 54
  sheet: -0.15 (0.29), residues: 332
  loop : -0.34 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 100A
 HIS   0.004   0.001   HIS L 198 
 PHE   0.011   0.001   PHE H 122 
 TYR   0.016   0.001   TYR L  49 
 ARG   0.006   0.001   ARG C  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03310 (  254)
  hydrogen bonds       : angle       5.93014 (  660)
  SS BOND              : bond        0.00322 (   11)
  SS BOND              : angle       0.77816 (   22)
  covalent geometry    : bond        0.00392 ( 7100)
  covalent geometry    : angle       0.57908 ( 9637)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5555.64 seconds
wall clock time: 99 minutes 7.53 seconds (5947.53 seconds total)