Starting phenix.real_space_refine
on Fri Mar 14 03:29:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8e40_27875/03_2025/8e40_27875.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8e40_27875/03_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_27875/03_2025/8e40_27875.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8e40_27875/03_2025/8e40_27875.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8e40_27875/03_2025/8e40_27875.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8e40_27875/03_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.90, per 1000 atoms: 0.78
  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 778.8 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: 1.99
  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: 2.05

  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:             3.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     21.620
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.780
-------------------------------------------------------------------------------
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      :  0.005   0.058   6570  Z= 0.323
  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 

*********************** 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  : 0.626 
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: 0.2408
  time to fit residues: 34.5423
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  : 0.623 
-------------------------------------------------------------------------------
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   6570  Z= 0.240
  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 

*********************** 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  : 0.709 
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: 0.1908
  time to fit residues: 21.2081
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  : 0.620 
-------------------------------------------------------------------------------
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:    3.9990
   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:    1.3388

-------------------------------------------------------------------------------
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 = 0.4131 r_free = 0.4131 target = 0.079748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.060802 restraints weight = 34921.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.062627 restraints weight = 18687.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.063794 restraints weight = 13121.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.3198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6570  Z= 0.270
  Angle     :  0.662   8.947   9111  Z= 0.328
  Chirality :  0.040   0.220    978
  Planarity :  0.005   0.043   1008
  Dihedral  : 14.414 133.426   1355
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 24.78 %
    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: -1.70 (0.33), residues: 626
  helix: -0.06 (0.35), residues: 219
  sheet: -1.86 (0.44), residues: 139
  loop : -1.50 (0.37), 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   0.022   0.002   PHE A 241 
 TYR   0.013   0.002   TYR A  91 
 ARG   0.009   0.000   ARG A 375 

*********************** 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: 29
    poor density    : 57
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 TRP cc_start: 0.8214 (t60) cc_final: 0.7991 (t-100)
REVERT: A   86 TYR cc_start: 0.8013 (m-10) cc_final: 0.7630 (m-10)
REVERT: A  197 MET cc_start: 0.8749 (ppp) cc_final: 0.8345 (ppp)
REVERT: A  371 SER cc_start: 0.9353 (OUTLIER) cc_final: 0.9056 (p)
REVERT: B   37 ASP cc_start: 0.7816 (t0) cc_final: 0.7595 (t0)
REVERT: B   39 PHE cc_start: 0.8673 (m-80) cc_final: 0.8406 (m-80)
REVERT: B   54 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8225 (tt0)
REVERT: C   13 GLU cc_start: 0.9444 (mt-10) cc_final: 0.9094 (pp20)
  outliers start: 29
  outliers final: 17
  residues processed: 82
  average time/residue: 0.2021
  time to fit residues: 21.9118
Evaluate side-chains
  69 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
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  149 MET
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:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0050
   chunk 56 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0970
   chunk 40 optimal weight:    3.9990
   overall best weight:    0.7996

-------------------------------------------------------------------------------
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 = 0.4153 r_free = 0.4153 target = 0.080673 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.061738 restraints weight = 34616.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.063599 restraints weight = 18359.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.064766 restraints weight = 12897.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6570  Z= 0.199
  Angle     :  0.621   9.412   9111  Z= 0.309
  Chirality :  0.039   0.224    978
  Planarity :  0.005   0.055   1008
  Dihedral  : 14.343 131.541   1353
  Min Nonbonded Distance : 1.265

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 25.84 %
    Favored  : 68.85 %
  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: -1.44 (0.34), residues: 626
  helix:  0.23 (0.35), residues: 215
  sheet: -1.80 (0.44), residues: 141
  loop : -1.33 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  70 
 HIS   0.052   0.002   HIS A 257 
 PHE   0.022   0.002   PHE A 241 
 TYR   0.009   0.001   TYR A  91 
 ARG   0.005   0.000   ARG A 375 

*********************** 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
  82 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 52
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 TYR cc_start: 0.7984 (m-10) cc_final: 0.7770 (m-10)
REVERT: A  197 MET cc_start: 0.8738 (ppp) cc_final: 0.8291 (ppp)
REVERT: A  371 SER cc_start: 0.9285 (OUTLIER) cc_final: 0.9011 (p)
REVERT: B   37 ASP cc_start: 0.7761 (t0) cc_final: 0.7517 (t0)
REVERT: B   39 PHE cc_start: 0.8576 (m-80) cc_final: 0.8303 (m-80)
REVERT: B   54 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8218 (tt0)
REVERT: C   13 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9083 (pp20)
  outliers start: 30
  outliers final: 22
  residues processed: 78
  average time/residue: 0.1834
  time to fit residues: 19.2233
Evaluate side-chains
  71 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 48
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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  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  261 CYS
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain A residue  338 ASN
Chi-restraints excluded: chain A residue  371 SER
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:    4.9990
   chunk 7 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 16 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   chunk 65 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 64 optimal weight:    5.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  19 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.080594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.061779 restraints weight = 34545.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.063647 restraints weight = 18401.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.064810 restraints weight = 12924.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6570  Z= 0.184
  Angle     :  0.591  10.106   9111  Z= 0.289
  Chirality :  0.038   0.222    978
  Planarity :  0.004   0.032   1008
  Dihedral  : 14.257 130.136   1353
  Min Nonbonded Distance : 1.579

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 24.60 %
    Favored  : 69.20 %
  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: -1.27 (0.34), residues: 626
  helix:  0.35 (0.35), residues: 216
  sheet: -1.70 (0.45), residues: 141
  loop : -1.23 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  38 
 HIS   0.004   0.001   HIS A 250 
 PHE   0.018   0.002   PHE C  12 
 TYR   0.009   0.001   TYR A  91 
 ARG   0.004   0.000   ARG A 375 

*********************** 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
  88 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 53
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 TYR cc_start: 0.7975 (m-10) cc_final: 0.7719 (m-10)
REVERT: A  197 MET cc_start: 0.8767 (ppp) cc_final: 0.8377 (ppp)
REVERT: B   54 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8239 (tt0)
REVERT: C   13 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9092 (pp20)
  outliers start: 35
  outliers final: 22
  residues processed: 84
  average time/residue: 0.1796
  time to fit residues: 20.1174
Evaluate side-chains
  70 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 48
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
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  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  306 LEU
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   53 SER
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0870
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0970
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.4956

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.081223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.062472 restraints weight = 34563.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.064379 restraints weight = 18286.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.065545 restraints weight = 12819.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.3805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6570  Z= 0.161
  Angle     :  0.585   8.541   9111  Z= 0.283
  Chirality :  0.039   0.222    978
  Planarity :  0.004   0.028   1008
  Dihedral  : 14.106 129.069   1353
  Min Nonbonded Distance : 1.760

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  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: -1.13 (0.34), residues: 626
  helix:  0.53 (0.35), residues: 217
  sheet: -1.58 (0.45), residues: 143
  loop : -1.22 (0.39), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 232 
 HIS   0.006   0.001   HIS A 257 
 PHE   0.017   0.002   PHE C  12 
 TYR   0.008   0.001   TYR A 339 
 ARG   0.008   0.000   ARG C  40 

*********************** 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
  80 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 52
  time to evaluate  : 0.943 
Fit side-chains
   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: 0.7951 (tt0)
REVERT: A   86 TYR cc_start: 0.7894 (m-10) cc_final: 0.7642 (m-10)
REVERT: A  197 MET cc_start: 0.8780 (ppp) cc_final: 0.8417 (ppp)
REVERT: B   54 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8232 (tt0)
REVERT: C   13 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9101 (pp20)
  outliers start: 28
  outliers final: 23
  residues processed: 77
  average time/residue: 0.2195
  time to fit residues: 22.8646
Evaluate side-chains
  73 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 49
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
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   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  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  306 LEU
Chi-restraints excluded: chain A residue  338 ASN
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 5 optimal weight:    0.2980
   chunk 60 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  20 ASN
A 205 ASN
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.079512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.060733 restraints weight = 34458.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.062552 restraints weight = 18427.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.063692 restraints weight = 13065.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6570  Z= 0.222
  Angle     :  0.616  11.495   9111  Z= 0.300
  Chirality :  0.039   0.218    978
  Planarity :  0.004   0.035   1008
  Dihedral  : 14.281 128.724   1353
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 25.84 %
    Favored  : 69.03 %
  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: -1.01 (0.35), residues: 626
  helix:  0.66 (0.35), residues: 217
  sheet: -1.65 (0.45), residues: 143
  loop : -1.11 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B   5 
 HIS   0.004   0.001   HIS A 250 
 PHE   0.018   0.002   PHE C  12 
 TYR   0.010   0.001   TYR A  91 
 ARG   0.003   0.000   ARG A 375 

*********************** 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
  78 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 49
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7964 (tt0)
REVERT: A   86 TYR cc_start: 0.7788 (m-10) cc_final: 0.7537 (m-10)
REVERT: A  197 MET cc_start: 0.8727 (ppp) cc_final: 0.8300 (ppp)
REVERT: B   54 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8178 (tt0)
REVERT: C   13 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9108 (pp20)
  outliers start: 29
  outliers final: 26
  residues processed: 74
  average time/residue: 0.1879
  time to fit residues: 18.8305
Evaluate side-chains
  75 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 48
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  306 LEU
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   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:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 229 ASN
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 303 HIS ** 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 = 0.4103 r_free = 0.4103 target = 0.077837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.059071 restraints weight = 34382.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.060865 restraints weight = 18656.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.061976 restraints weight = 13260.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.4415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6570  Z= 0.262
  Angle     :  0.647  12.401   9111  Z= 0.316
  Chirality :  0.039   0.219    978
  Planarity :  0.004   0.030   1008
  Dihedral  : 14.789 126.298   1353
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 26.19 %
    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: -1.01 (0.35), residues: 626
  helix:  0.58 (0.35), residues: 223
  sheet: -1.70 (0.44), residues: 140
  loop : -1.04 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 113 
 HIS   0.004   0.001   HIS A 250 
 PHE   0.019   0.002   PHE C  12 
 TYR   0.011   0.001   TYR C  29 
 ARG   0.003   0.000   ARG A 168 

*********************** 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
  81 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 52
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7821 (tt0)
REVERT: A  197 MET cc_start: 0.8816 (ppp) cc_final: 0.8268 (ppp)
REVERT: B   37 ASP cc_start: 0.7935 (t0) cc_final: 0.7622 (t0)
REVERT: B   54 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8207 (tt0)
REVERT: C   13 GLU cc_start: 0.9473 (mt-10) cc_final: 0.9123 (pp20)
  outliers start: 29
  outliers final: 26
  residues processed: 77
  average time/residue: 0.1833
  time to fit residues: 19.0126
Evaluate side-chains
  77 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 50
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
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   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  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  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   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:    0.8980
   chunk 5 optimal weight:    0.0670
   chunk 60 optimal weight:    5.9990
   chunk 64 optimal weight:    8.9990
   chunk 51 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.9520

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.078454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.059876 restraints weight = 34612.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.061727 restraints weight = 18540.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.062876 restraints weight = 13022.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.4489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6570  Z= 0.209
  Angle     :  0.617   8.956   9111  Z= 0.301
  Chirality :  0.039   0.218    978
  Planarity :  0.004   0.032   1008
  Dihedral  : 14.787 123.964   1353
  Min Nonbonded Distance : 1.847

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 26.19 %
    Favored  : 69.20 %
  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: -1.09 (0.35), residues: 626
  helix:  0.48 (0.35), residues: 229
  sheet: -1.57 (0.45), residues: 141
  loop : -1.20 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  94 
 HIS   0.004   0.001   HIS B  27 
 PHE   0.018   0.002   PHE C  12 
 TYR   0.010   0.001   TYR B  30 
 ARG   0.003   0.000   ARG C 131 

*********************** 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
  77 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 51
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7944 (tt0)
REVERT: A  197 MET cc_start: 0.8789 (ppp) cc_final: 0.8278 (ppp)
REVERT: B   37 ASP cc_start: 0.7872 (t0) cc_final: 0.7561 (t0)
REVERT: B   54 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8193 (tt0)
  outliers start: 26
  outliers final: 24
  residues processed: 73
  average time/residue: 0.1897
  time to fit residues: 18.6192
Evaluate side-chains
  75 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 50
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
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   88 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  138 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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   chunk 12 optimal weight:    0.3980
   chunk 54 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   chunk 41 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.079533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.061001 restraints weight = 34171.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.062850 restraints weight = 18406.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.064010 restraints weight = 12965.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.4555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6570  Z= 0.176
  Angle     :  0.611   9.321   9111  Z= 0.296
  Chirality :  0.039   0.215    978
  Planarity :  0.003   0.031   1008
  Dihedral  : 14.600 121.859   1353
  Min Nonbonded Distance : 1.820

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 27.26 %
    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: -0.87 (0.35), residues: 626
  helix:  0.71 (0.36), residues: 223
  sheet: -1.44 (0.46), residues: 141
  loop : -1.10 (0.40), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  94 
 HIS   0.003   0.001   HIS A 250 
 PHE   0.016   0.001   PHE C  12 
 TYR   0.009   0.001   TYR B  30 
 ARG   0.003   0.000   ARG C  83 

********************** 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: 23
    poor density    : 53
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7901 (tt0)
REVERT: A   77 TRP cc_start: 0.8142 (t60) cc_final: 0.7872 (t-100)
REVERT: A  197 MET cc_start: 0.8760 (ppp) cc_final: 0.8279 (ppp)
REVERT: B   37 ASP cc_start: 0.7873 (t0) cc_final: 0.7589 (t0)
REVERT: B   54 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8172 (tt0)
  outliers start: 23
  outliers final: 22
  residues processed: 72
  average time/residue: 0.1690
  time to fit residues: 16.7110
Evaluate side-chains
  75 residues out of total 567 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 52
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
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   88 VAL
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  138 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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 63 optimal weight:    5.9990
   chunk 18 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0030
   overall best weight:    0.9592

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.078632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.060066 restraints weight = 34989.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.061907 restraints weight = 18552.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.063060 restraints weight = 13067.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6570  Z= 0.215
  Angle     :  0.631  12.753   9111  Z= 0.305
  Chirality :  0.039   0.211    978
  Planarity :  0.003   0.032   1008
  Dihedral  : 14.657 121.119   1353
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 27.26 %
    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: -0.93 (0.35), residues: 626
  helix:  0.61 (0.35), residues: 229
  sheet: -1.41 (0.46), residues: 141
  loop : -1.15 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  94 
 HIS   0.004   0.001   HIS A 250 
 PHE   0.016   0.002   PHE A 164 
 TYR   0.010   0.001   TYR B  30 
 ARG   0.003   0.000   ARG C  19 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3659.64 seconds
wall clock time: 66 minutes 42.51 seconds (4002.51 seconds total)