Starting phenix.real_space_refine
on Sun Jul 27 16:30:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e40_27875/07_2025/8e40_27875.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e40_27875/07_2025/8e40_27875.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8e40_27875/07_2025/8e40_27875.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e40_27875/07_2025/8e40_27875.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e40_27875/07_2025/8e40_27875.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e40_27875/07_2025/8e40_27875.cif"
  }
  resolution = 3.57
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3868 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      47      5.49       5
     S      30      5.16       5
     C    3835      2.51       5
     N    1122      2.21       5
     O    1261      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6297
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3085
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 3085
          Classifications: {'peptide': 371}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 347}
    Chain: "B"
      Number of atoms: 1000
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 1000
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 111}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "C"
      Number of atoms: 1220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1220
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 5, 'TRANS': 141}
    Chain: "R"
      Number of atoms: 456
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 456
          Classifications: {'RNA': 22}
          Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 14}
          Link IDs: {'rna3p': 21}
    Chain: "r"
      Number of atoms: 534
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 534
          Classifications: {'RNA': 25}
          Modifications used: {'rna2p_pur': 4, 'rna3p_pur': 13, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 3, 'rna3p': 21}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    757  SG  CYS A  97      34.707  53.781  84.146  1.00 27.23           S
  ATOM    781  SG  CYS A 100      30.843  53.501  86.010  1.00 32.88           S
  ATOM   2300  SG  CYS A 287      59.635  23.728  72.488  1.00 60.84           S

  Time building chain proxies: 5.16, per 1000 atoms: 0.82
  Number of scatterers: 6297
  At special positions: 0
  Unit cell: (92.92, 98.44, 134.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      30     16.00
     P      47     15.00
     O    1261      8.00
     N    1122      7.00
     C    3835      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.48
  Conformation dependent library (CDL) restraints added in 770.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 501 "
        pdb="ZN    ZN A 501 " - pdb=" ND1 HIS A  65 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A  97 "
        pdb="ZN    ZN A 501 " - pdb=" SG  CYS A 100 "
      pdb="  ZN A 502 "
        pdb="ZN    ZN A 502 " - pdb=" SG  CYS A 287 "
        pdb="ZN    ZN A 502 " - pdb=" ND1 HIS A 257 "


  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1206

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 5 sheets defined
      38.5% alpha, 16.7% beta
      17 base pairs and 31 stacking pairs defined.
    Time for finding SS restraints: 2.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 21
    Processing helix  chain 'A' and resid 65 through 79
    Processing helix  chain 'A' and resid 97 through 111
      removed outlier: 4.056A  pdb=" N   THR A 106 " --> pdb=" O   ASN A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 142
      removed outlier: 3.851A  pdb=" N   ALA A 134 " --> pdb=" O   ASP A 130 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLY A 142 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 165
      removed outlier: 3.825A  pdb=" N   VAL A 165 " --> pdb=" O   TRP A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 193
      removed outlier: 3.962A  pdb=" N   THR A 188 " --> pdb=" O   LEU A 184 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLU A 191 " --> pdb=" O   ALA A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 206
    Processing helix  chain 'A' and resid 259 through 266
      removed outlier: 3.890A  pdb=" N   LEU A 263 " --> pdb=" O   GLN A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 270
    Processing helix  chain 'A' and resid 290 through 301
      removed outlier: 3.758A  pdb=" N   MET A 294 " --> pdb=" O   CYS A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 331
      removed outlier: 4.049A  pdb=" N   GLY A 323 " --> pdb=" O   ARG A 319 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ASP A 330 " --> pdb=" O   THR A 326 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLY A 331 " --> pdb=" O   LEU A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 349
    Processing helix  chain 'A' and resid 362 through 379
    Processing helix  chain 'B' and resid 14 through 31
    Processing helix  chain 'B' and resid 99 through 109
    Processing helix  chain 'B' and resid 166 through 171
    Processing helix  chain 'C' and resid 6 through 13
    Processing helix  chain 'C' and resid 15 through 22
      removed outlier: 3.866A  pdb=" N   ARG C  19 " --> pdb=" O   GLU C  15 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   LYS C  20 " --> pdb=" O   GLU C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 36 through 50
    Processing helix  chain 'C' and resid 70 through 75
      removed outlier: 4.295A  pdb=" N   GLN C  74 " --> pdb=" O   PRO C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 135
      removed outlier: 3.916A  pdb=" N   GLU C 135 " --> pdb=" O   ARG C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 149
      removed outlier: 3.677A  pdb=" N   ARG C 149 " --> pdb=" O   GLU C 145 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 87
      removed outlier: 6.767A  pdb=" N   TYR A  86 " --> pdb=" O   THR A 115 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92
    Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 240
      removed outlier: 5.035A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 9.432A  pdb=" N   GLN A 237 " --> pdb=" O   TYR A 222 " (cutoff:3.500A)
      removed outlier: 11.077A  pdb=" N   TYR A 222 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 4.869A  pdb=" N   ARG A 277 " --> pdb=" O   GLU A 225 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   TYR A 276 " --> pdb=" O   SER A 305 " (cutoff:3.500A)
      removed outlier: 7.458A  pdb=" N   CYS A 307 " --> pdb=" O   TYR A 276 " (cutoff:3.500A)
      removed outlier: 5.790A  pdb=" N   VAL A 278 " --> pdb=" O   CYS A 307 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   PHE A 309 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      removed outlier: 6.222A  pdb=" N   CYS A 280 " --> pdb=" O   PHE A 309 " (cutoff:3.500A)
      removed outlier: 7.772A  pdb=" N   ALA A 335 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   ILE A 308 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 41
      removed outlier: 6.492A  pdb=" N   THR B  68 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
      removed outlier: 4.358A  pdb=" N   GLU B  54 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ILE B  66 " --> pdb=" O   GLU B  54 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   HIS B  56 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   LEU B  64 " --> pdb=" O   HIS B  56 " (cutoff:3.500A)
      removed outlier: 6.519A  pdb=" N   ALA B  62 " --> pdb=" O   PRO B  58 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL B  65 " --> pdb=" O   GLU B  88 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   GLY B  84 " --> pdb=" O   TYR B  69 " (cutoff:3.500A)
      removed outlier: 5.529A  pdb=" N   ILE B  87 " --> pdb=" O   ILE B   9 " (cutoff:3.500A)
      removed outlier: 7.178A  pdb=" N   ILE B   9 " --> pdb=" O   ILE B  87 " (cutoff:3.500A)
      removed outlier: 11.161A  pdb=" N   TRP B  89 " --> pdb=" O   VAL B   7 " (cutoff:3.500A)
      removed outlier: 14.398A  pdb=" N   VAL B   7 " --> pdb=" O   TRP B  89 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE C  55 " --> pdb=" O   PHE C  68 " (cutoff:3.500A)

    204 hydrogen bonds defined for protein.
    585 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      34 hydrogen bonds
      68 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      31 stacking parallelities
  Total time for adding SS restraints: 2.23

  Time building geometry restraints manager: 1.79 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1818
        1.34 -     1.46: 1791
        1.46 -     1.58: 2826
        1.58 -     1.70: 92
        1.70 -     1.82: 43
  Bond restraints: 6570
  Sorted by residual:
  bond pdb=" N   LEU C 119 "
       pdb=" CA  LEU C 119 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.29e-02 6.01e+03 7.18e+00
  bond pdb=" N   ASP C  34 "
       pdb=" CA  ASP C  34 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.35e-02 5.49e+03 6.11e+00
  bond pdb=" C   VAL C   5 "
       pdb=" N   PRO C   6 "
    ideal  model  delta    sigma   weight residual
    1.334  1.392 -0.058 2.34e-02 1.83e+03 6.08e+00
  bond pdb=" N   ASP C 120 "
       pdb=" CA  ASP C 120 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.030 1.25e-02 6.40e+03 5.82e+00
  bond pdb=" N   ARG C 118 "
       pdb=" CA  ARG C 118 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.33e-02 5.65e+03 4.32e+00
  ... (remaining 6565 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 8712
        2.02 -     4.05: 321
        4.05 -     6.07: 56
        6.07 -     8.09: 15
        8.09 -    10.12: 7
  Bond angle restraints: 9111
  Sorted by residual:
  angle pdb=" CA  LYS A 113 "
        pdb=" CB  LYS A 113 "
        pdb=" CG  LYS A 113 "
      ideal   model   delta    sigma   weight residual
     114.10  124.22  -10.12 2.00e+00 2.50e-01 2.56e+01
  angle pdb=" CA  GLU C  38 "
        pdb=" CB  GLU C  38 "
        pdb=" CG  GLU C  38 "
      ideal   model   delta    sigma   weight residual
     114.10  123.28   -9.18 2.00e+00 2.50e-01 2.11e+01
  angle pdb=" CA  GLU A 302 "
        pdb=" CB  GLU A 302 "
        pdb=" CG  GLU A 302 "
      ideal   model   delta    sigma   weight residual
     114.10  123.07   -8.97 2.00e+00 2.50e-01 2.01e+01
  angle pdb=" N   LEU A 260 "
        pdb=" CA  LEU A 260 "
        pdb=" C   LEU A 260 "
      ideal   model   delta    sigma   weight residual
     111.36  106.48    4.88 1.09e+00 8.42e-01 2.01e+01
  angle pdb=" O3'   U r   2 "
        pdb=" C3'   U r   2 "
        pdb=" C2'   U r   2 "
      ideal   model   delta    sigma   weight residual
     113.70  120.40   -6.70 1.50e+00 4.44e-01 2.00e+01
  ... (remaining 9106 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.56: 3447
       26.56 -    53.11: 357
       53.11 -    79.67: 65
       79.67 -   106.23: 4
      106.23 -   132.79: 2
  Dihedral angle restraints: 3875
    sinusoidal: 2013
      harmonic: 1862
  Sorted by residual:
  dihedral pdb=" CA  LYS B 161 "
           pdb=" C   LYS B 161 "
           pdb=" N   PRO B 162 "
           pdb=" CA  PRO B 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.24   26.76     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  THR B  68 "
           pdb=" C   THR B  68 "
           pdb=" N   TYR B  69 "
           pdb=" CA  TYR B  69 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.49  -22.51     0      5.00e+00 4.00e-02 2.03e+01
  dihedral pdb=" CA  THR A  32 "
           pdb=" C   THR A  32 "
           pdb=" N   VAL A  33 "
           pdb=" CA  VAL A  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.48   20.52     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 3872 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 828
       0.067 -    0.135: 132
       0.135 -    0.202: 16
       0.202 -    0.269: 1
       0.269 -    0.336: 1
  Chirality restraints: 978
  Sorted by residual:
  chirality pdb=" C3'   U r   2 "
            pdb=" C4'   U r   2 "
            pdb=" O3'   U r   2 "
            pdb=" C2'   U r   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.14   -0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" CB  THR A 231 "
            pdb=" CA  THR A 231 "
            pdb=" OG1 THR A 231 "
            pdb=" CG2 THR A 231 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  THR C  62 "
            pdb=" N   THR C  62 "
            pdb=" C   THR C  62 "
            pdb=" CB  THR C  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 8.19e-01
  ... (remaining 975 not shown)

  Planarity restraints: 1008
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A  13 "   -0.080 5.00e-02 4.00e+02   1.18e-01 2.24e+01
        pdb=" N   PRO A  14 "    0.205 5.00e-02 4.00e+02
        pdb=" CA  PRO A  14 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO A  14 "   -0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 198 "    0.060 5.00e-02 4.00e+02   9.11e-02 1.33e+01
        pdb=" N   PRO A 199 "   -0.158 5.00e-02 4.00e+02
        pdb=" CA  PRO A 199 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 199 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 233 "    0.053 5.00e-02 4.00e+02   8.15e-02 1.06e+01
        pdb=" N   PRO A 234 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO A 234 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO A 234 "    0.044 5.00e-02 4.00e+02
  ... (remaining 1005 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 837
        2.76 -     3.29: 5650
        3.29 -     3.83: 11067
        3.83 -     4.36: 12501
        4.36 -     4.90: 20514
  Nonbonded interactions: 50569
  Sorted by model distance:
  nonbonded pdb=" CB  ALA A 258 "
            pdb=" SG  CYS A 290 "
     model   vdw
     2.225 3.820
  nonbonded pdb=" O   ASP A  31 "
            pdb=" CG1 VAL A  58 "
     model   vdw
     2.235 3.460
  nonbonded pdb=" N   TYR A  59 "
            pdb=" CD  PRO A  60 "
     model   vdw
     2.278 3.520
  nonbonded pdb=" O   PHE A 268 "
            pdb=" N6    A r  17 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" N   GLN A 259 "
            pdb=" OE1 GLN A 259 "
     model   vdw
     2.316 3.120
  ... (remaining 50564 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     22.540
  Find NCS groups from input model:        0.060
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6150
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      :  0.009   0.585   6575  Z= 0.354
  Angle     :  0.932  10.118   9111  Z= 0.510
  Chirality :  0.050   0.336    978
  Planarity :  0.008   0.118   1008
  Dihedral  : 19.336 132.785   2669
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 18.73
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  5.91 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 27.43 %
    Favored  : 70.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.30), residues: 626
  helix: -1.56 (0.30), residues: 205
  sheet: -1.40 (0.55), residues: 109
  loop : -2.27 (0.30), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 211 
 HIS   0.007   0.001   HIS A  75 
 PHE   0.034   0.002   PHE C  12 
 TYR   0.018   0.002   TYR A 219 
 ARG   0.010   0.001   ARG A  24 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14650 (  238)
  hydrogen bonds       : angle       7.55533 (  653)
  metal coordination   : bond        0.28053 (    5)
  covalent geometry    : bond        0.00520 ( 6570)
  covalent geometry    : angle       0.93189 ( 9111)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.593 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7123 (t0)
  outliers start: 12
  outliers final: 4
  residues processed: 114
  average time/residue: 0.2450
  time to fit residues: 34.8880
Evaluate side-chains
  59 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.650 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   61 LYS
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  266 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A  20 ASN
A 195 HIS
** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 133 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.082671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.063389 restraints weight = 34113.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.065143 restraints weight = 18762.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.066274 restraints weight = 13368.402|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6575  Z= 0.166
  Angle     :  0.675  10.297   9111  Z= 0.338
  Chirality :  0.040   0.221    978
  Planarity :  0.006   0.069   1008
  Dihedral  : 13.982 133.856   1363
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 27.79 %
    Favored  : 67.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.13 (0.32), residues: 626
  helix: -0.48 (0.34), residues: 218
  sheet: -1.77 (0.46), residues: 131
  loop : -1.90 (0.34), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  70 
 HIS   0.004   0.001   HIS A 250 
 PHE   0.022   0.002   PHE A 241 
 TYR   0.013   0.001   TYR A  91 
 ARG   0.007   0.001   ARG B  15 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04496 (  238)
  hydrogen bonds       : angle       5.55203 (  653)
  metal coordination   : bond        0.00397 (    5)
  covalent geometry    : bond        0.00377 ( 6570)
  covalent geometry    : angle       0.67516 ( 9111)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 59
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 TRP cc_start: 0.8354 (t60) cc_final: 0.8006 (t-100)
REVERT: A   86 TYR cc_start: 0.7982 (m-10) cc_final: 0.7622 (m-10)
REVERT: A  197 MET cc_start: 0.8701 (ppp) cc_final: 0.8340 (ppp)
REVERT: A  371 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.9002 (p)
REVERT: B   37 ASP cc_start: 0.7768 (t0) cc_final: 0.7475 (t0)
REVERT: B   54 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8227 (tt0)
REVERT: C   13 GLU cc_start: 0.9430 (mt-10) cc_final: 0.9101 (pp20)
  outliers start: 27
  outliers final: 13
  residues processed: 83
  average time/residue: 0.2152
  time to fit residues: 23.5337
Evaluate side-chains
  66 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue  117 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 36 optimal weight:    7.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
A 257 HIS
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.080836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.061921 restraints weight = 34813.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.063745 restraints weight = 18478.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.064924 restraints weight = 13014.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.016   1.246   6575  Z= 0.538
  Angle     :  0.637   8.746   9111  Z= 0.314
  Chirality :  0.040   0.221    978
  Planarity :  0.005   0.044   1008
  Dihedral  : 14.218 133.200   1355
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 24.96 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.33), residues: 626
  helix: -0.04 (0.35), residues: 219
  sheet: -1.76 (0.45), residues: 139
  loop : -1.54 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  70 
 HIS   0.005   0.001   HIS A 250 
 PHE   0.023   0.002   PHE A 241 
 TYR   0.011   0.001   TYR A  91 
 ARG   0.007   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04271 (  238)
  hydrogen bonds       : angle       5.13447 (  653)
  metal coordination   : bond        0.55740 (    5)
  covalent geometry    : bond        0.00365 ( 6570)
  covalent geometry    : angle       0.63654 ( 9111)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 58
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 TRP cc_start: 0.8229 (t60) cc_final: 0.8029 (t-100)
REVERT: A   86 TYR cc_start: 0.7971 (m-10) cc_final: 0.7608 (m-10)
REVERT: A  197 MET cc_start: 0.8738 (ppp) cc_final: 0.8353 (ppp)
REVERT: A  371 SER cc_start: 0.9317 (OUTLIER) cc_final: 0.9029 (p)
REVERT: B   37 ASP cc_start: 0.7788 (t0) cc_final: 0.7571 (t0)
REVERT: B   39 PHE cc_start: 0.8668 (m-80) cc_final: 0.8394 (m-80)
REVERT: B   54 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8217 (tt0)
REVERT: C   13 GLU cc_start: 0.9445 (mt-10) cc_final: 0.9093 (pp20)
  outliers start: 28
  outliers final: 16
  residues processed: 83
  average time/residue: 0.1913
  time to fit residues: 20.8274
Evaluate side-chains
  68 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 51
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   55 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0010
   chunk 29 optimal weight:    3.9990
   chunk 3 optimal weight:    0.5980
   chunk 56 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 195 HIS
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  45 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.079510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.060603 restraints weight = 34770.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.062379 restraints weight = 18571.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.063506 restraints weight = 13075.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6575  Z= 0.186
  Angle     :  0.645   9.605   9111  Z= 0.320
  Chirality :  0.040   0.222    978
  Planarity :  0.005   0.056   1008
  Dihedral  : 14.431 131.986   1353
  Min Nonbonded Distance : 1.370

Molprobity Statistics.
  All-atom Clashscore : 15.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 26.02 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.34), residues: 626
  helix:  0.18 (0.35), residues: 221
  sheet: -1.84 (0.44), residues: 141
  loop : -1.47 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  70 
 HIS   0.049   0.002   HIS A 257 
 PHE   0.019   0.002   PHE A 241 
 TYR   0.012   0.001   TYR A  91 
 ARG   0.005   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04475 (  238)
  hydrogen bonds       : angle       5.01723 (  653)
  metal coordination   : bond        0.03521 (    5)
  covalent geometry    : bond        0.00403 ( 6570)
  covalent geometry    : angle       0.64486 ( 9111)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 53
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 TYR cc_start: 0.7759 (m-10) cc_final: 0.7539 (m-10)
REVERT: A  197 MET cc_start: 0.8721 (ppp) cc_final: 0.8421 (ppp)
REVERT: B   37 ASP cc_start: 0.7708 (t0) cc_final: 0.7497 (t0)
REVERT: B   54 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8214 (tt0)
REVERT: C   13 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9089 (pp20)
  outliers start: 30
  outliers final: 25
  residues processed: 79
  average time/residue: 0.1873
  time to fit residues: 20.1962
Evaluate side-chains
  73 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 48
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  379 GLN
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue   12 PHE
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   55 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 52 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 65 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 205 ASN
A 301 ASN
B  19 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.077036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.058374 restraints weight = 34818.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.060098 restraints weight = 18755.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.061204 restraints weight = 13301.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.095   6575  Z= 0.224
  Angle     :  0.672   9.951   9111  Z= 0.336
  Chirality :  0.041   0.221    978
  Planarity :  0.005   0.049   1008
  Dihedral  : 15.082 129.018   1353
  Min Nonbonded Distance : 1.260

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.43 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 24.60 %
    Favored  : 68.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.34), residues: 626
  helix:  0.21 (0.35), residues: 217
  sheet: -1.94 (0.44), residues: 140
  loop : -1.30 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B   5 
 HIS   0.043   0.002   HIS A 257 
 PHE   0.023   0.002   PHE C  12 
 TYR   0.012   0.002   TYR A  91 
 ARG   0.003   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05180 (  238)
  hydrogen bonds       : angle       5.19864 (  653)
  metal coordination   : bond        0.05680 (    5)
  covalent geometry    : bond        0.00480 ( 6570)
  covalent geometry    : angle       0.67214 ( 9111)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 51
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7782 (tt0)
REVERT: A  197 MET cc_start: 0.8799 (ppp) cc_final: 0.8269 (ppp)
REVERT: B   39 PHE cc_start: 0.8611 (m-80) cc_final: 0.8292 (m-80)
REVERT: B   54 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8244 (tt0)
REVERT: B   96 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7990 (m)
REVERT: C   13 GLU cc_start: 0.9453 (mt-10) cc_final: 0.9123 (pp20)
REVERT: C   39 GLU cc_start: 0.8920 (tp30) cc_final: 0.8537 (tt0)
  outliers start: 38
  outliers final: 29
  residues processed: 83
  average time/residue: 0.1973
  time to fit residues: 22.0695
Evaluate side-chains
  77 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 46
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   16 THR
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  261 CYS
Chi-restraints excluded: chain A residue  324 LEU
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  379 GLN
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   53 SER
Chi-restraints excluded: chain B residue   93 ARG
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue   12 PHE
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   44 PHE
Chi-restraints excluded: chain C residue   55 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 41 optimal weight:    0.4980
   chunk 38 optimal weight:    0.6980
   chunk 63 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0970
   chunk 22 optimal weight:    0.0980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A  20 ASN
A 303 HIS
B  19 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.079666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.061207 restraints weight = 34231.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.063026 restraints weight = 18192.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.064171 restraints weight = 12813.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.4179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   6575  Z= 0.123
  Angle     :  0.613  11.225   9111  Z= 0.299
  Chirality :  0.039   0.224    978
  Planarity :  0.004   0.045   1008
  Dihedral  : 14.738 125.490   1353
  Min Nonbonded Distance : 1.324

Molprobity Statistics.
  All-atom Clashscore : 12.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 26.55 %
    Favored  : 68.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.34), residues: 626
  helix:  0.46 (0.35), residues: 217
  sheet: -1.69 (0.45), residues: 142
  loop : -1.21 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 232 
 HIS   0.041   0.002   HIS A 257 
 PHE   0.017   0.002   PHE C  12 
 TYR   0.009   0.001   TYR C  29 
 ARG   0.003   0.000   ARG A 375 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  238)
  hydrogen bonds       : angle       4.90104 (  653)
  metal coordination   : bond        0.04253 (    5)
  covalent geometry    : bond        0.00258 ( 6570)
  covalent geometry    : angle       0.61311 ( 9111)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 54
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 TYR cc_start: 0.8014 (m-10) cc_final: 0.7761 (m-10)
REVERT: A  197 MET cc_start: 0.8803 (ppp) cc_final: 0.8370 (ppp)
REVERT: B   37 ASP cc_start: 0.7893 (t0) cc_final: 0.7618 (t0)
REVERT: B   54 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8217 (tt0)
REVERT: C   39 GLU cc_start: 0.8835 (tp30) cc_final: 0.8536 (tt0)
  outliers start: 28
  outliers final: 19
  residues processed: 78
  average time/residue: 0.3084
  time to fit residues: 31.4048
Evaluate side-chains
  68 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 49
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  122 ARG
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue   12 PHE
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue  144 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 60 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 56 optimal weight:    9.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 229 ASN
C  41 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.077555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.058238 restraints weight = 35480.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.059975 restraints weight = 19426.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.061077 restraints weight = 13962.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.4617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   6575  Z= 0.241
  Angle     :  0.687   8.012   9111  Z= 0.343
  Chirality :  0.041   0.214    978
  Planarity :  0.004   0.042   1008
  Dihedral  : 15.190 125.393   1353
  Min Nonbonded Distance : 1.296

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 27.43 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.34), residues: 626
  helix:  0.51 (0.36), residues: 223
  sheet: -1.92 (0.43), residues: 140
  loop : -1.31 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 360 
 HIS   0.037   0.002   HIS A 257 
 PHE   0.020   0.002   PHE C  12 
 TYR   0.012   0.002   TYR A 320 
 ARG   0.012   0.001   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05597 (  238)
  hydrogen bonds       : angle       5.20823 (  653)
  metal coordination   : bond        0.04201 (    5)
  covalent geometry    : bond        0.00520 ( 6570)
  covalent geometry    : angle       0.68750 ( 9111)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 47
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LEU cc_start: 0.9614 (tp) cc_final: 0.9365 (tt)
REVERT: A  197 MET cc_start: 0.8784 (ppp) cc_final: 0.8253 (ppp)
REVERT: B   54 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8192 (tt0)
REVERT: C   39 GLU cc_start: 0.8981 (tp30) cc_final: 0.8665 (tt0)
  outliers start: 27
  outliers final: 25
  residues processed: 70
  average time/residue: 0.1903
  time to fit residues: 19.0060
Evaluate side-chains
  70 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 45
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   75 HIS
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  149 MET
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  276 TYR
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  379 GLN
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue   12 PHE
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue  144 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0370
   chunk 42 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
C  46 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.078538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.060063 restraints weight = 34412.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.061909 restraints weight = 18379.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.063037 restraints weight = 12946.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6575  Z= 0.132
  Angle     :  0.629  13.017   9111  Z= 0.306
  Chirality :  0.039   0.217    978
  Planarity :  0.004   0.032   1008
  Dihedral  : 15.032 121.826   1353
  Min Nonbonded Distance : 1.408

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 27.96 %
    Favored  : 67.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.35), residues: 626
  helix:  0.55 (0.35), residues: 223
  sheet: -1.73 (0.44), residues: 142
  loop : -1.28 (0.39), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  94 
 HIS   0.030   0.001   HIS A 257 
 PHE   0.020   0.002   PHE C  44 
 TYR   0.010   0.001   TYR A 339 
 ARG   0.005   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03948 (  238)
  hydrogen bonds       : angle       4.99853 (  653)
  metal coordination   : bond        0.02572 (    5)
  covalent geometry    : bond        0.00289 ( 6570)
  covalent geometry    : angle       0.62906 ( 9111)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 52
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.7960 (tt0)
REVERT: A  197 MET cc_start: 0.8776 (ppp) cc_final: 0.8238 (ppp)
REVERT: B   37 ASP cc_start: 0.7946 (t0) cc_final: 0.7649 (t0)
REVERT: B   54 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8179 (tt0)
REVERT: C   39 GLU cc_start: 0.8928 (tp30) cc_final: 0.8599 (tt0)
  outliers start: 25
  outliers final: 22
  residues processed: 73
  average time/residue: 0.1808
  time to fit residues: 18.2196
Evaluate side-chains
  73 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 50
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  379 GLN
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue   12 PHE
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   55 ILE
Chi-restraints excluded: chain C residue  144 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 60 optimal weight:    0.8980
   chunk 64 optimal weight:    8.9990
   chunk 51 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0980
   chunk 24 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.079370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.061019 restraints weight = 34821.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.062908 restraints weight = 18396.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.064101 restraints weight = 12826.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.4686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6575  Z= 0.123
  Angle     :  0.609   9.447   9111  Z= 0.296
  Chirality :  0.039   0.209    978
  Planarity :  0.004   0.031   1008
  Dihedral  : 14.725 119.604   1353
  Min Nonbonded Distance : 1.407

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 27.61 %
    Favored  : 68.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.35), residues: 626
  helix:  0.68 (0.35), residues: 226
  sheet: -1.29 (0.48), residues: 134
  loop : -1.27 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  38 
 HIS   0.028   0.001   HIS A 257 
 PHE   0.019   0.002   PHE C  44 
 TYR   0.008   0.001   TYR B  30 
 ARG   0.005   0.000   ARG C  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  238)
  hydrogen bonds       : angle       4.80918 (  653)
  metal coordination   : bond        0.02384 (    5)
  covalent geometry    : bond        0.00275 ( 6570)
  covalent geometry    : angle       0.60858 ( 9111)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7987 (tt0)
REVERT: A  197 MET cc_start: 0.8715 (ppp) cc_final: 0.8280 (ppp)
REVERT: B   54 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8185 (tt0)
  outliers start: 23
  outliers final: 22
  residues processed: 74
  average time/residue: 0.1730
  time to fit residues: 17.5254
Evaluate side-chains
  74 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 51
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   75 HIS
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue   12 PHE
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   55 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 54 optimal weight:    0.8980
   chunk 10 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   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 238 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.079059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.060563 restraints weight = 34408.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.062421 restraints weight = 18373.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.063575 restraints weight = 12932.956|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.4790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6575  Z= 0.142
  Angle     :  0.647  12.322   9111  Z= 0.315
  Chirality :  0.039   0.207    978
  Planarity :  0.004   0.032   1008
  Dihedral  : 14.700 119.039   1353
  Min Nonbonded Distance : 1.418

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 28.32 %
    Favored  : 67.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.35), residues: 626
  helix:  0.72 (0.36), residues: 226
  sheet: -1.29 (0.48), residues: 134
  loop : -1.25 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  38 
 HIS   0.029   0.001   HIS A 257 
 PHE   0.018   0.002   PHE A 262 
 TYR   0.009   0.001   TYR B  30 
 ARG   0.004   0.000   ARG C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04075 (  238)
  hydrogen bonds       : angle       4.83468 (  653)
  metal coordination   : bond        0.02160 (    5)
  covalent geometry    : bond        0.00318 ( 6570)
  covalent geometry    : angle       0.64674 ( 9111)

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

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

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1252 Ramachandran restraints generated.
    626 Oldfield, 0 Emsley, 626 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 52
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7935 (tt0)
REVERT: A  197 MET cc_start: 0.8714 (ppp) cc_final: 0.8278 (ppp)
REVERT: B   37 ASP cc_start: 0.7842 (t0) cc_final: 0.7594 (t0)
REVERT: B   54 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8177 (tt0)
  outliers start: 24
  outliers final: 22
  residues processed: 72
  average time/residue: 0.1619
  time to fit residues: 16.3236
Evaluate side-chains
  73 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 50
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 VAL
Chi-restraints excluded: chain A residue   53 ILE
Chi-restraints excluded: chain A residue   55 GLN
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   65 HIS
Chi-restraints excluded: chain A residue   75 HIS
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  257 HIS
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue   10 VAL
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  166 SER
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain C residue   12 PHE
Chi-restraints excluded: chain C residue   32 PHE
Chi-restraints excluded: chain C residue   55 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   overall best weight:    1.0382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.078060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.059563 restraints weight = 35177.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.061436 restraints weight = 18617.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.062584 restraints weight = 13055.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.4938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6575  Z= 0.161
  Angle     :  0.655  11.994   9111  Z= 0.319
  Chirality :  0.039   0.205    978
  Planarity :  0.004   0.032   1008
  Dihedral  : 14.813 118.005   1353
  Min Nonbonded Distance : 1.416

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 28.14 %
    Favored  : 67.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.35), residues: 626
  helix:  0.87 (0.36), residues: 220
  sheet: -1.32 (0.48), residues: 134
  loop : -1.19 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B   5 
 HIS   0.029   0.001   HIS A 257 
 PHE   0.017   0.002   PHE C  44 
 TYR   0.010   0.001   TYR B  30 
 ARG   0.003   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04444 (  238)
  hydrogen bonds       : angle       4.91469 (  653)
  metal coordination   : bond        0.02006 (    5)
  covalent geometry    : bond        0.00359 ( 6570)
  covalent geometry    : angle       0.65451 ( 9111)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2878.02 seconds
wall clock time: 51 minutes 59.64 seconds (3119.64 seconds total)