Starting phenix.real_space_refine
on Wed Mar 12 03:27:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vul_43532/03_2025/8vul_43532.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vul_43532/03_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_43532/03_2025/8vul_43532.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vul_43532/03_2025/8vul_43532.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vul_43532/03_2025/8vul_43532.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vul_43532/03_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-5624/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: 5.48, per 1000 atoms: 0.77
  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: 0.84
  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: 1.74

  Time building geometry restraints manager: 2.03 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:             5.060
  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:             0.000
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     20.600
  Find NCS groups from input model:        0.090
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.150
-------------------------------------------------------------------------------
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  : 0.779 
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: 0.1470
  time to fit residues: 29.6623
Evaluate side-chains
  134 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
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 = 0.108331 restraints weight = 11506.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.109126 restraints weight = 9722.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.110790 restraints weight = 8794.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
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  : 0.886 
Fit side-chains
REVERT: A  323 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7243 (mtm-85)
REVERT: B  193 ASN cc_start: 0.7438 (t0) cc_final: 0.7005 (t0)
REVERT: B  286 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.6825 (t80)
  outliers start: 37
  outliers final: 25
  residues processed: 164
  average time/residue: 0.1709
  time to fit residues: 39.6941
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  : 0.845 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 28 optimal weight:    0.1980
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.140850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.110230 restraints weight = 11658.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.111195 restraints weight = 9564.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.112680 restraints weight = 8726.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.1199

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= 0.204
  Angle     :  0.615  10.049  10009  Z= 0.319
  Chirality :  0.043   0.158   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.379  32.111   1027
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.69 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 30.42 %
    Favored  : 63.85 %
  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:  1.82 (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
  173 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 131
  time to evaluate  : 0.825 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 ASP cc_start: 0.8241 (t0) cc_final: 0.8003 (t0)
REVERT: B  286 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.6776 (t80)
  outliers start: 42
  outliers final: 23
  residues processed: 162
  average time/residue: 0.1452
  time to fit residues: 34.1052
Evaluate side-chains
  148 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 46 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 90 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 62 optimal weight:    0.4980
   chunk 6 optimal weight:    0.7980
   chunk 7 optimal weight:    0.2980
   chunk 30 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.5580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.141052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.110433 restraints weight = 11746.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.111501 restraints weight = 9773.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.113279 restraints weight = 8686.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1301

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= 0.199
  Angle     :  0.614   9.960  10009  Z= 0.316
  Chirality :  0.043   0.152   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.282  29.618   1027
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.63 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 30.56 %
    Favored  : 64.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.28), residues: 955
  helix:  1.79 (0.35), residues: 245
  sheet: -1.27 (0.33), residues: 239
  loop : -2.66 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 255 
 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
  164 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 128
  time to evaluate  : 0.791 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8204 (t0) cc_final: 0.7995 (t0)
REVERT: A  323 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7281 (mtm-85)
REVERT: A  326 MET cc_start: 0.7752 (mmm) cc_final: 0.7473 (mmm)
REVERT: A  332 ASP cc_start: 0.6883 (p0) cc_final: 0.6657 (t0)
REVERT: B  193 ASN cc_start: 0.7426 (t0) cc_final: 0.6845 (t0)
REVERT: B  286 TYR cc_start: 0.8262 (OUTLIER) cc_final: 0.6917 (t80)
REVERT: H   64 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.7941 (pp)
  outliers start: 36
  outliers final: 24
  residues processed: 156
  average time/residue: 0.1480
  time to fit residues: 32.8717
Evaluate side-chains
  149 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0970
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0670
   chunk 49 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.5516

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.140607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.110416 restraints weight = 11487.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.111319 restraints weight = 9589.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.113128 restraints weight = 8624.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1387

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= 0.198
  Angle     :  0.607   9.871  10009  Z= 0.313
  Chirality :  0.042   0.149   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.232  28.830   1027
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.90 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 30.29 %
    Favored  : 64.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.60 (0.28), residues: 955
  helix:  1.83 (0.35), residues: 245
  sheet: -1.23 (0.34), residues: 239
  loop : -2.67 (0.26), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 381 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.013   0.001   PHE B 396 
 TYR   0.010   0.001   TYR A 367 
 ARG   0.006   0.000   ARG B 244 

*********************** 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
  169 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 129
  time to evaluate  : 0.864 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8192 (t0) cc_final: 0.7969 (t0)
REVERT: A  323 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7266 (mtm-85)
REVERT: A  326 MET cc_start: 0.7666 (mmm) cc_final: 0.7425 (mmm)
REVERT: B  193 ASN cc_start: 0.7601 (t0) cc_final: 0.7039 (t0)
REVERT: B  286 TYR cc_start: 0.8339 (OUTLIER) cc_final: 0.7082 (t80)
REVERT: B  365 VAL cc_start: 0.9258 (p) cc_final: 0.8963 (m)
REVERT: H   64 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7882 (pp)
  outliers start: 40
  outliers final: 27
  residues processed: 160
  average time/residue: 0.1427
  time to fit residues: 32.8871
Evaluate side-chains
  152 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 122
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
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   36 ILE
Chi-restraints excluded: chain B residue   40 LEU
Chi-restraints excluded: chain B residue   77 THR
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  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:    0.5980
   chunk 87 optimal weight:    0.4980
   chunk 41 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 85 optimal weight:    7.9990
   chunk 37 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   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**
L  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.140983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.110412 restraints weight = 11650.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.111244 restraints weight = 9669.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.113113 restraints weight = 8711.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7327  Z= 0.219
  Angle     :  0.622   9.888  10009  Z= 0.321
  Chirality :  0.043   0.153   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.280  31.365   1027
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.21 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  5.87 %
    Allowed  : 30.15 %
    Favored  : 63.98 %
  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: -1.60 (0.28), residues: 955
  helix:  1.82 (0.35), residues: 245
  sheet: -1.21 (0.34), residues: 234
  loop : -2.67 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 381 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.014   0.001   PHE B 186 
 TYR   0.010   0.001   TYR H  60 
 ARG   0.003   0.000   ARG L  55 

*********************** 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
  160 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 117
  time to evaluate  : 0.901 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.4490 (OUTLIER) cc_final: 0.3678 (p0)
REVERT: A  130 ASP cc_start: 0.8188 (t0) cc_final: 0.7962 (t0)
REVERT: A  323 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7316 (mtm-85)
REVERT: B  193 ASN cc_start: 0.7640 (t0) cc_final: 0.7131 (t0)
REVERT: B  286 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7092 (t80)
REVERT: H   64 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7895 (pp)
  outliers start: 43
  outliers final: 32
  residues processed: 151
  average time/residue: 0.1574
  time to fit residues: 34.6278
Evaluate side-chains
  158 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  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   38 GLN
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:    0.9990
   chunk 89 optimal weight:    0.0670
   chunk 60 optimal weight:    0.7980
   chunk 48 optimal weight:    0.4980
   chunk 11 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 63 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.140527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.110344 restraints weight = 11650.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.110826 restraints weight = 9603.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.112110 restraints weight = 9594.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7327  Z= 0.206
  Angle     :  0.613   9.851  10009  Z= 0.318
  Chirality :  0.042   0.145   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.252  30.896   1027
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.32 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 31.24 %
    Favored  : 63.03 %
  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: -1.56 (0.28), residues: 955
  helix:  1.85 (0.35), residues: 245
  sheet: -1.15 (0.34), residues: 234
  loop : -2.67 (0.26), residues: 476

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   0.014   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
  168 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 126
  time to evaluate  : 0.805 
Fit side-chains
REVERT: A  130 ASP cc_start: 0.8187 (t0) cc_final: 0.7972 (t0)
REVERT: A  323 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7281 (mtm-85)
REVERT: A  385 GLU cc_start: 0.7919 (pm20) cc_final: 0.7489 (pm20)
REVERT: B  193 ASN cc_start: 0.7621 (t0) cc_final: 0.7127 (t0)
REVERT: B  286 TYR cc_start: 0.8349 (OUTLIER) cc_final: 0.7096 (t80)
REVERT: B  315 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7047 (mp0)
REVERT: H   64 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7932 (pp)
REVERT: L   89 TYR cc_start: 0.8465 (OUTLIER) cc_final: 0.8148 (m-80)
REVERT: L   90 TYR cc_start: 0.8409 (m-80) cc_final: 0.8143 (m-80)
  outliers start: 42
  outliers final: 28
  residues processed: 158
  average time/residue: 0.1456
  time to fit residues: 32.9834
Evaluate side-chains
  154 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  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   89 TYR
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:    0.0060
   chunk 65 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0030
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.5606

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.141255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.111089 restraints weight = 11721.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.111963 restraints weight = 9590.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.113676 restraints weight = 8571.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1568

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= 0.205
  Angle     :  0.623   9.836  10009  Z= 0.321
  Chirality :  0.042   0.143   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.260  31.643   1027
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.01 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 31.51 %
    Favored  : 62.89 %
  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:  1.89 (0.35), residues: 245
  sheet: -1.14 (0.35), residues: 234
  loop : -2.67 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  35 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.015   0.001   PHE B 186 
 TYR   0.009   0.001   TYR A 367 
 ARG   0.003   0.000   ARG L  55 

*********************** 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
  167 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 126
  time to evaluate  : 0.797 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.4413 (OUTLIER) cc_final: 0.3697 (p0)
REVERT: A  323 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7280 (mtm-85)
REVERT: B  193 ASN cc_start: 0.7627 (t0) cc_final: 0.7164 (t0)
REVERT: B  286 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7123 (t80)
REVERT: B  315 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7069 (mp0)
REVERT: B  396 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.7158 (p90)
REVERT: H   64 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7934 (pp)
REVERT: L   89 TYR cc_start: 0.8458 (m-10) cc_final: 0.8166 (m-80)
  outliers start: 41
  outliers final: 29
  residues processed: 157
  average time/residue: 0.1439
  time to fit residues: 32.8761
Evaluate side-chains
  154 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 119
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   35 THR
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain A residue  204 VAL
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  266 ILE
Chi-restraints excluded: chain A residue  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   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  315 GLU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  396 PHE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 93
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 70 optimal weight:    0.8980
   chunk 28 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3654 r_free = 0.3654 target = 0.140036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.109703 restraints weight = 11859.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.109764 restraints weight = 9549.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.111319 restraints weight = 9426.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.1639

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= 0.255
  Angle     :  0.658  10.097  10009  Z= 0.339
  Chirality :  0.043   0.174   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.349  26.460   1027
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.74 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 32.06 %
    Favored  : 62.62 %
  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: -1.60 (0.28), residues: 955
  helix:  1.86 (0.35), residues: 245
  sheet: -1.21 (0.34), residues: 234
  loop : -2.70 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  37 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.015   0.001   PHE B 396 
 TYR   0.010   0.001   TYR B 286 
 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: 39
    poor density    : 119
  time to evaluate  : 0.874 
Fit side-chains
REVERT: A   81 ASP cc_start: 0.4351 (OUTLIER) cc_final: 0.3339 (p0)
REVERT: A  323 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7339 (mtm-85)
REVERT: A  379 ILE cc_start: 0.9028 (pt) cc_final: 0.8754 (pt)
REVERT: B  193 ASN cc_start: 0.7693 (t0) cc_final: 0.7266 (t0)
REVERT: B  286 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7577 (t80)
REVERT: B  315 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7131 (mp0)
REVERT: B  360 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7959 (mmt90)
REVERT: B  396 PHE cc_start: 0.7793 (p90) cc_final: 0.7590 (p90)
REVERT: H   20 LEU cc_start: 0.8482 (mt) cc_final: 0.8217 (mp)
REVERT: H   64 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7948 (pp)
  outliers start: 39
  outliers final: 29
  residues processed: 151
  average time/residue: 0.1514
  time to fit residues: 32.4409
Evaluate side-chains
  154 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 119
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
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  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  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  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:    0.9980
   chunk 78 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 64 optimal weight:    0.4980
   chunk 48 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3658 r_free = 0.3658 target = 0.140223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.110518 restraints weight = 11899.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.110733 restraints weight = 9764.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.112149 restraints weight = 9718.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1667

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= 0.217
  Angle     :  0.649   9.968  10009  Z= 0.334
  Chirality :  0.043   0.166   1163
  Planarity :  0.004   0.045   1274
  Dihedral  :  4.289  25.901   1027
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.21 %
    Favored  : 90.47 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 32.33 %
    Favored  : 62.62 %
  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: -1.56 (0.28), residues: 955
  helix:  1.88 (0.35), residues: 245
  sheet: -1.17 (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 B 255 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.015   0.001   PHE B 186 
 TYR   0.009   0.001   TYR A 367 
 ARG   0.002   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
  164 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 127
  time to evaluate  : 0.853 
Fit side-chains
REVERT: A  323 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7317 (mtm-85)
REVERT: B  193 ASN cc_start: 0.7661 (t0) cc_final: 0.7249 (t0)
REVERT: B  286 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7554 (t80)
REVERT: B  315 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7132 (mp0)
REVERT: B  360 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7972 (mmt90)
REVERT: B  396 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7692 (p90)
REVERT: H   20 LEU cc_start: 0.8432 (mt) cc_final: 0.8177 (mp)
REVERT: H   64 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7937 (pp)
REVERT: L   89 TYR cc_start: 0.8466 (m-10) cc_final: 0.8214 (m-80)
  outliers start: 37
  outliers final: 29
  residues processed: 157
  average time/residue: 0.1557
  time to fit residues: 34.5857
Evaluate side-chains
  160 residues out of total 839 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 125
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
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  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  109 VAL
Chi-restraints excluded: chain B residue  135 MET
Chi-restraints excluded: chain B residue  161 ILE
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  175 THR
Chi-restraints excluded: chain B residue  203 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  276 LEU
Chi-restraints excluded: chain B residue  286 TYR
Chi-restraints excluded: chain B residue  298 ILE
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 B residue  396 PHE
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 69 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 72 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 55 optimal weight:    0.5980
   chunk 73 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0770
   chunk 37 optimal weight:    0.0570
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.4456

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.141257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.111220 restraints weight = 11664.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.112086 restraints weight = 9911.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.113565 restraints weight = 8982.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1693

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= 0.196
  Angle     :  0.649   9.823  10009  Z= 0.333
  Chirality :  0.043   0.165   1163
  Planarity :  0.004   0.044   1274
  Dihedral  :  4.220  26.280   1027
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.11 %
    Favored  : 90.58 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 32.61 %
    Favored  : 62.62 %
  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: -1.52 (0.28), residues: 955
  helix:  1.94 (0.35), residues: 245
  sheet: -1.16 (0.34), residues: 234
  loop : -2.65 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 255 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.014   0.001   PHE B 186 
 TYR   0.010   0.001   TYR L  94 
 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: 2282.61 seconds
wall clock time: 40 minutes 20.98 seconds (2420.98 seconds total)