Starting phenix.real_space_refine
on Mon Apr 28 22:48:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9enb_19830/04_2025/9enb_19830.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9enb_19830/04_2025/9enb_19830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9enb_19830/04_2025/9enb_19830.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9enb_19830/04_2025/9enb_19830.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9enb_19830/04_2025/9enb_19830.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9enb_19830/04_2025/9enb_19830.cif"
  }
  resolution = 2.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.036
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P     142      5.49       5
     Mg      6      5.21       5
     S      34      5.16       5
     C    4700      2.51       5
     N    1440      2.21       5
     O    1942      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8264
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2602
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 14, 'TRANS': 303}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 2602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2602
          Classifications: {'peptide': 318}
          Link IDs: {'PTRANS': 14, 'TRANS': 303}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 1527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1527
          Classifications: {'RNA': 72}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 29, 'rna3p_pyr': 31}
          Link IDs: {'rna2p': 12, 'rna3p': 59}
    Chain: "D"
      Number of atoms: 1527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1527
          Classifications: {'RNA': 72}
          Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 7, 'rna3p_pur': 30, 'rna3p_pyr': 30}
          Link IDs: {'rna2p': 12, 'rna3p': 59}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.67, per 1000 atoms: 0.69
  Number of scatterers: 8264
  At special positions: 0
  Unit cell: (104.009, 131.068, 68.4936, 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)
     S      34     16.00
     P     142     15.00
     Mg      6     11.99
     O    1942      8.00
     N    1440      7.00
     C    4700      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 114 " - pdb=" SG  CYS A 327 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 114 " - pdb=" SG  CYS B 327 " distance=2.04

  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: 2.00
  Conformation dependent library (CDL) restraints added in 561.1 milliseconds
  

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1208

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 4 sheets defined
      36.6% alpha, 24.2% beta
      45 base pairs and 66 stacking pairs defined.
    Time for finding SS restraints: 3.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 60
      removed outlier: 3.725A  pdb=" N   ALA A  59 " --> pdb=" O   ASP A  56 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   HIS A  60 " --> pdb=" O   PHE A  57 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 56 through 60'
    Processing helix  chain 'A' and resid 72 through 76
      removed outlier: 4.442A  pdb=" N   GLY A  75 " --> pdb=" O   MET A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 100
      removed outlier: 3.514A  pdb=" N   LYS A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 109
      removed outlier: 3.531A  pdb=" N   SER A 109 " --> pdb=" O   ARG A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 168
      removed outlier: 4.059A  pdb=" N   VAL A 167 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 214
    Processing helix  chain 'A' and resid 223 through 226
      removed outlier: 4.248A  pdb=" N   CYS A 226 " --> pdb=" O   ARG A 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 223 through 226'
    Processing helix  chain 'A' and resid 229 through 233
    Processing helix  chain 'A' and resid 277 through 291
      removed outlier: 3.536A  pdb=" N   LEU A 288 " --> pdb=" O   ALA A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 303
      removed outlier: 3.577A  pdb=" N   GLU A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 369
    Processing helix  chain 'B' and resid 56 through 60
      removed outlier: 3.723A  pdb=" N   ALA B  59 " --> pdb=" O   ASP B  56 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   HIS B  60 " --> pdb=" O   PHE B  57 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 56 through 60'
    Processing helix  chain 'B' and resid 72 through 76
      removed outlier: 4.425A  pdb=" N   GLY B  75 " --> pdb=" O   MET B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 100
      removed outlier: 3.564A  pdb=" N   LYS B  92 " --> pdb=" O   THR B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 109
      removed outlier: 3.501A  pdb=" N   THR B 108 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 168
      removed outlier: 4.046A  pdb=" N   VAL B 167 " --> pdb=" O   ILE B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 214
      removed outlier: 3.553A  pdb=" N   GLN B 214 " --> pdb=" O   ASP B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 226
      removed outlier: 4.206A  pdb=" N   CYS B 226 " --> pdb=" O   ARG B 223 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 223 through 226'
    Processing helix  chain 'B' and resid 229 through 233
    Processing helix  chain 'B' and resid 259 through 262
    Processing helix  chain 'B' and resid 277 through 291
      removed outlier: 3.534A  pdb=" N   LEU B 288 " --> pdb=" O   ALA B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 297 through 303
      removed outlier: 3.526A  pdb=" N   GLU B 301 " --> pdb=" O   GLU B 297 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 369
    Processing helix  chain 'B' and resid 413 through 417
    Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 113
      removed outlier: 5.269A  pdb=" N   PHE A 124 " --> pdb=" O   TYR A  71 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   TYR A  71 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY A  61 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   HIS A  64 " --> pdb=" O   PRO A 179 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ALA A  66 " --> pdb=" O   TRP A 177 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   TRP A 177 " --> pdb=" O   ALA A  66 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ARG A  68 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 112 through 113
      removed outlier: 6.426A  pdb=" N   ASP A 326 " --> pdb=" O   PHE A 124 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   GLN A 126 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
      removed outlier: 8.924A  pdb=" N   LYS A 328 " --> pdb=" O   GLN A 126 " (cutoff:3.500A)
      removed outlier: 10.976A  pdb=" N   ILE A 128 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   THR A 194 " --> pdb=" O   TYR A 325 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   CYS A 327 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   GLU A 192 " --> pdb=" O   CYS A 327 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   LEU A 264 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   GLN A 266 " --> pdb=" O   VAL A 246 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   VAL A 246 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 6.818A  pdb=" N   GLU A 268 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   ALA A 244 " --> pdb=" O   GLU A 268 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   THR A 270 " --> pdb=" O   LEU A 242 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 113
      removed outlier: 5.349A  pdb=" N   PHE B 124 " --> pdb=" O   TYR B  71 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   TYR B  71 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLY B  61 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 8.004A  pdb=" N   HIS B  64 " --> pdb=" O   PRO B 179 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ALA B  66 " --> pdb=" O   TRP B 177 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   TRP B 177 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   ARG B  68 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 112 through 113
      removed outlier: 6.447A  pdb=" N   ASP B 326 " --> pdb=" O   PHE B 124 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   GLN B 126 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
      removed outlier: 8.939A  pdb=" N   LYS B 328 " --> pdb=" O   GLN B 126 " (cutoff:3.500A)
      removed outlier: 10.960A  pdb=" N   ILE B 128 " --> pdb=" O   LYS B 328 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   THR B 194 " --> pdb=" O   TYR B 325 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   CYS B 327 " --> pdb=" O   GLU B 192 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   GLU B 192 " --> pdb=" O   CYS B 327 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   LEU B 264 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 5.107A  pdb=" N   LEU B 248 " --> pdb=" O   LEU B 264 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   GLN B 266 " --> pdb=" O   VAL B 246 " (cutoff:3.500A)
      removed outlier: 4.431A  pdb=" N   VAL B 246 " --> pdb=" O   GLN B 266 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   GLU B 268 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ALA B 244 " --> pdb=" O   GLU B 268 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   THR B 270 " --> pdb=" O   LEU B 242 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ARG B 239 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)

    199 hydrogen bonds defined for protein.
    534 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      118 hydrogen bonds
      208 hydrogen bond angles
      0 basepair planarities
      45 basepair parallelities
      66 stacking parallelities
  Total time for adding SS restraints: 2.79

  Time building geometry restraints manager: 2.39 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1876
        1.33 -     1.45: 2667
        1.45 -     1.57: 3859
        1.57 -     1.69: 284
        1.69 -     1.81: 54
  Bond restraints: 8740
  Sorted by residual:
  bond pdb=" CB  MET A 316 "
       pdb=" CG  MET A 316 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.36e+00
  bond pdb=" CG  PRO A 321 "
       pdb=" CD  PRO A 321 "
    ideal  model  delta    sigma   weight residual
    1.503  1.465  0.038 3.40e-02 8.65e+02 1.22e+00
  bond pdb=" CG  PRO B 321 "
       pdb=" CD  PRO B 321 "
    ideal  model  delta    sigma   weight residual
    1.503  1.466  0.037 3.40e-02 8.65e+02 1.18e+00
  bond pdb=" CB  TRP B  74 "
       pdb=" CG  TRP B  74 "
    ideal  model  delta    sigma   weight residual
    1.498  1.470  0.028 3.10e-02 1.04e+03 8.41e-01
  bond pdb=" C4'   A D  38 "
       pdb=" O4'   A D  38 "
    ideal  model  delta    sigma   weight residual
    1.451  1.438  0.013 1.50e-02 4.44e+03 8.00e-01
  ... (remaining 8735 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 12032
        1.23 -     2.46: 390
        2.46 -     3.69: 68
        3.69 -     4.92: 16
        4.92 -     6.15: 4
  Bond angle restraints: 12510
  Sorted by residual:
  angle pdb=" C2'   U C  39 "
        pdb=" C1'   U C  39 "
        pdb=" N1    U C  39 "
      ideal   model   delta    sigma   weight residual
     112.00  116.38   -4.38 1.50e+00 4.44e-01 8.53e+00
  angle pdb=" N   PHE A 320 "
        pdb=" CA  PHE A 320 "
        pdb=" C   PHE A 320 "
      ideal   model   delta    sigma   weight residual
     109.81  115.96   -6.15 2.21e+00 2.05e-01 7.74e+00
  angle pdb=" N   PHE B 320 "
        pdb=" CA  PHE B 320 "
        pdb=" C   PHE B 320 "
      ideal   model   delta    sigma   weight residual
     109.81  115.72   -5.91 2.21e+00 2.05e-01 7.15e+00
  angle pdb=" C2'   A D  38 "
        pdb=" C1'   A D  38 "
        pdb=" N9    A D  38 "
      ideal   model   delta    sigma   weight residual
     112.00  115.62   -3.62 1.50e+00 4.44e-01 5.81e+00
  angle pdb=" CA  PHE A 320 "
        pdb=" C   PHE A 320 "
        pdb=" N   PRO A 321 "
      ideal   model   delta    sigma   weight residual
     118.44  121.76   -3.32 1.59e+00 3.96e-01 4.37e+00
  ... (remaining 12505 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.54: 4977
       35.54 -    71.08: 401
       71.08 -   106.62: 56
      106.62 -   142.16: 3
      142.16 -   177.70: 5
  Dihedral angle restraints: 5442
    sinusoidal: 3578
      harmonic: 1864
  Sorted by residual:
  dihedral pdb=" O4'   C C  48 "
           pdb=" C1'   C C  48 "
           pdb=" N1    C C  48 "
           pdb=" C2    C C  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -8.90 -151.10     1      1.50e+01 4.44e-03 8.00e+01
  dihedral pdb=" O4'   C D  48 "
           pdb=" C1'   C D  48 "
           pdb=" N1    C D  48 "
           pdb=" C2    C D  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00   -9.07 -150.93     1      1.50e+01 4.44e-03 8.00e+01
  dihedral pdb=" O4'   U C  34 "
           pdb=" C1'   U C  34 "
           pdb=" N1    U C  34 "
           pdb=" C2    U C  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   48.64 -176.64     1      1.70e+01 3.46e-03 6.64e+01
  ... (remaining 5439 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1217
       0.048 -    0.096: 214
       0.096 -    0.145: 47
       0.145 -    0.193: 2
       0.193 -    0.241: 2
  Chirality restraints: 1482
  Sorted by residual:
  chirality pdb=" C1'   A D  38 "
            pdb=" O4'   A D  38 "
            pdb=" C2'   A D  38 "
            pdb=" N9    A D  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.22    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" C1'   U C  39 "
            pdb=" O4'   U C  39 "
            pdb=" C2'   U C  39 "
            pdb=" N1    U C  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.23    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality pdb=" CA  PHE A 320 "
            pdb=" N   PHE A 320 "
            pdb=" C   PHE A 320 "
            pdb=" CB  PHE A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.97e-01
  ... (remaining 1479 not shown)

  Planarity restraints: 1076
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  38 "   -0.027 2.00e-02 2.50e+03   1.35e-02 5.03e+00
        pdb=" N9    A D  38 "    0.035 2.00e-02 2.50e+03
        pdb=" C8    A D  38 "    0.001 2.00e-02 2.50e+03
        pdb=" N7    A D  38 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    A D  38 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  38 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A D  38 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A D  38 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2    A D  38 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A D  38 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  38 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U C  39 "    0.022 2.00e-02 2.50e+03   1.33e-02 3.97e+00
        pdb=" N1    U C  39 "   -0.032 2.00e-02 2.50e+03
        pdb=" C2    U C  39 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    U C  39 "    0.000 2.00e-02 2.50e+03
        pdb=" N3    U C  39 "    0.001 2.00e-02 2.50e+03
        pdb=" C4    U C  39 "    0.003 2.00e-02 2.50e+03
        pdb=" O4    U C  39 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    U C  39 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    U C  39 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 320 "   -0.028 5.00e-02 4.00e+02   4.23e-02 2.86e+00
        pdb=" N   PRO B 321 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B 321 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 321 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1073 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 429
        2.70 -     3.25: 7178
        3.25 -     3.80: 14293
        3.80 -     4.35: 18866
        4.35 -     4.90: 28528
  Nonbonded interactions: 69294
  Sorted by model distance:
  nonbonded pdb=" OP2   G D   9 "
            pdb="MG    MG D 102 "
     model   vdw
     2.149 2.170
  nonbonded pdb=" OP2   G C   9 "
            pdb="MG    MG C 102 "
     model   vdw
     2.162 2.170
  nonbonded pdb=" OE2 GLU B 294 "
            pdb=" OH  TYR B 411 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O2'   G C  36 "
            pdb=" OP2   A C  37 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OE2 GLU A 294 "
            pdb=" OH  TYR A 411 "
     model   vdw
     2.250 3.040
  ... (remaining 69289 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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 individual isotropic
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:             2.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     24.320
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.050
  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:14.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
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      :  0.006   0.042   8742  Z= 0.261
  Angle     :  0.554   6.147  12514  Z= 0.292
  Chirality :  0.039   0.241   1482
  Planarity :  0.004   0.042   1076
  Dihedral  : 22.369 177.702   4228
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 25.27 %
    Favored  : 74.01 %
  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: -0.08 (0.33), residues: 620
  helix:  0.93 (0.39), residues: 166
  sheet:  1.03 (0.56), residues: 82
  loop : -0.78 (0.32), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.016   0.001   PHE B 320 
 TYR   0.009   0.001   TYR A 216 
 ARG   0.002   0.000   ARG B 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17213 (  313)
  hydrogen bonds       : angle       5.56689 (  742)
  SS BOND              : bond        0.00888 (    2)
  SS BOND              : angle       1.17487 (    4)
  covalent geometry    : bond        0.00590 ( 8740)
  covalent geometry    : angle       0.55375 (12510)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 27
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.7892 (mt0) cc_final: 0.7497 (mt0)
REVERT: A  412 LYS cc_start: 0.7486 (ttpp) cc_final: 0.7278 (ttpp)
REVERT: B   72 MET cc_start: 0.8292 (mmm) cc_final: 0.7783 (mmm)
  outliers start: 4
  outliers final: 3
  residues processed: 30
  average time/residue: 1.3450
  time to fit residues: 43.3194
Evaluate side-chains
  28 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 25
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  122 SER
Chi-restraints excluded: chain B residue  171 ASP
Chi-restraints excluded: chain B residue  415 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 57 optimal weight:    0.2980
   chunk 31 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 23 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 69 optimal weight:    8.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 259 GLN
** B 251 GLN ** 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 = 0.3594 r_free = 0.3594 target = 0.093105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.064890 restraints weight = 17571.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 2.17
r_work: 0.2917 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.0816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8742  Z= 0.141
  Angle     :  0.511   6.056  12514  Z= 0.268
  Chirality :  0.036   0.251   1482
  Planarity :  0.004   0.040   1076
  Dihedral  : 22.099 176.600   2954
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 22.94 %
    Favored  : 74.91 %
  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:  0.45 (0.34), residues: 620
  helix:  1.66 (0.39), residues: 166
  sheet:  1.68 (0.58), residues: 68
  loop : -0.60 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  74 
 HIS   0.003   0.001   HIS B 360 
 PHE   0.017   0.001   PHE B 320 
 TYR   0.005   0.001   TYR A 216 
 ARG   0.001   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05458 (  313)
  hydrogen bonds       : angle       3.84053 (  742)
  SS BOND              : bond        0.00710 (    2)
  SS BOND              : angle       0.93750 (    4)
  covalent geometry    : bond        0.00306 ( 8740)
  covalent geometry    : angle       0.51091 (12510)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 26
  time to evaluate  : 0.658 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8513 (mt0) cc_final: 0.7790 (mt0)
REVERT: A  412 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.7080 (ttpt)
REVERT: B   72 MET cc_start: 0.8632 (mmm) cc_final: 0.8168 (mmm)
REVERT: B  335 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8725 (mm)
  outliers start: 12
  outliers final: 1
  residues processed: 37
  average time/residue: 1.1517
  time to fit residues: 46.0545
Evaluate side-chains
  29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue  335 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 1 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 38 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** B 251 GLN ** 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 = 0.3569 r_free = 0.3569 target = 0.091758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.063248 restraints weight = 17991.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 2.23
r_work: 0.2875 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.0728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8742  Z= 0.225
  Angle     :  0.554   6.156  12514  Z= 0.291
  Chirality :  0.039   0.250   1482
  Planarity :  0.004   0.043   1076
  Dihedral  : 22.094 176.808   2948
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 23.66 %
    Favored  : 74.55 %
  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:  0.39 (0.33), residues: 620
  helix:  1.58 (0.39), residues: 166
  sheet:  1.52 (0.55), residues: 72
  loop : -0.62 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.016   0.001   PHE B 320 
 TYR   0.009   0.001   TYR A 216 
 ARG   0.001   0.000   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06219 (  313)
  hydrogen bonds       : angle       3.82152 (  742)
  SS BOND              : bond        0.00965 (    2)
  SS BOND              : angle       1.25402 (    4)
  covalent geometry    : bond        0.00506 ( 8740)
  covalent geometry    : angle       0.55335 (12510)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  36 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 26
  time to evaluate  : 0.674 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8436 (mt0) cc_final: 0.7797 (mt0)
REVERT: A  412 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.7237 (ttpt)
REVERT: B   72 MET cc_start: 0.8721 (mmm) cc_final: 0.8102 (mmm)
  outliers start: 10
  outliers final: 3
  residues processed: 32
  average time/residue: 1.3577
  time to fit residues: 46.6283
Evaluate side-chains
  30 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.666 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 47 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** B 251 GLN ** 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 = 0.3588 r_free = 0.3588 target = 0.092911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.064471 restraints weight = 17703.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 2.22
r_work: 0.2910 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.0956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8742  Z= 0.154
  Angle     :  0.507   5.993  12514  Z= 0.266
  Chirality :  0.037   0.248   1482
  Planarity :  0.004   0.042   1076
  Dihedral  : 22.042 176.678   2948
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 23.48 %
    Favored  : 74.73 %
  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:  0.40 (0.33), residues: 620
  helix:  1.77 (0.38), residues: 166
  sheet:  1.57 (0.58), residues: 60
  loop : -0.63 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  74 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.018   0.001   PHE B 320 
 TYR   0.007   0.001   TYR A 197 
 ARG   0.001   0.000   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05406 (  313)
  hydrogen bonds       : angle       3.63490 (  742)
  SS BOND              : bond        0.00787 (    2)
  SS BOND              : angle       1.02009 (    4)
  covalent geometry    : bond        0.00340 ( 8740)
  covalent geometry    : angle       0.50660 (12510)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.633 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8408 (mtp)
REVERT: A  259 GLN cc_start: 0.8465 (mt0) cc_final: 0.7850 (mt0)
REVERT: A  412 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7173 (ttpp)
REVERT: B   72 MET cc_start: 0.8674 (mmm) cc_final: 0.7996 (mmm)
REVERT: B  228 MET cc_start: 0.8612 (mtp) cc_final: 0.8144 (mtm)
  outliers start: 10
  outliers final: 3
  residues processed: 35
  average time/residue: 1.3126
  time to fit residues: 49.2923
Evaluate side-chains
  32 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  412 LYS
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 57 optimal weight:    3.9990
   chunk 73 optimal weight:    5.9990
   chunk 68 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 6 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B 251 GLN ** 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 = 0.3555 r_free = 0.3555 target = 0.090842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.062566 restraints weight = 17690.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.15
r_work: 0.2861 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.0768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051   8742  Z= 0.317
  Angle     :  0.605   6.303  12514  Z= 0.318
  Chirality :  0.042   0.241   1482
  Planarity :  0.004   0.046   1076
  Dihedral  : 22.089 176.941   2948
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 23.84 %
    Favored  : 74.19 %
  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:  0.22 (0.33), residues: 620
  helix:  1.43 (0.38), residues: 166
  sheet:  1.46 (0.54), residues: 72
  loop : -0.72 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  74 
 HIS   0.004   0.002   HIS A 220 
 PHE   0.019   0.002   PHE A  94 
 TYR   0.011   0.001   TYR A 216 
 ARG   0.002   0.000   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06896 (  313)
  hydrogen bonds       : angle       3.87666 (  742)
  SS BOND              : bond        0.01166 (    2)
  SS BOND              : angle       1.48263 (    4)
  covalent geometry    : bond        0.00720 ( 8740)
  covalent geometry    : angle       0.60486 (12510)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 27
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A   72 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8458 (mtp)
REVERT: A  259 GLN cc_start: 0.8388 (mt0) cc_final: 0.7744 (mt0)
REVERT: A  412 LYS cc_start: 0.7463 (ttpp) cc_final: 0.7258 (ttpp)
REVERT: B   72 MET cc_start: 0.8762 (mmm) cc_final: 0.8070 (mmm)
  outliers start: 11
  outliers final: 4
  residues processed: 37
  average time/residue: 1.3702
  time to fit residues: 54.2367
Evaluate side-chains
  32 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 27
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    0.4980
   chunk 51 optimal weight:    1.9990
   chunk 25 optimal weight:    0.2980
   chunk 31 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B 251 GLN ** 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 = 0.3659 r_free = 0.3659 target = 0.096339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.068317 restraints weight = 17810.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.20
r_work: 0.3009 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8742  Z= 0.102
  Angle     :  0.480   7.856  12514  Z= 0.250
  Chirality :  0.034   0.242   1482
  Planarity :  0.004   0.040   1076
  Dihedral  : 22.025 176.895   2948
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 24.91 %
    Favored  : 73.84 %
  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:  0.57 (0.33), residues: 620
  helix:  2.06 (0.38), residues: 166
  sheet:  1.71 (0.60), residues: 60
  loop : -0.60 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  74 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.019   0.001   PHE B 320 
 TYR   0.005   0.001   TYR B 276 
 ARG   0.002   0.000   ARG A 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04642 (  313)
  hydrogen bonds       : angle       3.48927 (  742)
  SS BOND              : bond        0.00570 (    2)
  SS BOND              : angle       0.63060 (    4)
  covalent geometry    : bond        0.00210 ( 8740)
  covalent geometry    : angle       0.47956 (12510)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.690 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8467 (mt0) cc_final: 0.7819 (mt0)
REVERT: B   72 MET cc_start: 0.8698 (mmm) cc_final: 0.7950 (mmm)
REVERT: B  228 MET cc_start: 0.8670 (mtp) cc_final: 0.8269 (mtm)
REVERT: B  412 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7199 (ttpp)
  outliers start: 7
  outliers final: 3
  residues processed: 33
  average time/residue: 1.6473
  time to fit residues: 58.2981
Evaluate side-chains
  30 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  412 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 70 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 69 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
** B 251 GLN ** 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 = 0.3619 r_free = 0.3619 target = 0.093877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.065640 restraints weight = 17851.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 2.20
r_work: 0.2942 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.0963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8742  Z= 0.217
  Angle     :  0.538   6.441  12514  Z= 0.282
  Chirality :  0.038   0.232   1482
  Planarity :  0.004   0.044   1076
  Dihedral  : 22.009 177.109   2948
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 24.73 %
    Favored  : 74.19 %
  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:  0.49 (0.33), residues: 620
  helix:  1.79 (0.38), residues: 166
  sheet:  1.57 (0.55), residues: 72
  loop : -0.62 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.016   0.001   PHE B  94 
 TYR   0.009   0.001   TYR A 216 
 ARG   0.001   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05986 (  313)
  hydrogen bonds       : angle       3.66305 (  742)
  SS BOND              : bond        0.00947 (    2)
  SS BOND              : angle       1.25598 (    4)
  covalent geometry    : bond        0.00489 ( 8740)
  covalent geometry    : angle       0.53796 (12510)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 25
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8431 (mt0) cc_final: 0.7839 (mt0)
REVERT: B   72 MET cc_start: 0.8768 (mmm) cc_final: 0.8053 (mmm)
REVERT: B  228 MET cc_start: 0.8679 (mtp) cc_final: 0.8315 (mtm)
REVERT: B  412 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7226 (ttpp)
  outliers start: 6
  outliers final: 4
  residues processed: 30
  average time/residue: 1.3604
  time to fit residues: 43.9040
Evaluate side-chains
  30 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Chi-restraints excluded: chain B residue  412 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0870
   chunk 3 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 74 optimal weight:    5.9990
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.8760

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

Flipped N/Q/H residues before XYZ refinement:
** B 251 GLN ** 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 = 0.3642 r_free = 0.3642 target = 0.095418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.067275 restraints weight = 17828.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3131 rms_B_bonded: 2.19
r_work: 0.2979 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.1280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8742  Z= 0.116
  Angle     :  0.477   5.984  12514  Z= 0.249
  Chirality :  0.035   0.230   1482
  Planarity :  0.003   0.040   1076
  Dihedral  : 21.974 177.154   2948
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 25.45 %
    Favored  : 74.01 %
  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:  0.63 (0.33), residues: 620
  helix:  2.15 (0.38), residues: 166
  sheet:  1.75 (0.61), residues: 60
  loop : -0.59 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  74 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.017   0.001   PHE B 320 
 TYR   0.006   0.001   TYR B 197 
 ARG   0.001   0.000   ARG A  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04846 (  313)
  hydrogen bonds       : angle       3.48591 (  742)
  SS BOND              : bond        0.00640 (    2)
  SS BOND              : angle       0.76026 (    4)
  covalent geometry    : bond        0.00249 ( 8740)
  covalent geometry    : angle       0.47722 (12510)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 1.355 
Fit side-chains
   revert: symmetry clash
REVERT: B   72 MET cc_start: 0.8708 (mmm) cc_final: 0.7989 (mmm)
REVERT: B  228 MET cc_start: 0.8659 (mtp) cc_final: 0.8242 (mtm)
  outliers start: 3
  outliers final: 2
  residues processed: 29
  average time/residue: 1.9363
  time to fit residues: 59.8085
Evaluate side-chains
  28 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 26
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   83 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 62 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B 251 GLN ** 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 = 0.3605 r_free = 0.3605 target = 0.094073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.066012 restraints weight = 17918.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 2.25
r_work: 0.2915 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.0987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8742  Z= 0.225
  Angle     :  0.544   6.071  12514  Z= 0.285
  Chirality :  0.039   0.225   1482
  Planarity :  0.004   0.044   1076
  Dihedral  : 21.991 177.365   2948
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 25.09 %
    Favored  : 74.01 %
  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:  0.52 (0.33), residues: 620
  helix:  1.86 (0.38), residues: 166
  sheet:  1.57 (0.55), residues: 72
  loop : -0.61 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.016   0.001   PHE B  94 
 TYR   0.009   0.001   TYR A 216 
 ARG   0.001   0.000   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06101 (  313)
  hydrogen bonds       : angle       3.67738 (  742)
  SS BOND              : bond        0.00967 (    2)
  SS BOND              : angle       1.32934 (    4)
  covalent geometry    : bond        0.00507 ( 8740)
  covalent geometry    : angle       0.54330 (12510)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8417 (mt0) cc_final: 0.7758 (mt0)
REVERT: B   72 MET cc_start: 0.8776 (mmm) cc_final: 0.8051 (mmm)
REVERT: B  228 MET cc_start: 0.8671 (mtp) cc_final: 0.8289 (mtm)
  outliers start: 5
  outliers final: 4
  residues processed: 29
  average time/residue: 1.6100
  time to fit residues: 49.9601
Evaluate side-chains
  29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 25
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   74 TRP
Chi-restraints excluded: chain B residue   83 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B 251 GLN ** 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 = 0.3628 r_free = 0.3628 target = 0.094729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.066716 restraints weight = 17566.530|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 2.16
r_work: 0.2962 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8742  Z= 0.125
  Angle     :  0.486   6.044  12514  Z= 0.254
  Chirality :  0.035   0.223   1482
  Planarity :  0.004   0.042   1076
  Dihedral  : 21.949 177.422   2948
  Min Nonbonded Distance : 2.051

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 25.45 %
    Favored  : 74.01 %
  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:  0.61 (0.33), residues: 620
  helix:  2.14 (0.38), residues: 166
  sheet:  1.72 (0.60), residues: 60
  loop : -0.60 (0.31), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  74 
 HIS   0.003   0.001   HIS A 360 
 PHE   0.017   0.001   PHE B 320 
 TYR   0.005   0.001   TYR A 216 
 ARG   0.001   0.000   ARG A 193 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05033 (  313)
  hydrogen bonds       : angle       3.50327 (  742)
  SS BOND              : bond        0.00695 (    2)
  SS BOND              : angle       0.90634 (    4)
  covalent geometry    : bond        0.00269 ( 8740)
  covalent geometry    : angle       0.48542 (12510)

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

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

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1240 Ramachandran restraints generated.
    620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 26
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A  259 GLN cc_start: 0.8471 (mt0) cc_final: 0.7862 (mt0)
REVERT: B   72 MET cc_start: 0.8674 (mmm) cc_final: 0.7950 (mmm)
REVERT: B  228 MET cc_start: 0.8643 (mtp) cc_final: 0.8232 (mtm)
  outliers start: 3
  outliers final: 2
  residues processed: 29
  average time/residue: 1.4890
  time to fit residues: 46.6641
Evaluate side-chains
  27 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 25
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain B residue   83 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 75 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    0.3980
   chunk 12 optimal weight:    3.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** B 251 GLN ** 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 = 0.3606 r_free = 0.3606 target = 0.093242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.065082 restraints weight = 17922.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 2.18
r_work: 0.2918 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.1034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   8742  Z= 0.212
  Angle     :  0.535   6.100  12514  Z= 0.280
  Chirality :  0.038   0.221   1482
  Planarity :  0.004   0.042   1076
  Dihedral  : 21.972 177.576   2948
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 25.45 %
    Favored  : 74.01 %
  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:  0.53 (0.33), residues: 620
  helix:  1.88 (0.38), residues: 166
  sheet:  1.59 (0.55), residues: 72
  loop : -0.62 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  74 
 HIS   0.004   0.001   HIS A 360 
 PHE   0.016   0.001   PHE B 320 
 TYR   0.008   0.001   TYR A 216 
 ARG   0.001   0.000   ARG A 187 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05958 (  313)
  hydrogen bonds       : angle       3.65749 (  742)
  SS BOND              : bond        0.00928 (    2)
  SS BOND              : angle       1.25440 (    4)
  covalent geometry    : bond        0.00477 ( 8740)
  covalent geometry    : angle       0.53424 (12510)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4462.89 seconds
wall clock time: 79 minutes 20.77 seconds (4760.77 seconds total)