Starting phenix.real_space_refine
on Wed Sep 17 08:30:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vul_43532/09_2025/8vul_43532.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vul_43532/09_2025/8vul_43532.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vul_43532/09_2025/8vul_43532.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vul_43532/09_2025/8vul_43532.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vul_43532/09_2025/8vul_43532.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vul_43532/09_2025/8vul_43532.cif"
  }
  resolution = 3.83
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    4560      2.51       5
     N    1244      2.21       5
     O    1329      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7158
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 369, 2800
          Classifications: {'peptide': 369}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 17, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 104
          Unresolved non-hydrogen angles: 127
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 1, 'HIS:plan': 2, 'ASP:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 71
    Chain: "B"
      Number of atoms: 2665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 366, 2665
          Classifications: {'peptide': 366}
          Incomplete info: {'truncation_to_alanine': 71}
          Link IDs: {'PTRANS': 15, 'TRANS': 350}
          Unresolved non-hydrogen bonds: 243
          Unresolved non-hydrogen angles: 301
          Unresolved non-hydrogen dihedrals: 194
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'HIS:plan': 2, 'ASP:plan': 15, 'GLU:plan': 15, 'ARG:plan': 5, 'GLN:plan1': 3, 'PHE:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 168
    Chain: "H"
      Number of atoms: 894
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 894
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "L"
      Number of atoms: 799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 799
          Classifications: {'peptide': 109}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 13
  Time building chain proxies: 1.94, per 1000 atoms: 0.27
  Number of scatterers: 7158
  At special positions: 0
  Unit cell: (107.8, 126.5, 85.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    1329      8.00
     N    1244      7.00
     C    4560      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  79 " - pdb=" SG  CYS A 308 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  87 " - pdb=" SG  CYS B 320 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  91 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.55
  Conformation dependent library (CDL) restraints added in 502.3 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1790

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 12 sheets defined
      29.2% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 53
      removed outlier: 3.792A  pdb=" N   LYS A  51 " --> pdb=" O   ASN A  47 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ARG A  52 " --> pdb=" O   GLN A  48 " (cutoff:3.500A)
      removed outlier: 4.426A  pdb=" N   HIS A  53 " --> pdb=" O   ALA A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 86
      removed outlier: 4.442A  pdb=" N   ALA A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   LEU A  76 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 114
      removed outlier: 3.624A  pdb=" N   PHE A 113 " --> pdb=" O   TYR A 109 " (cutoff:3.500A)
      removed outlier: 4.248A  pdb=" N   TYR A 114 " --> pdb=" O   THR A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.862A  pdb=" N   TYR A 128 " --> pdb=" O   MET A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 146
    Processing helix  chain 'A' and resid 147 through 159
    Processing helix  chain 'A' and resid 170 through 186
    Processing helix  chain 'A' and resid 204 through 213
      removed outlier: 3.779A  pdb=" N   GLU A 213 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 238
      removed outlier: 3.853A  pdb=" N   THR A 230 " --> pdb=" O   ASP A 226 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   MET A 237 " --> pdb=" O   ARG A 233 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LEU A 238 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.935A  pdb=" N   LEU A 259 " --> pdb=" O   GLY A 256 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ARG A 260 " --> pdb=" O   ASN A 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 256 through 260'
    Processing helix  chain 'A' and resid 277 through 296
    Processing helix  chain 'A' and resid 317 through 327
    Processing helix  chain 'B' and resid 50 through 55
    Processing helix  chain 'B' and resid 78 through 94
      removed outlier: 3.682A  pdb=" N   ILE B  83 " --> pdb=" O   PRO B  79 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   THR B  84 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ARG B  94 " --> pdb=" O   MET B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 107 through 121
      removed outlier: 4.304A  pdb=" N   GLN B 111 " --> pdb=" O   GLU B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 133
      removed outlier: 3.757A  pdb=" N   MET B 133 " --> pdb=" O   GLY B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 165
      removed outlier: 3.507A  pdb=" N   GLN B 154 " --> pdb=" O   SER B 150 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 193
    Processing helix  chain 'B' and resid 214 through 221
    Processing helix  chain 'B' and resid 232 through 247
    Processing helix  chain 'B' and resid 287 through 310
    Processing helix  chain 'H' and resid 62 through 68
      removed outlier: 3.638A  pdb=" N   LYS H  65 " --> pdb=" O   PRO H  62 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   SER H  66 " --> pdb=" O   SER H  63 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   VAL H  68 " --> pdb=" O   LYS H  65 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 86
      removed outlier: 3.881A  pdb=" N   ASP L  85 " --> pdb=" O   LYS L  82 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   GLU L  86 " --> pdb=" O   THR L  83 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 82 through 86'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66
      removed outlier: 6.423A  pdb=" N   ILE A  90 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 197
      removed outlier: 4.092A  pdb=" N   LYS A 193 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 6.682A  pdb=" N   ILE A 164 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 8.206A  pdb=" N   SER A 222 " --> pdb=" O   ILE A 164 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   LEU A 166 " --> pdb=" O   SER A 222 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   ILE A 219 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271
      removed outlier: 6.178A  pdb=" N   ASN A 355 " --> pdb=" O   GLN A 363 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   GLN A 363 " --> pdb=" O   ASN A 355 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 70
      removed outlier: 9.340A  pdb=" N   VAL B  99 " --> pdb=" O   ASN B  35 " (cutoff:3.500A)
      removed outlier: 6.989A  pdb=" N   ALA B  37 " --> pdb=" O   VAL B  99 " (cutoff:3.500A)
      removed outlier: 8.704A  pdb=" N   GLY B 101 " --> pdb=" O   ALA B  37 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   MET B  39 " --> pdb=" O   GLY B 101 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 227 through 228
      removed outlier: 6.248A  pdb=" N   ILE B 227 " --> pdb=" O   ILE B 256 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   VAL B 279 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   VAL B 363 " --> pdb=" O   VAL B 375 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LYS B 377 " --> pdb=" O   SER B 384 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   SER B 384 " --> pdb=" O   LYS B 377 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.439A  pdb=" N   TRP H  48 " --> pdb=" O   ARG H  39 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ARG H  39 " --> pdb=" O   TRP H  48 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLY H  50 " --> pdb=" O   TRP H  37 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TRP H  35 " --> pdb=" O   ILE H  52 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 110 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   TRP H 110 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 108 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60
      removed outlier: 5.439A  pdb=" N   TRP H  48 " --> pdb=" O   ARG H  39 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ARG H  39 " --> pdb=" O   TRP H  48 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLY H  50 " --> pdb=" O   TRP H  37 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TRP H  35 " --> pdb=" O   ILE H  52 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 5
      removed outlier: 3.544A  pdb=" N   THR L   5 " --> pdb=" O   THR L  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 11
      removed outlier: 6.805A  pdb=" N   VAL L  10 " --> pdb=" O   THR L 108 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'L' and resid 46 through 49
      removed outlier: 6.557A  pdb=" N   TRP L  36 " --> pdb=" O   VAL L  48 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   SER L  93 " --> pdb=" O   VAL L 100 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL L 100 " --> pdb=" O   SER L  93 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 63 through 64

    258 hydrogen bonds defined for protein.
    720 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.03

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2329
        1.35 -     1.47: 1858
        1.47 -     1.59: 3097
        1.59 -     1.72: 2
        1.72 -     1.84: 41
  Bond restraints: 7327
  Sorted by residual:
  bond pdb=" N   PRO A 304 "
       pdb=" CA  PRO A 304 "
    ideal  model  delta    sigma   weight residual
    1.465  1.407  0.058 2.03e-02 2.43e+03 8.25e+00
  bond pdb=" CB  PRO A 304 "
       pdb=" CG  PRO A 304 "
    ideal  model  delta    sigma   weight residual
    1.492  1.635 -0.143 5.00e-02 4.00e+02 8.23e+00
  bond pdb=" CG  PRO A 304 "
       pdb=" CD  PRO A 304 "
    ideal  model  delta    sigma   weight residual
    1.503  1.408  0.095 3.40e-02 8.65e+02 7.74e+00
  bond pdb=" N   PRO A 304 "
       pdb=" CD  PRO A 304 "
    ideal  model  delta    sigma   weight residual
    1.473  1.507 -0.034 1.40e-02 5.10e+03 5.78e+00
  bond pdb=" CB  PRO B 336 "
       pdb=" CG  PRO B 336 "
    ideal  model  delta    sigma   weight residual
    1.492  1.612 -0.120 5.00e-02 4.00e+02 5.78e+00
  ... (remaining 7322 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.19: 9950
        3.19 -     6.37: 42
        6.37 -     9.56: 14
        9.56 -    12.75: 2
       12.75 -    15.94: 1
  Bond angle restraints: 10009
  Sorted by residual:
  angle pdb=" CA  PRO A 304 "
        pdb=" N   PRO A 304 "
        pdb=" CD  PRO A 304 "
      ideal   model   delta    sigma   weight residual
     112.00   96.06   15.94 1.40e+00 5.10e-01 1.30e+02
  angle pdb=" CA  PRO B 336 "
        pdb=" N   PRO B 336 "
        pdb=" CD  PRO B 336 "
      ideal   model   delta    sigma   weight residual
     112.00  102.92    9.08 1.40e+00 5.10e-01 4.21e+01
  angle pdb=" N   PRO A 304 "
        pdb=" CD  PRO A 304 "
        pdb=" CG  PRO A 304 "
      ideal   model   delta    sigma   weight residual
     103.20   94.35    8.85 1.50e+00 4.44e-01 3.48e+01
  angle pdb=" C   SER B 225 "
        pdb=" N   VAL B 226 "
        pdb=" CA  VAL B 226 "
      ideal   model   delta    sigma   weight residual
     121.95  129.15   -7.20 1.53e+00 4.27e-01 2.21e+01
  angle pdb=" N   PRO B 336 "
        pdb=" CD  PRO B 336 "
        pdb=" CG  PRO B 336 "
      ideal   model   delta    sigma   weight residual
     103.20   96.36    6.84 1.50e+00 4.44e-01 2.08e+01
  ... (remaining 10004 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 3690
       17.92 -    35.84: 478
       35.84 -    53.76: 119
       53.76 -    71.68: 18
       71.68 -    89.60: 7
  Dihedral angle restraints: 4312
    sinusoidal: 1531
      harmonic: 2781
  Sorted by residual:
  dihedral pdb=" CB  CYS A  79 "
           pdb=" SG  CYS A  79 "
           pdb=" SG  CYS A 308 "
           pdb=" CB  CYS A 308 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -28.09  -57.91     1      1.00e+01 1.00e-02 4.50e+01
  dihedral pdb=" CA  SER B 225 "
           pdb=" C   SER B 225 "
           pdb=" N   VAL B 226 "
           pdb=" CA  VAL B 226 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.09   26.91     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" CA  PRO A  98 "
           pdb=" C   PRO A  98 "
           pdb=" N   ASN A  99 "
           pdb=" CA  ASN A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.91   22.09     0      5.00e+00 4.00e-02 1.95e+01
  ... (remaining 4309 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 739
       0.032 -    0.065: 274
       0.065 -    0.097: 100
       0.097 -    0.129: 43
       0.129 -    0.161: 7
  Chirality restraints: 1163
  Sorted by residual:
  chirality pdb=" CA  VAL B 226 "
            pdb=" N   VAL B 226 "
            pdb=" C   VAL B 226 "
            pdb=" CB  VAL B 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.50e-01
  chirality pdb=" CA  ASN L  53 "
            pdb=" N   ASN L  53 "
            pdb=" C   ASN L  53 "
            pdb=" CB  ASN L  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.00e-01
  chirality pdb=" CA  VAL A  32 "
            pdb=" N   VAL A  32 "
            pdb=" C   VAL A  32 "
            pdb=" CB  VAL A  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.63e-01
  ... (remaining 1160 not shown)

  Planarity restraints: 1274
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 303 "   -0.117 5.00e-02 4.00e+02   1.64e-01 4.29e+01
        pdb=" N   PRO A 304 "    0.283 5.00e-02 4.00e+02
        pdb=" CA  PRO A 304 "   -0.087 5.00e-02 4.00e+02
        pdb=" CD  PRO A 304 "   -0.078 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 204 "    0.010 2.00e-02 2.50e+03   1.90e-02 3.62e+00
        pdb=" C   VAL A 204 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   VAL A 204 "    0.012 2.00e-02 2.50e+03
        pdb=" N   THR A 205 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  63 "   -0.030 5.00e-02 4.00e+02   4.50e-02 3.24e+00
        pdb=" N   PRO B  64 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO B  64 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B  64 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1271 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 958
        2.75 -     3.29: 6671
        3.29 -     3.83: 10992
        3.83 -     4.36: 11212
        4.36 -     4.90: 21177
  Nonbonded interactions: 51010
  Sorted by model distance:
  nonbonded pdb=" OG  SER L  64 "
            pdb=" OG1 THR L  77 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   ILE B 116 "
            pdb=" OG1 THR B 120 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   SER H  32 "
            pdb=" OG  SER H  32 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" NE1 TRP H 106 "
            pdb=" OG1 THR L  47 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" OD1 ASN B 367 "
            pdb=" N   LYS B 368 "
     model   vdw
     2.290 3.120
  ... (remaining 51005 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:             4.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     8.110
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
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      :  0.004   0.143   7331  Z= 0.133
  Angle     :  0.682  15.935  10017  Z= 0.364
  Chirality :  0.042   0.161   1163
  Planarity :  0.006   0.164   1274
  Dihedral  : 16.798  89.605   2510
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.80 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  : 35.74 %
    Favored  : 63.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.27), residues: 955
  helix:  1.71 (0.36), residues: 234
  sheet: -1.14 (0.36), residues: 209
  loop : -2.59 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 306 
 TYR   0.012   0.001   TYR L  94 
 PHE   0.013   0.001   PHE B 396 
 TRP   0.008   0.001   TRP B 255 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 7327)
  covalent geometry    : angle       0.67979 (10009)
  SS BOND              : bond        0.00610 (    4)
  SS BOND              : angle       2.05202 (    8)
  hydrogen bonds       : bond        0.18575 (  246)
  hydrogen bonds       : angle       7.13572 (  720)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 140
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7274 (mp0) cc_final: 0.6961 (mp0)
  outliers start: 2
  outliers final: 0
  residues processed: 141
  average time/residue: 0.0684
  time to fit residues: 13.9562
Evaluate side-chains
  134 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.2980
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  38 HIS
A 177 GLN
A 196 GLN
A 358 ASN
H 105 ASN
L  38 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.142175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.111331 restraints weight = 11668.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.112374 restraints weight = 9762.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.114081 restraints weight = 8834.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.114518 restraints weight = 6897.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.115258 restraints weight = 6266.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.0916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7331  Z= 0.126
  Angle     :  0.608  10.080  10017  Z= 0.315
  Chirality :  0.043   0.141   1163
  Planarity :  0.004   0.046   1274
  Dihedral  :  4.183  27.024   1027
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.11 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 32.33 %
    Favored  : 63.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.63 (0.27), residues: 955
  helix:  1.75 (0.35), residues: 245
  sheet: -1.27 (0.34), residues: 232
  loop : -2.63 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  55 
 TYR   0.012   0.001   TYR H  95 
 PHE   0.021   0.001   PHE B 186 
 TRP   0.006   0.001   TRP H  34 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7327)
  covalent geometry    : angle       0.60682 (10009)
  SS BOND              : bond        0.00505 (    4)
  SS BOND              : angle       1.47063 (    8)
  hydrogen bonds       : bond        0.03969 (  246)
  hydrogen bonds       : angle       4.99216 (  720)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 134
  time to evaluate  : 0.259 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7716 (mp0) cc_final: 0.7258 (mp0)
REVERT: B  286 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.6703 (t80)
  outliers start: 32
  outliers final: 16
  residues processed: 157
  average time/residue: 0.0603
  time to fit residues: 13.7839
Evaluate side-chains
  141 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue  105 ASN
Chi-restraints excluded: chain H residue  108 ASP
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 18 optimal weight:    3.9990
   chunk 84 optimal weight:    0.4980
   chunk 58 optimal weight:    0.8980
   chunk 60 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 82 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0050
   chunk 1 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
** B  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 105 ASN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.141413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.111117 restraints weight = 11512.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.112096 restraints weight = 9588.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.113745 restraints weight = 8751.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.114350 restraints weight = 6760.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.114409 restraints weight = 6705.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7331  Z= 0.123
  Angle     :  0.598   9.878  10017  Z= 0.309
  Chirality :  0.042   0.159   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.217  31.368   1027
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.90 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 31.11 %
    Favored  : 64.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.58 (0.28), residues: 955
  helix:  1.83 (0.35), residues: 245
  sheet: -1.18 (0.34), residues: 233
  loop : -2.65 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  55 
 TYR   0.009   0.001   TYR L  89 
 PHE   0.009   0.001   PHE B 186 
 TRP   0.005   0.001   TRP H 106 
 HIS   0.003   0.001   HIS B  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7327)
  covalent geometry    : angle       0.59679 (10009)
  SS BOND              : bond        0.00386 (    4)
  SS BOND              : angle       1.20788 (    8)
  hydrogen bonds       : bond        0.03619 (  246)
  hydrogen bonds       : angle       4.66419 (  720)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 129
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7731 (mp0) cc_final: 0.7251 (mp0)
REVERT: A  323 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7285 (mtm-85)
REVERT: B  286 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.6838 (t80)
REVERT: B  365 VAL cc_start: 0.9245 (p) cc_final: 0.8939 (m)
  outliers start: 32
  outliers final: 18
  residues processed: 151
  average time/residue: 0.0671
  time to fit residues: 14.7294
Evaluate side-chains
  140 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  323 ARG
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  298 ILE
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue  105 ASN
Chi-restraints excluded: chain H residue  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue   38 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 46 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 73 optimal weight:    0.0970
   chunk 20 optimal weight:    0.0970
   chunk 28 optimal weight:   10.0000
   chunk 30 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.4976

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

Flipped N/Q/H residues before XYZ refinement:
** B  96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 105 ASN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.142121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.111494 restraints weight = 11699.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.112681 restraints weight = 9596.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.114132 restraints weight = 8619.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.114573 restraints weight = 6788.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.115176 restraints weight = 6139.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7331  Z= 0.119
  Angle     :  0.595   9.866  10017  Z= 0.308
  Chirality :  0.042   0.155   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.139  28.928   1027
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.90 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 30.70 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.28), residues: 955
  helix:  1.85 (0.35), residues: 245
  sheet: -1.21 (0.33), residues: 238
  loop : -2.63 (0.26), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.009   0.001   TYR A 367 
 PHE   0.010   0.001   PHE B 186 
 TRP   0.006   0.001   TRP H 106 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7327)
  covalent geometry    : angle       0.59423 (10009)
  SS BOND              : bond        0.00316 (    4)
  SS BOND              : angle       1.06275 (    8)
  hydrogen bonds       : bond        0.03395 (  246)
  hydrogen bonds       : angle       4.49503 (  720)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 124
  time to evaluate  : 0.188 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7706 (mp0) cc_final: 0.7236 (mp0)
REVERT: A  323 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7292 (mtm-85)
REVERT: B  286 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.6827 (t80)
REVERT: H   64 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.7948 (pp)
REVERT: L   89 TYR cc_start: 0.8494 (m-80) cc_final: 0.8178 (m-80)
  outliers start: 37
  outliers final: 22
  residues processed: 152
  average time/residue: 0.0649
  time to fit residues: 14.2174
Evaluate side-chains
  145 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  323 ARG
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain H residue  105 ASN
Chi-restraints excluded: chain H residue  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   chunk 23 optimal weight:    0.1980
   chunk 12 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0870
   chunk 54 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0470
   overall best weight:    0.4056

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

Flipped N/Q/H residues before XYZ refinement:
H 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.143055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.112663 restraints weight = 11707.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.113910 restraints weight = 9829.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.115505 restraints weight = 8735.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.115885 restraints weight = 6740.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.116472 restraints weight = 6182.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7331  Z= 0.112
  Angle     :  0.586   9.771  10017  Z= 0.304
  Chirality :  0.042   0.145   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.093  27.943   1027
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.21 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 31.51 %
    Favored  : 64.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.28), residues: 955
  helix:  1.91 (0.35), residues: 245
  sheet: -1.17 (0.33), residues: 244
  loop : -2.68 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.009   0.001   TYR A 367 
 PHE   0.016   0.001   PHE B 396 
 TRP   0.006   0.001   TRP H 106 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7327)
  covalent geometry    : angle       0.58583 (10009)
  SS BOND              : bond        0.00297 (    4)
  SS BOND              : angle       0.97146 (    8)
  hydrogen bonds       : bond        0.03171 (  246)
  hydrogen bonds       : angle       4.31189 (  720)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 127
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7638 (mp0) cc_final: 0.7201 (mp0)
REVERT: A  323 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7485 (mtm-85)
REVERT: A  332 ASP cc_start: 0.6871 (p0) cc_final: 0.6632 (t0)
REVERT: B  286 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.6843 (t80)
REVERT: B  365 VAL cc_start: 0.9291 (p) cc_final: 0.9004 (m)
REVERT: H   64 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7933 (pp)
REVERT: L   89 TYR cc_start: 0.8541 (m-80) cc_final: 0.8250 (m-80)
  outliers start: 29
  outliers final: 22
  residues processed: 149
  average time/residue: 0.0610
  time to fit residues: 13.5097
Evaluate side-chains
  145 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 ARG
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain H residue  105 ASN
Chi-restraints excluded: chain H residue  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 85 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0070
   chunk 80 optimal weight:    0.0970
   chunk 81 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
H 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.142454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.112085 restraints weight = 11726.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.113216 restraints weight = 9712.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.114922 restraints weight = 8621.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.115297 restraints weight = 6629.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.115455 restraints weight = 6091.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7331  Z= 0.122
  Angle     :  0.601   9.741  10017  Z= 0.311
  Chirality :  0.042   0.144   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.121  30.608   1027
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.80 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 30.29 %
    Favored  : 64.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.28), residues: 955
  helix:  1.91 (0.35), residues: 245
  sheet: -1.15 (0.34), residues: 239
  loop : -2.69 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  55 
 TYR   0.010   0.001   TYR H  60 
 PHE   0.014   0.001   PHE B 396 
 TRP   0.006   0.001   TRP B 255 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7327)
  covalent geometry    : angle       0.59843 (10009)
  SS BOND              : bond        0.00402 (    4)
  SS BOND              : angle       2.05841 (    8)
  hydrogen bonds       : bond        0.03336 (  246)
  hydrogen bonds       : angle       4.32527 (  720)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  323 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7235 (mtm-85)
REVERT: B  193 ASN cc_start: 0.7529 (t0) cc_final: 0.6928 (t0)
REVERT: B  286 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.6879 (t80)
REVERT: H   64 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.7907 (pp)
REVERT: L   89 TYR cc_start: 0.8582 (m-80) cc_final: 0.8283 (m-80)
  outliers start: 38
  outliers final: 27
  residues processed: 147
  average time/residue: 0.0616
  time to fit residues: 13.3803
Evaluate side-chains
  147 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 117
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 ARG
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue   36 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain H residue  105 ASN
Chi-restraints excluded: chain H residue  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0070
   chunk 48 optimal weight:    0.5980
   chunk 71 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   chunk 87 optimal weight:    0.2980
   chunk 50 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.3998

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

Flipped N/Q/H residues before XYZ refinement:
H 105 ASN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.143387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.112852 restraints weight = 11658.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.113638 restraints weight = 9562.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.115235 restraints weight = 8728.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.115616 restraints weight = 6900.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.116205 restraints weight = 6257.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7331  Z= 0.114
  Angle     :  0.599   9.719  10017  Z= 0.308
  Chirality :  0.042   0.155   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.093  29.880   1027
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.32 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 31.38 %
    Favored  : 63.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.53 (0.28), residues: 955
  helix:  1.94 (0.35), residues: 245
  sheet: -1.17 (0.33), residues: 244
  loop : -2.67 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 244 
 TYR   0.010   0.001   TYR L  94 
 PHE   0.018   0.001   PHE B 396 
 TRP   0.006   0.001   TRP B 255 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7327)
  covalent geometry    : angle       0.59711 (10009)
  SS BOND              : bond        0.00475 (    4)
  SS BOND              : angle       1.73960 (    8)
  hydrogen bonds       : bond        0.03130 (  246)
  hydrogen bonds       : angle       4.29692 (  720)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  323 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7274 (mtm-85)
REVERT: B  193 ASN cc_start: 0.7559 (t0) cc_final: 0.6977 (t0)
REVERT: B  286 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.6888 (t80)
REVERT: B  365 VAL cc_start: 0.9318 (p) cc_final: 0.9038 (m)
REVERT: H   64 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7957 (pp)
REVERT: L   89 TYR cc_start: 0.8555 (m-80) cc_final: 0.8245 (m-80)
  outliers start: 36
  outliers final: 28
  residues processed: 149
  average time/residue: 0.0652
  time to fit residues: 14.1465
Evaluate side-chains
  147 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 ARG
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain H residue  105 ASN
Chi-restraints excluded: chain H residue  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0050
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 63 optimal weight:    5.9990
   chunk 48 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
H 105 ASN
L  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.142745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.112480 restraints weight = 11735.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.113251 restraints weight = 9850.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.115034 restraints weight = 8980.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.115309 restraints weight = 6898.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.116044 restraints weight = 6345.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7331  Z= 0.124
  Angle     :  0.614   9.702  10017  Z= 0.315
  Chirality :  0.042   0.142   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.099  30.953   1027
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.63 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 31.92 %
    Favored  : 63.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.28), residues: 955
  helix:  1.94 (0.35), residues: 245
  sheet: -1.19 (0.33), residues: 244
  loop : -2.68 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 244 
 TYR   0.010   0.001   TYR L  94 
 PHE   0.011   0.001   PHE B 396 
 TRP   0.005   0.001   TRP B 255 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 7327)
  covalent geometry    : angle       0.61278 (10009)
  SS BOND              : bond        0.00404 (    4)
  SS BOND              : angle       1.65291 (    8)
  hydrogen bonds       : bond        0.03227 (  246)
  hydrogen bonds       : angle       4.26769 (  720)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 115
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  323 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7281 (mtm-85)
REVERT: A  326 MET cc_start: 0.7750 (mmm) cc_final: 0.7351 (mmm)
REVERT: B  193 ASN cc_start: 0.7586 (t0) cc_final: 0.7032 (t0)
REVERT: B  244 ARG cc_start: 0.7741 (tpt-90) cc_final: 0.7397 (ttt90)
REVERT: B  286 TYR cc_start: 0.8246 (OUTLIER) cc_final: 0.6948 (t80)
REVERT: B  365 VAL cc_start: 0.9314 (p) cc_final: 0.9038 (m)
REVERT: H   20 LEU cc_start: 0.8279 (mt) cc_final: 0.8030 (mp)
REVERT: H   64 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7940 (pp)
  outliers start: 36
  outliers final: 30
  residues processed: 145
  average time/residue: 0.0636
  time to fit residues: 13.4535
Evaluate side-chains
  153 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 ARG
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  278 SER
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain H residue  105 ASN
Chi-restraints excluded: chain H residue  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   38 GLN
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0070
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
H 105 ASN
L  32 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.141495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.111239 restraints weight = 11625.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.111200 restraints weight = 9612.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.112703 restraints weight = 9827.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.113459 restraints weight = 7648.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.113630 restraints weight = 7158.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7331  Z= 0.133
  Angle     :  0.618   9.774  10017  Z= 0.317
  Chirality :  0.043   0.142   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.243  30.478   1027
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  9.63 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 32.61 %
    Favored  : 62.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.28), residues: 955
  helix:  1.94 (0.35), residues: 245
  sheet: -1.17 (0.33), residues: 244
  loop : -2.70 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  55 
 TYR   0.009   0.001   TYR L  94 
 PHE   0.012   0.001   PHE B 186 
 TRP   0.006   0.001   TRP H  35 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 7327)
  covalent geometry    : angle       0.61649 (10009)
  SS BOND              : bond        0.00377 (    4)
  SS BOND              : angle       1.65399 (    8)
  hydrogen bonds       : bond        0.03312 (  246)
  hydrogen bonds       : angle       4.27729 (  720)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 115
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A  323 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7285 (mtm-85)
REVERT: A  326 MET cc_start: 0.7736 (mmm) cc_final: 0.7343 (mmm)
REVERT: A  332 ASP cc_start: 0.6921 (p0) cc_final: 0.6654 (t0)
REVERT: B  193 ASN cc_start: 0.7608 (t0) cc_final: 0.7088 (t0)
REVERT: B  244 ARG cc_start: 0.7748 (tpt-90) cc_final: 0.7433 (ttt90)
REVERT: B  286 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.6981 (t80)
REVERT: B  365 VAL cc_start: 0.9306 (p) cc_final: 0.9023 (m)
REVERT: H   20 LEU cc_start: 0.8290 (mt) cc_final: 0.8056 (mp)
REVERT: H   64 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7911 (pp)
REVERT: L   89 TYR cc_start: 0.8440 (m-10) cc_final: 0.8150 (m-80)
  outliers start: 34
  outliers final: 29
  residues processed: 143
  average time/residue: 0.0712
  time to fit residues: 14.5554
Evaluate side-chains
  146 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 ARG
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  278 SER
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain H residue  105 ASN
Chi-restraints excluded: chain H residue  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 59 optimal weight:    0.1980
   chunk 68 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 35 optimal weight:    0.5980
   chunk 92 optimal weight:    0.4980
   chunk 25 optimal weight:    0.0980
   chunk 58 optimal weight:    0.0980
   chunk 69 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.2980

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

Flipped N/Q/H residues before XYZ refinement:
H 105 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.143684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.113702 restraints weight = 11681.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.114417 restraints weight = 9638.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.116284 restraints weight = 8932.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.116634 restraints weight = 6773.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.116807 restraints weight = 6243.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7331  Z= 0.112
  Angle     :  0.612   9.667  10017  Z= 0.314
  Chirality :  0.042   0.165   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.162  27.171   1027
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  9.84 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 32.74 %
    Favored  : 62.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.49 (0.28), residues: 955
  helix:  1.97 (0.35), residues: 245
  sheet: -1.06 (0.34), residues: 234
  loop : -2.69 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  55 
 TYR   0.011   0.001   TYR L  94 
 PHE   0.013   0.001   PHE B 186 
 TRP   0.008   0.001   TRP H  35 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 7327)
  covalent geometry    : angle       0.61025 (10009)
  SS BOND              : bond        0.00430 (    4)
  SS BOND              : angle       1.62674 (    8)
  hydrogen bonds       : bond        0.02972 (  246)
  hydrogen bonds       : angle       4.20577 (  720)

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

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

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1910 Ramachandran restraints generated.
    955 Oldfield, 0 Emsley, 955 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A  323 ARG cc_start: 0.8047 (OUTLIER) cc_final: 0.7304 (mtm-85)
REVERT: A  332 ASP cc_start: 0.6892 (p0) cc_final: 0.6627 (t0)
REVERT: B  193 ASN cc_start: 0.7587 (t0) cc_final: 0.7077 (t0)
REVERT: B  286 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7043 (t80)
REVERT: H   20 LEU cc_start: 0.8273 (mt) cc_final: 0.8032 (mp)
REVERT: H   64 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7876 (pp)
REVERT: L   62 ARG cc_start: 0.8359 (mpp80) cc_final: 0.8155 (mtm180)
REVERT: L   89 TYR cc_start: 0.8428 (m-10) cc_final: 0.8121 (m-80)
  outliers start: 33
  outliers final: 25
  residues processed: 146
  average time/residue: 0.0705
  time to fit residues: 14.5995
Evaluate side-chains
  142 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  301 ILE
Chi-restraints excluded: chain A residue  323 ARG
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain H residue   21 THR
Chi-restraints excluded: chain H residue   23 THR
Chi-restraints excluded: chain H residue   58 THR
Chi-restraints excluded: chain H residue   64 LEU
Chi-restraints excluded: chain H residue  105 ASN
Chi-restraints excluded: chain H residue  108 ASP
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue  109 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** H 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.140482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.110391 restraints weight = 11756.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.111063 restraints weight = 10026.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.112682 restraints weight = 8853.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.112995 restraints weight = 7187.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.113590 restraints weight = 6534.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   7331  Z= 0.170
  Angle     :  0.658   9.955  10017  Z= 0.339
  Chirality :  0.043   0.165   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.341  25.091   1027
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 10.47 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 33.02 %
    Favored  : 62.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.60 (0.28), residues: 955
  helix:  1.88 (0.35), residues: 245
  sheet: -1.18 (0.34), residues: 234
  loop : -2.72 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 244 
 TYR   0.010   0.001   TYR B 286 
 PHE   0.015   0.001   PHE B 186 
 TRP   0.007   0.001   TRP H 110 
 HIS   0.003   0.001   HIS B  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 7327)
  covalent geometry    : angle       0.65660 (10009)
  SS BOND              : bond        0.00372 (    4)
  SS BOND              : angle       1.68911 (    8)
  hydrogen bonds       : bond        0.03797 (  246)
  hydrogen bonds       : angle       4.32212 (  720)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1256.95 seconds
wall clock time: 22 minutes 27.75 seconds (1347.75 seconds total)