Starting phenix.real_space_refine
on Tue Jan 14 18:51:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vul_43532/01_2025/8vul_43532.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vul_43532/01_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_43532/01_2025/8vul_43532.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vul_43532/01_2025/8vul_43532.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vul_43532/01_2025/8vul_43532.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vul_43532/01_2025/8vul_43532.cif"
  }
  resolution = 3.83
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.024
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: {'GLN:plan1': 1, 'GLU:plan': 12, 'ASP:plan': 1, 'PHE:plan': 1, 'HIS:plan': 2}
          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: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 15, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5}
          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: {'GLN:plan1': 1, 'GLU:plan': 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: {'GLU:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 13
  Time building chain proxies: 5.26, per 1000 atoms: 0.73
  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: 1.70
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.79
  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: 1.97

  Time building geometry restraints manager: 2.00 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:             3.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.030
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.490
-------------------------------------------------------------------------------
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   7327  Z= 0.243
  Angle     :  0.680  15.935  10009  Z= 0.363
  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 : 7.73
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.008   0.001   TRP B 255 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.013   0.001   PHE B 396 
 TYR   0.012   0.001   TYR L  94 
 ARG   0.004   0.000   ARG A 306 

*********************** 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  : 0.785 
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: 0.1537
  time to fit residues: 30.9134
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  : 1.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0040
   chunk 28 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0270
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.0056

-------------------------------------------------------------------------------
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 = 0.3644 r_free = 0.3644 target = 0.139074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.108329 restraints weight = 11506.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.109149 restraints weight = 9723.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.111031 restraints weight = 8784.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.1109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7327  Z= 0.297
  Angle     :  0.658  10.908  10009  Z= 0.342
  Chirality :  0.044   0.147   1163
  Planarity :  0.005   0.046   1274
  Dihedral  :  4.444  27.786   1027
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 10.16 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 32.47 %
    Favored  : 62.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.27), residues: 955
  helix:  1.89 (0.35), residues: 239
  sheet: -1.33 (0.34), residues: 228
  loop : -2.61 (0.25), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  34 
 HIS   0.004   0.001   HIS H  54 
 PHE   0.020   0.002   PHE B 186 
 TYR   0.012   0.001   TYR H  53 
 ARG   0.005   0.001   ARG L  55 

*********************** 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
  173 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 136
  time to evaluate  : 0.854 
Fit side-chains
REVERT: A  323 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7243 (mtm-85)
REVERT: B  193 ASN cc_start: 0.7437 (t0) cc_final: 0.7002 (t0)
REVERT: B  286 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.6835 (t80)
  outliers start: 37
  outliers final: 25
  residues processed: 164
  average time/residue: 0.1596
  time to fit residues: 37.3131
Evaluate side-chains
  147 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 ILE
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  323 ARG
Chi-restraints excluded: chain A residue  356 LEU
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain B residue   40 LEU
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 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  105 ASN
Chi-restraints excluded: chain H residue  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain H residue  117 THR
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 2 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 43 optimal weight:    0.3980
   chunk 18 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.140740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.110243 restraints weight = 11663.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.111177 restraints weight = 9543.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.112704 restraints weight = 8717.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7327  Z= 0.208
  Angle     :  0.616  10.043  10009  Z= 0.319
  Chirality :  0.043   0.159   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.387  32.138   1027
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.69 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 30.56 %
    Favored  : 63.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.28), residues: 955
  helix:  1.81 (0.35), residues: 246
  sheet: -1.30 (0.34), residues: 239
  loop : -2.69 (0.26), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H 106 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.018   0.001   PHE B 396 
 TYR   0.010   0.001   TYR A 367 
 ARG   0.004   0.000   ARG L  55 

*********************** 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
  172 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 130
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 ASP cc_start: 0.8244 (t0) cc_final: 0.8001 (t0)
REVERT: B  286 TYR cc_start: 0.8293 (OUTLIER) cc_final: 0.6776 (t80)
  outliers start: 42
  outliers final: 23
  residues processed: 162
  average time/residue: 0.1490
  time to fit residues: 34.5600
Evaluate side-chains
  146 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
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  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  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  244 ARG
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  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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 58 optimal weight:    0.4980
   chunk 46 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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**
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.140152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.109435 restraints weight = 11785.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.110688 restraints weight = 9836.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.112314 restraints weight = 8675.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7327  Z= 0.230
  Angle     :  0.627  10.201  10009  Z= 0.323
  Chirality :  0.043   0.151   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.357  29.817   1027
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  : 10.16 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 30.83 %
    Favored  : 63.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.28), residues: 955
  helix:  1.79 (0.35), residues: 246
  sheet: -1.26 (0.34), residues: 234
  loop : -2.69 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 381 
 HIS   0.003   0.001   HIS B  42 
 PHE   0.010   0.001   PHE B 186 
 TYR   0.009   0.001   TYR A 367 
 ARG   0.003   0.000   ARG L  55 

*********************** 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
  168 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8231 (t0) cc_final: 0.8024 (t0)
REVERT: A  323 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7299 (mtm-85)
REVERT: A  326 MET cc_start: 0.7710 (mmm) cc_final: 0.7435 (mmm)
REVERT: A  332 ASP cc_start: 0.6919 (p0) cc_final: 0.6682 (t0)
REVERT: B  193 ASN cc_start: 0.7466 (t0) cc_final: 0.6901 (t0)
REVERT: B  286 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.7051 (t80)
REVERT: H   64 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.7967 (pp)
  outliers start: 39
  outliers final: 26
  residues processed: 160
  average time/residue: 0.1731
  time to fit residues: 39.4933
Evaluate side-chains
  153 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
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  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  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  298 ILE
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  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   91 CYS
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 30 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0870
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  96 HIS ** 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 = 0.3661 r_free = 0.3661 target = 0.140602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.110157 restraints weight = 11568.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.111001 restraints weight = 9651.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.112647 restraints weight = 8671.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7327  Z= 0.215
  Angle     :  0.617   9.978  10009  Z= 0.318
  Chirality :  0.043   0.148   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.331  29.307   1027
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.01 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 30.83 %
    Favored  : 63.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.28), residues: 955
  helix:  1.79 (0.35), residues: 245
  sheet: -1.19 (0.34), residues: 234
  loop : -2.68 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 381 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.014   0.001   PHE B 396 
 TYR   0.010   0.001   TYR A 367 
 ARG   0.002   0.000   ARG L  55 

*********************** 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
  167 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 128
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8212 (t0) cc_final: 0.8003 (t0)
REVERT: A  323 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7306 (mtm-85)
REVERT: A  326 MET cc_start: 0.7612 (mmm) cc_final: 0.7342 (mmm)
REVERT: B  193 ASN cc_start: 0.7581 (t0) cc_final: 0.7027 (t0)
REVERT: B  286 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.7055 (t80)
REVERT: H   64 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7905 (pp)
  outliers start: 39
  outliers final: 25
  residues processed: 158
  average time/residue: 0.1489
  time to fit residues: 33.9481
Evaluate side-chains
  146 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 118
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
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  266 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   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  276 LEU
Chi-restraints excluded: chain B residue  278 SER
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  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   91 CYS
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 66 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 41 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 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 = 0.3651 r_free = 0.3651 target = 0.139631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.109287 restraints weight = 11641.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.109631 restraints weight = 9537.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.110836 restraints weight = 9682.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   7327  Z= 0.237
  Angle     :  0.635  10.040  10009  Z= 0.327
  Chirality :  0.043   0.148   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.364  31.307   1027
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.53 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 30.97 %
    Favored  : 63.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.28), residues: 955
  helix:  1.81 (0.35), residues: 246
  sheet: -1.21 (0.34), residues: 234
  loop : -2.69 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 381 
 HIS   0.003   0.001   HIS B  42 
 PHE   0.018   0.001   PHE B 396 
 TYR   0.010   0.001   TYR H  60 
 ARG   0.005   0.000   ARG B 244 

*********************** 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
  162 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 121
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.4359 (OUTLIER) cc_final: 0.3499 (p0)
REVERT: A  130 ASP cc_start: 0.8234 (t0) cc_final: 0.8018 (t0)
REVERT: A  323 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7326 (mtm-85)
REVERT: B  193 ASN cc_start: 0.7636 (t0) cc_final: 0.7157 (t0)
REVERT: B  286 TYR cc_start: 0.8330 (OUTLIER) cc_final: 0.7097 (t80)
REVERT: H   64 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7876 (pp)
  outliers start: 41
  outliers final: 31
  residues processed: 154
  average time/residue: 0.1509
  time to fit residues: 33.2138
Evaluate side-chains
  155 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 120
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
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  309 VAL
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   36 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue   89 LEU
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  298 ILE
Chi-restraints excluded: chain B residue  389 VAL
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  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   91 CYS
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 72 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0270
   chunk 60 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 11 optimal weight:    0.6980
   chunk 24 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 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 = 0.3673 r_free = 0.3673 target = 0.141736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.111353 restraints weight = 11735.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.111842 restraints weight = 9458.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.113195 restraints weight = 9325.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7327  Z= 0.194
  Angle     :  0.611   9.845  10009  Z= 0.316
  Chirality :  0.042   0.143   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.265  30.955   1027
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.80 %
    Favored  : 90.89 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 32.20 %
    Favored  : 62.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.28), residues: 955
  helix:  1.85 (0.35), residues: 245
  sheet: -1.13 (0.35), residues: 234
  loop : -2.65 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  35 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.014   0.001   PHE B 186 
 TYR   0.010   0.001   TYR A 367 
 ARG   0.003   0.000   ARG L  55 

*********************** 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: 38
    poor density    : 118
  time to evaluate  : 0.929 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8194 (t0) cc_final: 0.7976 (t0)
REVERT: A  323 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7288 (mtm-85)
REVERT: B  193 ASN cc_start: 0.7608 (t0) cc_final: 0.7151 (t0)
REVERT: B  286 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.7190 (t80)
REVERT: B  315 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7120 (mp0)
REVERT: H   64 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7929 (pp)
REVERT: L   89 TYR cc_start: 0.8645 (m-80) cc_final: 0.8370 (m-80)
  outliers start: 38
  outliers final: 26
  residues processed: 146
  average time/residue: 0.1600
  time to fit residues: 33.5093
Evaluate side-chains
  141 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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   89 LEU
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  315 GLU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain H residue    4 LEU
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  108 ASP
Chi-restraints excluded: chain H residue  114 THR
Chi-restraints excluded: chain L residue   34 VAL
Chi-restraints excluded: chain L residue   91 CYS
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 73 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0570
   chunk 33 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0060
   chunk 90 optimal weight:    5.9990
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.3914

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 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 = 0.3681 r_free = 0.3681 target = 0.142282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.112220 restraints weight = 11731.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.113111 restraints weight = 9927.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.115155 restraints weight = 8796.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.1575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7327  Z= 0.181
  Angle     :  0.617   9.718  10009  Z= 0.316
  Chirality :  0.042   0.141   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.197  31.502   1027
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.90 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 33.15 %
    Favored  : 62.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.28), residues: 955
  helix:  1.88 (0.35), residues: 245
  sheet: -1.16 (0.34), residues: 239
  loop : -2.63 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  35 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.017   0.001   PHE B 396 
 TYR   0.011   0.001   TYR L  94 
 ARG   0.004   0.000   ARG B 244 

*********************** 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
  150 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 118
  time to evaluate  : 0.814 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8136 (t0) cc_final: 0.7935 (t0)
REVERT: A  323 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7345 (mtm-85)
REVERT: A  332 ASP cc_start: 0.6918 (p0) cc_final: 0.6682 (t0)
REVERT: A  379 ILE cc_start: 0.8953 (pt) cc_final: 0.8689 (pt)
REVERT: B  193 ASN cc_start: 0.7619 (t0) cc_final: 0.7153 (t0)
REVERT: B  286 TYR cc_start: 0.8273 (OUTLIER) cc_final: 0.7179 (t80)
REVERT: B  315 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7074 (mp0)
REVERT: B  365 VAL cc_start: 0.9262 (p) cc_final: 0.8991 (m)
REVERT: H   64 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.7903 (pp)
REVERT: L   89 TYR cc_start: 0.8660 (m-80) cc_final: 0.8395 (m-80)
  outliers start: 32
  outliers final: 25
  residues processed: 143
  average time/residue: 0.1482
  time to fit residues: 30.8011
Evaluate side-chains
  143 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 114
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  266 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   89 LEU
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  315 GLU
Chi-restraints excluded: chain B residue  389 VAL
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   83 LEU
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   91 CYS
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 62 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 70 optimal weight:    0.3980
   chunk 28 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 10 optimal weight:    0.4980
   chunk 19 optimal weight:    0.8980
   chunk 66 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 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 = 0.3660 r_free = 0.3660 target = 0.140289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.110398 restraints weight = 11737.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.110595 restraints weight = 9661.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.111848 restraints weight = 9978.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7327  Z= 0.225
  Angle     :  0.640   9.864  10009  Z= 0.329
  Chirality :  0.043   0.168   1163
  Planarity :  0.004   0.043   1274
  Dihedral  :  4.232  26.628   1027
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.63 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 32.88 %
    Favored  : 62.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.28), residues: 955
  helix:  1.87 (0.35), residues: 245
  sheet: -1.13 (0.34), residues: 234
  loop : -2.65 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 381 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.016   0.001   PHE B 396 
 TYR   0.009   0.001   TYR A 367 
 ARG   0.003   0.000   ARG L  55 

*********************** 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
  158 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 121
  time to evaluate  : 0.826 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8285 (mmtm)
REVERT: A  227 ASP cc_start: 0.8246 (p0) cc_final: 0.7792 (p0)
REVERT: A  323 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7366 (mtm-85)
REVERT: A  332 ASP cc_start: 0.6851 (p0) cc_final: 0.6618 (t0)
REVERT: B  193 ASN cc_start: 0.7683 (t0) cc_final: 0.7261 (t0)
REVERT: B  286 TYR cc_start: 0.8346 (OUTLIER) cc_final: 0.7529 (t80)
REVERT: B  315 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7059 (mp0)
REVERT: B  360 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7991 (mmt90)
REVERT: H   20 LEU cc_start: 0.8413 (mt) cc_final: 0.8151 (mp)
REVERT: H   64 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7928 (pp)
  outliers start: 37
  outliers final: 26
  residues processed: 151
  average time/residue: 0.1634
  time to fit residues: 34.9725
Evaluate side-chains
  149 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 117
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LYS
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  230 THR
Chi-restraints excluded: chain A residue  266 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   40 LEU
Chi-restraints excluded: chain B residue   89 LEU
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  279 VAL
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  360 ARG
Chi-restraints excluded: chain B residue  389 VAL
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   83 LEU
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   91 CYS
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 24 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0060
   chunk 64 optimal weight:    0.9990
   chunk 48 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0010
   chunk 13 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0570
   overall best weight:    0.2520

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 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 = 0.3689 r_free = 0.3689 target = 0.142598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.112671 restraints weight = 11780.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.113742 restraints weight = 9873.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.115233 restraints weight = 9193.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.1691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7327  Z= 0.175
  Angle     :  0.633   9.674  10009  Z= 0.325
  Chirality :  0.042   0.173   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.100  25.522   1027
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.21 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 34.38 %
    Favored  : 61.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.28), residues: 955
  helix:  1.94 (0.35), residues: 245
  sheet: -1.04 (0.34), residues: 234
  loop : -2.62 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  35 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.013   0.001   PHE B 396 
 TYR   0.011   0.001   TYR L  94 
 ARG   0.003   0.000   ARG L  55 

********************** 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
  145 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 117
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8258 (mmtm)
REVERT: A  227 ASP cc_start: 0.8223 (p0) cc_final: 0.7186 (p0)
REVERT: A  323 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7328 (mtm-85)
REVERT: A  332 ASP cc_start: 0.6915 (p0) cc_final: 0.6618 (t0)
REVERT: B  193 ASN cc_start: 0.7638 (t0) cc_final: 0.7220 (t0)
REVERT: B  286 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7148 (t80)
REVERT: B  315 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7052 (mp0)
REVERT: H   20 LEU cc_start: 0.8375 (mt) cc_final: 0.8123 (mp)
REVERT: H   64 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.7863 (pp)
REVERT: L   89 TYR cc_start: 0.8438 (m-10) cc_final: 0.8233 (m-80)
  outliers start: 28
  outliers final: 18
  residues processed: 139
  average time/residue: 0.1547
  time to fit residues: 30.6411
Evaluate side-chains
  138 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 LYS
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  230 THR
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   89 LEU
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  215 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  315 GLU
Chi-restraints excluded: chain B residue  389 VAL
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   83 LEU
Chi-restraints excluded: chain H residue  108 ASP
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 69 optimal weight:    0.6980
   chunk 48 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 73 optimal weight:    0.5980
   chunk 40 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 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 = 0.3664 r_free = 0.3664 target = 0.140502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.110183 restraints weight = 11618.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.111366 restraints weight = 9939.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.112878 restraints weight = 8450.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7327  Z= 0.230
  Angle     :  0.666   9.867  10009  Z= 0.340
  Chirality :  0.043   0.174   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.207  26.515   1027
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.74 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 34.65 %
    Favored  : 61.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.28), residues: 955
  helix:  2.07 (0.36), residues: 238
  sheet: -1.14 (0.34), residues: 234
  loop : -2.54 (0.26), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 255 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.016   0.001   PHE B 396 
 TYR   0.016   0.001   TYR L  89 
 ARG   0.003   0.000   ARG L  55 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2149.06 seconds
wall clock time: 40 minutes 48.58 seconds (2448.58 seconds total)