Starting phenix.real_space_refine
on Fri Aug 22 18:26:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8un2_42391/08_2025/8un2_42391.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8un2_42391/08_2025/8un2_42391.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8un2_42391/08_2025/8un2_42391.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8un2_42391/08_2025/8un2_42391.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8un2_42391/08_2025/8un2_42391.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8un2_42391/08_2025/8un2_42391.cif"
  }
  resolution = 2.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.025
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: 5
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     S      20      5.16       5
     C    4378      2.51       5
     N    1172      2.21       5
     O    1282      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6854
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 3426
          Classifications: {'peptide': 433}
          Link IDs: {'PCIS': 4, 'PTRANS': 29, 'TRANS': 399}
    Chain: "B"
      Number of atoms: 3426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 3426
          Classifications: {'peptide': 433}
          Link IDs: {'PCIS': 4, 'PTRANS': 29, 'TRANS': 399}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.47, per 1000 atoms: 0.21
  Number of scatterers: 6854
  At special positions: 0
  Unit cell: (92.3832, 108.626, 68.0184, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Mn      2     24.99
     S      20     16.00
     O    1282      8.00
     N    1172      7.00
     C    4378      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: 0.44
  Conformation dependent library (CDL) restraints added in 276.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 8 sheets defined
      34.9% alpha, 20.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 70 through 77
    Processing helix  chain 'A' and resid 117 through 121
    Processing helix  chain 'A' and resid 149 through 151
      No H-bonds generated for 'chain 'A' and resid 149 through 151'
    Processing helix  chain 'A' and resid 160 through 171
    Processing helix  chain 'A' and resid 180 through 184
    Processing helix  chain 'A' and resid 191 through 206
      removed outlier: 3.524A  pdb=" N   SER A 203 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
      removed outlier: 3.568A  pdb=" N   ALA A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 286
      removed outlier: 3.670A  pdb=" N   GLU A 276 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      Proline residue:  A 280  - end of helix
    Processing helix  chain 'A' and resid 301 through 315
    Processing helix  chain 'A' and resid 326 through 329
    Processing helix  chain 'A' and resid 345 through 350
      removed outlier: 3.596A  pdb=" N   ASP A 349 " --> pdb=" O   ALA A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 360
      removed outlier: 3.555A  pdb=" N   VAL A 358 " --> pdb=" O   PRO A 355 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASP A 360 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 396
    Processing helix  chain 'A' and resid 413 through 433
      removed outlier: 4.141A  pdb=" N   GLU A 417 " --> pdb=" O   TRP A 413 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 77
    Processing helix  chain 'B' and resid 117 through 121
    Processing helix  chain 'B' and resid 149 through 151
      No H-bonds generated for 'chain 'B' and resid 149 through 151'
    Processing helix  chain 'B' and resid 160 through 171
    Processing helix  chain 'B' and resid 180 through 184
    Processing helix  chain 'B' and resid 191 through 206
      removed outlier: 3.524A  pdb=" N   SER B 203 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 250
      removed outlier: 3.569A  pdb=" N   ALA B 238 " --> pdb=" O   GLU B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 270 through 286
      removed outlier: 3.670A  pdb=" N   GLU B 276 " --> pdb=" O   THR B 272 " (cutoff:3.500A)
      Proline residue:  B 280  - end of helix
    Processing helix  chain 'B' and resid 301 through 315
    Processing helix  chain 'B' and resid 326 through 329
    Processing helix  chain 'B' and resid 345 through 350
      removed outlier: 3.596A  pdb=" N   ASP B 349 " --> pdb=" O   ALA B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 360
      removed outlier: 3.556A  pdb=" N   VAL B 358 " --> pdb=" O   PRO B 355 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ASP B 360 " --> pdb=" O   ASP B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 396
    Processing helix  chain 'B' and resid 413 through 433
      removed outlier: 4.142A  pdb=" N   GLU B 417 " --> pdb=" O   TRP B 413 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18
      removed outlier: 3.671A  pdb=" N   GLY A  24 " --> pdb=" O   VAL A  16 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   GLU A  18 " --> pdb=" O   ILE A  22 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   ILE A  22 " --> pdb=" O   GLU A  18 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE A  89 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 38
    Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.640A  pdb=" N   GLY A  44 " --> pdb=" O   ARG A 110 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A 127 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 289
      removed outlier: 7.582A  pdb=" N   ILE A 176 " --> pdb=" O   THR A 210 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   MET A 212 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ILE A 178 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   SER A 214 " --> pdb=" O   ILE A 178 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   TYR A 144 " --> pdb=" O   GLY A 175 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   GLU A 177 " --> pdb=" O   TYR A 144 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL A 146 " --> pdb=" O   GLU A 177 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   LEU A 179 " --> pdb=" O   VAL A 146 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   TYR A 406 " --> pdb=" O   SER A 147 " (cutoff:3.500A)
      removed outlier: 5.104A  pdb=" N   TYR A 401 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE A 368 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   LEU A 321 " --> pdb=" O   VAL A 366 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   ILE A 368 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LEU A 323 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   ALA A 370 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE A 293 " --> pdb=" O   ASP A 324 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 18
      removed outlier: 3.672A  pdb=" N   GLY B  24 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   GLU B  18 " --> pdb=" O   ILE B  22 " (cutoff:3.500A)
      removed outlier: 5.698A  pdb=" N   ILE B  22 " --> pdb=" O   GLU B  18 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ILE B  89 " --> pdb=" O   THR B  63 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 38
    Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54
      removed outlier: 3.641A  pdb=" N   GLY B  44 " --> pdb=" O   ARG B 110 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL B 127 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 288 through 289
      removed outlier: 7.582A  pdb=" N   ILE B 176 " --> pdb=" O   THR B 210 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   MET B 212 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ILE B 178 " --> pdb=" O   MET B 212 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   SER B 214 " --> pdb=" O   ILE B 178 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   TYR B 144 " --> pdb=" O   GLY B 175 " (cutoff:3.500A)
      removed outlier: 8.417A  pdb=" N   GLU B 177 " --> pdb=" O   TYR B 144 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL B 146 " --> pdb=" O   GLU B 177 " (cutoff:3.500A)
      removed outlier: 8.501A  pdb=" N   LEU B 179 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   TYR B 406 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   TYR B 401 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE B 368 " --> pdb=" O   TYR B 401 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   LEU B 321 " --> pdb=" O   VAL B 366 " (cutoff:3.500A)
      removed outlier: 6.016A  pdb=" N   ILE B 368 " --> pdb=" O   LEU B 321 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   LEU B 323 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   ALA B 370 " --> pdb=" O   LEU B 323 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ILE B 293 " --> pdb=" O   ASP B 324 " (cutoff:3.500A)

    278 hydrogen bonds defined for protein.
    744 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.80

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2204
        1.33 -     1.45: 989
        1.45 -     1.57: 3801
        1.57 -     1.69: 0
        1.69 -     1.80: 38
  Bond restraints: 7032
  Sorted by residual:
  bond pdb=" CB  ARG B   5 "
       pdb=" CG  ARG B   5 "
    ideal  model  delta    sigma   weight residual
    1.520  1.459  0.061 3.00e-02 1.11e+03 4.18e+00
  bond pdb=" CB  ARG A   5 "
       pdb=" CG  ARG A   5 "
    ideal  model  delta    sigma   weight residual
    1.520  1.459  0.061 3.00e-02 1.11e+03 4.18e+00
  bond pdb=" CB  VAL B 254 "
       pdb=" CG2 VAL B 254 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.71e+00
  bond pdb=" CB  VAL A 254 "
       pdb=" CG2 VAL A 254 "
    ideal  model  delta    sigma   weight residual
    1.521  1.467  0.054 3.30e-02 9.18e+02 2.63e+00
  bond pdb=" CB  PRO B 122 "
       pdb=" CG  PRO B 122 "
    ideal  model  delta    sigma   weight residual
    1.506  1.449  0.057 3.90e-02 6.57e+02 2.11e+00
  ... (remaining 7027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 9021
        1.49 -     2.98: 467
        2.98 -     4.46: 76
        4.46 -     5.95: 12
        5.95 -     7.44: 8
  Bond angle restraints: 9584
  Sorted by residual:
  angle pdb=" C   PRO B 412 "
        pdb=" N   TRP B 413 "
        pdb=" CA  TRP B 413 "
      ideal   model   delta    sigma   weight residual
     123.91  130.05   -6.14 1.66e+00 3.63e-01 1.37e+01
  angle pdb=" C   PRO A 412 "
        pdb=" N   TRP A 413 "
        pdb=" CA  TRP A 413 "
      ideal   model   delta    sigma   weight residual
     123.91  130.03   -6.12 1.66e+00 3.63e-01 1.36e+01
  angle pdb=" CA  PRO B  60 "
        pdb=" N   PRO B  60 "
        pdb=" CD  PRO B  60 "
      ideal   model   delta    sigma   weight residual
     112.00  108.19    3.81 1.40e+00 5.10e-01 7.39e+00
  angle pdb=" CA  PRO A  60 "
        pdb=" N   PRO A  60 "
        pdb=" CD  PRO A  60 "
      ideal   model   delta    sigma   weight residual
     112.00  108.23    3.77 1.40e+00 5.10e-01 7.26e+00
  angle pdb=" CA  VAL A  59 "
        pdb=" C   VAL A  59 "
        pdb=" N   PRO A  60 "
      ideal   model   delta    sigma   weight residual
     118.88  122.91   -4.03 1.54e+00 4.22e-01 6.86e+00
  ... (remaining 9579 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.57: 3756
       16.57 -    33.13: 338
       33.13 -    49.70: 78
       49.70 -    66.26: 18
       66.26 -    82.83: 10
  Dihedral angle restraints: 4200
    sinusoidal: 1724
      harmonic: 2476
  Sorted by residual:
  dihedral pdb=" CA  ILE B 178 "
           pdb=" C   ILE B 178 "
           pdb=" N   LEU B 179 "
           pdb=" CA  LEU B 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.57   18.43     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ALA A 134 "
           pdb=" C   ALA A 134 "
           pdb=" N   PRO A 135 "
           pdb=" CA  PRO A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.60  -18.40     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  ILE A 178 "
           pdb=" C   ILE A 178 "
           pdb=" N   LEU A 179 "
           pdb=" CA  LEU A 179 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.60   18.40     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 4197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 531
       0.035 -    0.070: 333
       0.070 -    0.105: 120
       0.105 -    0.140: 49
       0.140 -    0.174: 15
  Chirality restraints: 1048
  Sorted by residual:
  chirality pdb=" CA  GLU A 387 "
            pdb=" N   GLU A 387 "
            pdb=" C   GLU A 387 "
            pdb=" CB  GLU A 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.61e-01
  chirality pdb=" CA  GLU B 387 "
            pdb=" N   GLU B 387 "
            pdb=" C   GLU B 387 "
            pdb=" CB  GLU B 387 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.10e-01
  chirality pdb=" CB  ILE A 176 "
            pdb=" CA  ILE A 176 "
            pdb=" CG1 ILE A 176 "
            pdb=" CG2 ILE A 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.54e-01
  ... (remaining 1045 not shown)

  Planarity restraints: 1260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 279 "    0.051 5.00e-02 4.00e+02   7.60e-02 9.25e+00
        pdb=" N   PRO B 280 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO B 280 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 280 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 279 "   -0.050 5.00e-02 4.00e+02   7.56e-02 9.15e+00
        pdb=" N   PRO A 280 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 280 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 280 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 340 "    0.036 5.00e-02 4.00e+02   5.38e-02 4.63e+00
        pdb=" N   PRO A 341 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 341 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 341 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1257 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 40
        2.59 -     3.17: 5243
        3.17 -     3.74: 10501
        3.74 -     4.32: 16114
        4.32 -     4.90: 26060
  Nonbonded interactions: 57958
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 292 "
            pdb="MN    MN A 501 "
     model   vdw
     2.009 2.320
  nonbonded pdb=" OE2 GLU B 292 "
            pdb="MN    MN B 501 "
     model   vdw
     2.014 2.320
  nonbonded pdb=" OE1 GLN A 369 "
            pdb="MN    MN A 501 "
     model   vdw
     2.155 2.320
  nonbonded pdb=" OE1 GLN B 369 "
            pdb="MN    MN B 501 "
     model   vdw
     2.164 2.320
  nonbonded pdb=" OD2 ASP B 324 "
            pdb="MN    MN B 501 "
     model   vdw
     2.196 2.320
  ... (remaining 57953 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.530
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:5.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7583
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.061   7032  Z= 0.378
  Angle     :  0.795   7.438   9584  Z= 0.461
  Chirality :  0.054   0.174   1048
  Planarity :  0.008   0.076   1260
  Dihedral  : 14.149  82.828   2616
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.74 (0.25), residues: 862
  helix: -4.08 (0.13), residues: 230
  sheet: -0.94 (0.41), residues: 154
  loop : -0.81 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A   5 
 TYR   0.019   0.002   TYR A 144 
 PHE   0.013   0.002   PHE A 347 
 TRP   0.014   0.003   TRP B 198 
 HIS   0.010   0.002   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00910 ( 7032)
  covalent geometry    : angle       0.79500 ( 9584)
  hydrogen bonds       : bond        0.27668 (  278)
  hydrogen bonds       : angle       9.07532 (  744)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.217 
Fit side-chains
REVERT: A   43 ASP cc_start: 0.7893 (t70) cc_final: 0.7591 (m-30)
REVERT: A  119 GLU cc_start: 0.7450 (pm20) cc_final: 0.7136 (pm20)
REVERT: A  126 ARG cc_start: 0.7975 (mtt-85) cc_final: 0.7690 (mtt-85)
REVERT: A  273 GLU cc_start: 0.7066 (pm20) cc_final: 0.6475 (pm20)
REVERT: A  276 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7126 (mt-10)
REVERT: A  286 ASP cc_start: 0.7718 (t70) cc_final: 0.7445 (t0)
REVERT: A  349 ASP cc_start: 0.7296 (m-30) cc_final: 0.7054 (m-30)
REVERT: A  391 LYS cc_start: 0.7802 (tttm) cc_final: 0.7537 (tttm)
REVERT: A  428 GLN cc_start: 0.7918 (mt0) cc_final: 0.7485 (mt0)
REVERT: B   21 GLU cc_start: 0.7376 (mm-30) cc_final: 0.7141 (mm-30)
REVERT: B  118 GLN cc_start: 0.7459 (tp40) cc_final: 0.7125 (mm-40)
REVERT: B  119 GLU cc_start: 0.7410 (pm20) cc_final: 0.6998 (pm20)
REVERT: B  159 MET cc_start: 0.8620 (ttm) cc_final: 0.8350 (ttp)
REVERT: B  192 ASP cc_start: 0.8022 (m-30) cc_final: 0.7747 (m-30)
REVERT: B  241 ARG cc_start: 0.7833 (ttp-170) cc_final: 0.7544 (ttp-170)
REVERT: B  257 LYS cc_start: 0.8274 (tppp) cc_final: 0.8036 (tptm)
REVERT: B  273 GLU cc_start: 0.6856 (pm20) cc_final: 0.6465 (pm20)
REVERT: B  276 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7264 (mt-10)
REVERT: B  377 GLU cc_start: 0.7130 (mp0) cc_final: 0.6816 (mp0)
REVERT: B  431 ASP cc_start: 0.7113 (m-30) cc_final: 0.6815 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.7253
  time to fit residues: 120.1786
Evaluate side-chains
  140 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.2980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 121 GLN
A 186 ASN
A 221 HIS
A 343 GLN
A 356 ASN
A 369 GLN
B 121 GLN
B 221 HIS
B 343 GLN
B 423 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.113524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.103309 restraints weight = 8638.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.37
r_work: 0.3312 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7032  Z= 0.136
  Angle     :  0.535   5.073   9584  Z= 0.281
  Chirality :  0.045   0.139   1048
  Planarity :  0.006   0.044   1260
  Dihedral  :  4.803  17.378    950
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.81 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.97 (0.26), residues: 862
  helix: -0.94 (0.26), residues: 256
  sheet: -0.62 (0.42), residues: 154
  loop : -0.32 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 143 
 TYR   0.014   0.001   TYR B 144 
 PHE   0.010   0.001   PHE B 347 
 TRP   0.018   0.002   TRP A 198 
 HIS   0.003   0.001   HIS B 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7032)
  covalent geometry    : angle       0.53484 ( 9584)
  hydrogen bonds       : bond        0.04050 (  278)
  hydrogen bonds       : angle       5.72358 (  744)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 169
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  300 LYS cc_start: 0.8212 (mmtp) cc_final: 0.7986 (mmtp)
REVERT: B   31 MET cc_start: 0.8718 (tpt) cc_final: 0.8412 (tpt)
REVERT: B  242 ASP cc_start: 0.7505 (m-30) cc_final: 0.7284 (m-30)
  outliers start: 10
  outliers final: 3
  residues processed: 173
  average time/residue: 0.6806
  time to fit residues: 122.0541
Evaluate side-chains
  161 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain B residue  343 GLN
Chi-restraints excluded: chain B residue  394 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 423 HIS
A 428 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.111884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.101712 restraints weight = 8465.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.34
r_work: 0.3281 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7032  Z= 0.183
  Angle     :  0.549   5.146   9584  Z= 0.287
  Chirality :  0.048   0.137   1048
  Planarity :  0.005   0.036   1260
  Dihedral  :  4.800  17.463    950
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.38 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.27), residues: 862
  helix:  0.74 (0.30), residues: 256
  sheet: -0.48 (0.42), residues: 154
  loop : -0.03 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  17 
 TYR   0.017   0.001   TYR B 144 
 PHE   0.011   0.001   PHE B 347 
 TRP   0.012   0.002   TRP B 198 
 HIS   0.003   0.001   HIS A 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 7032)
  covalent geometry    : angle       0.54869 ( 9584)
  hydrogen bonds       : bond        0.04582 (  278)
  hydrogen bonds       : angle       5.36191 (  744)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6832 (mp0)
REVERT: A  300 LYS cc_start: 0.8261 (mmtp) cc_final: 0.8049 (mmtp)
REVERT: B   67 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7653 (tm-30)
REVERT: B  242 ASP cc_start: 0.7546 (m-30) cc_final: 0.7319 (m-30)
REVERT: B  369 GLN cc_start: 0.7961 (mt0) cc_final: 0.7722 (mt0)
  outliers start: 13
  outliers final: 3
  residues processed: 160
  average time/residue: 0.7265
  time to fit residues: 120.3028
Evaluate side-chains
  153 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 148
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 61 optimal weight:    0.1980
   chunk 19 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0870
   chunk 81 optimal weight:    0.0060
   chunk 6 optimal weight:    1.9990
   chunk 67 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.3174

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.114367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.104151 restraints weight = 8514.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 1.37
r_work: 0.3325 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.3190 rms_B_bonded: 3.09 restraints_weight: 0.2500
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7032  Z= 0.100
  Angle     :  0.494   7.000   9584  Z= 0.253
  Chirality :  0.045   0.139   1048
  Planarity :  0.005   0.039   1260
  Dihedral  :  4.387  16.532    950
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 14.32 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.28), residues: 862
  helix:  1.85 (0.31), residues: 242
  sheet: -0.28 (0.43), residues: 154
  loop :  0.30 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  17 
 TYR   0.011   0.001   TYR A 144 
 PHE   0.011   0.001   PHE B 347 
 TRP   0.012   0.001   TRP B 198 
 HIS   0.002   0.000   HIS B 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 7032)
  covalent geometry    : angle       0.49356 ( 9584)
  hydrogen bonds       : bond        0.03499 (  278)
  hydrogen bonds       : angle       5.03575 (  744)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 157
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6851 (mp0)
REVERT: B  242 ASP cc_start: 0.7500 (m-30) cc_final: 0.7271 (m-30)
REVERT: B  369 GLN cc_start: 0.7949 (mt0) cc_final: 0.7580 (mt0)
REVERT: B  405 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7211 (tt0)
  outliers start: 12
  outliers final: 7
  residues processed: 161
  average time/residue: 0.7200
  time to fit residues: 120.0344
Evaluate side-chains
  163 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 155
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 58 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0470
   chunk 36 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A 343 GLN
A 428 GLN
B 343 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.111279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.101173 restraints weight = 8565.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 1.37
r_work: 0.3306 rms_B_bonded: 1.69 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.3213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7032  Z= 0.142
  Angle     :  0.517   6.973   9584  Z= 0.266
  Chirality :  0.046   0.138   1048
  Planarity :  0.005   0.039   1260
  Dihedral  :  4.507  18.055    950
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.59 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.28), residues: 862
  helix:  1.83 (0.31), residues: 256
  sheet: -0.23 (0.43), residues: 154
  loop :  0.22 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  48 
 TYR   0.013   0.001   TYR B 144 
 PHE   0.014   0.001   PHE A 347 
 TRP   0.011   0.001   TRP B 198 
 HIS   0.003   0.001   HIS A 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 7032)
  covalent geometry    : angle       0.51691 ( 9584)
  hydrogen bonds       : bond        0.03948 (  278)
  hydrogen bonds       : angle       5.01269 (  744)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 0.269 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6884 (mp0)
REVERT: B  242 ASP cc_start: 0.7497 (m-30) cc_final: 0.7260 (m-30)
REVERT: B  364 ASN cc_start: 0.8770 (m-40) cc_final: 0.8433 (m-40)
REVERT: B  369 GLN cc_start: 0.7890 (mt0) cc_final: 0.7551 (mt0)
REVERT: B  405 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7301 (tt0)
  outliers start: 20
  outliers final: 10
  residues processed: 165
  average time/residue: 0.7337
  time to fit residues: 125.4333
Evaluate side-chains
  164 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 153
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  343 GLN
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 36 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0050
   chunk 6 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7596

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

Flipped N/Q/H residues before XYZ refinement:
A 428 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.111191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.101136 restraints weight = 8508.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3407 rms_B_bonded: 1.35
r_work: 0.3304 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7032  Z= 0.153
  Angle     :  0.534   8.251   9584  Z= 0.273
  Chirality :  0.047   0.137   1048
  Planarity :  0.005   0.040   1260
  Dihedral  :  4.546  18.171    950
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 15.41 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.29), residues: 862
  helix:  1.94 (0.31), residues: 256
  sheet: -0.22 (0.42), residues: 154
  loop :  0.32 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  17 
 TYR   0.014   0.001   TYR A 144 
 PHE   0.011   0.001   PHE B 347 
 TRP   0.011   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 7032)
  covalent geometry    : angle       0.53370 ( 9584)
  hydrogen bonds       : bond        0.03986 (  278)
  hydrogen bonds       : angle       4.99803 (  744)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 154
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6918 (mp0)
REVERT: B   67 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7705 (tm-30)
REVERT: B  242 ASP cc_start: 0.7509 (m-30) cc_final: 0.7272 (m-30)
REVERT: B  364 ASN cc_start: 0.8783 (m-40) cc_final: 0.8459 (m-40)
REVERT: B  369 GLN cc_start: 0.7917 (mt0) cc_final: 0.7567 (mt0)
REVERT: B  405 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7332 (tt0)
  outliers start: 20
  outliers final: 8
  residues processed: 160
  average time/residue: 0.7575
  time to fit residues: 125.5710
Evaluate side-chains
  161 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 151
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 343 GLN
A 428 GLN
B 343 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.110075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.099996 restraints weight = 8492.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3384 rms_B_bonded: 1.35
r_work: 0.3282 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7032  Z= 0.218
  Angle     :  0.582   7.058   9584  Z= 0.302
  Chirality :  0.049   0.137   1048
  Planarity :  0.005   0.042   1260
  Dihedral  :  4.806  19.784    950
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.35 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.85 (0.28), residues: 862
  helix:  1.74 (0.31), residues: 256
  sheet: -0.26 (0.42), residues: 154
  loop :  0.29 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A  17 
 TYR   0.018   0.002   TYR A 144 
 PHE   0.015   0.002   PHE A 347 
 TRP   0.013   0.002   TRP A 413 
 HIS   0.005   0.001   HIS B 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 7032)
  covalent geometry    : angle       0.58248 ( 9584)
  hydrogen bonds       : bond        0.04563 (  278)
  hydrogen bonds       : angle       5.13879 (  744)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 0.227 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.7025 (mp0)
REVERT: B   67 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7660 (tm-30)
REVERT: B  242 ASP cc_start: 0.7508 (m-30) cc_final: 0.7274 (m-30)
REVERT: B  312 ARG cc_start: 0.7920 (mtt180) cc_final: 0.7719 (mtt180)
REVERT: B  364 ASN cc_start: 0.8780 (m-40) cc_final: 0.8447 (m-40)
REVERT: B  369 GLN cc_start: 0.7872 (mt0) cc_final: 0.7530 (mt0)
REVERT: B  405 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7378 (tt0)
  outliers start: 19
  outliers final: 10
  residues processed: 162
  average time/residue: 0.7967
  time to fit residues: 133.7042
Evaluate side-chains
  170 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 158
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  159 MET
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  343 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 70 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 343 GLN
A 428 GLN
B 343 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.111294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.101252 restraints weight = 8529.353|
|-----------------------------------------------------------------------------|
r_work (start): 0.3410 rms_B_bonded: 1.36
r_work: 0.3307 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7032  Z= 0.137
  Angle     :  0.540   6.384   9584  Z= 0.280
  Chirality :  0.047   0.139   1048
  Planarity :  0.005   0.040   1260
  Dihedral  :  4.632  18.438    950
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.30 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.29), residues: 862
  helix:  1.97 (0.32), residues: 256
  sheet: -0.17 (0.43), residues: 154
  loop :  0.43 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  17 
 TYR   0.015   0.001   TYR A 144 
 PHE   0.014   0.001   PHE A 347 
 TRP   0.012   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7032)
  covalent geometry    : angle       0.53954 ( 9584)
  hydrogen bonds       : bond        0.03941 (  278)
  hydrogen bonds       : angle       4.99845 (  744)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  273 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6973 (mp0)
REVERT: B   67 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7666 (tm-30)
REVERT: B  242 ASP cc_start: 0.7500 (m-30) cc_final: 0.7258 (m-30)
REVERT: B  312 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7729 (mtt180)
REVERT: B  364 ASN cc_start: 0.8785 (m-40) cc_final: 0.8469 (m-40)
REVERT: B  369 GLN cc_start: 0.7892 (mt0) cc_final: 0.7550 (mt0)
REVERT: B  405 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7360 (tt0)
  outliers start: 16
  outliers final: 11
  residues processed: 166
  average time/residue: 0.7479
  time to fit residues: 128.5619
Evaluate side-chains
  168 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  343 GLN
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 5 optimal weight:    0.0770
   chunk 40 optimal weight:    3.9990
   chunk 38 optimal weight:    0.4980
   chunk 4 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.8942

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

Flipped N/Q/H residues before XYZ refinement:
A  67 GLN
A 428 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.110859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.100853 restraints weight = 8512.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.34
r_work: 0.3299 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3164 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7032  Z= 0.174
  Angle     :  0.564   8.205   9584  Z= 0.290
  Chirality :  0.048   0.139   1048
  Planarity :  0.005   0.039   1260
  Dihedral  :  4.698  18.870    950
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.97 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.29), residues: 862
  helix:  1.91 (0.31), residues: 256
  sheet: -0.16 (0.43), residues: 154
  loop :  0.48 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  17 
 TYR   0.015   0.001   TYR A 144 
 PHE   0.014   0.001   PHE A 347 
 TRP   0.011   0.001   TRP B 198 
 HIS   0.004   0.001   HIS B 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 7032)
  covalent geometry    : angle       0.56447 ( 9584)
  hydrogen bonds       : bond        0.04185 (  278)
  hydrogen bonds       : angle       5.03829 (  744)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A    1 MET cc_start: 0.8850 (mtm) cc_final: 0.8578 (mmm)
REVERT: A  273 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.7006 (mp0)
REVERT: B   67 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7632 (tm-30)
REVERT: B  242 ASP cc_start: 0.7518 (m-30) cc_final: 0.7278 (m-30)
REVERT: B  312 ARG cc_start: 0.7955 (mtt180) cc_final: 0.7753 (mtt180)
REVERT: B  364 ASN cc_start: 0.8789 (m-40) cc_final: 0.8469 (m-40)
REVERT: B  369 GLN cc_start: 0.7905 (mt0) cc_final: 0.7550 (mt0)
REVERT: B  405 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7396 (tt0)
  outliers start: 13
  outliers final: 8
  residues processed: 157
  average time/residue: 0.7575
  time to fit residues: 123.1086
Evaluate side-chains
  160 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  264 ASP
Chi-restraints excluded: chain A residue  273 GLU
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue   67 GLN
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   chunk 54 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   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  67 GLN
A 343 GLN
B 343 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.111710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.101707 restraints weight = 8462.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.35
r_work: 0.3313 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7032  Z= 0.138
  Angle     :  0.543   7.375   9584  Z= 0.279
  Chirality :  0.046   0.138   1048
  Planarity :  0.005   0.038   1260
  Dihedral  :  4.572  18.077    950
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.97 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.29), residues: 862
  helix:  2.08 (0.31), residues: 256
  sheet: -0.11 (0.43), residues: 154
  loop :  0.53 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  17 
 TYR   0.015   0.001   TYR A 187 
 PHE   0.014   0.001   PHE A 347 
 TRP   0.012   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7032)
  covalent geometry    : angle       0.54266 ( 9584)
  hydrogen bonds       : bond        0.03846 (  278)
  hydrogen bonds       : angle       4.94610 (  744)

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

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

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1724 Ramachandran restraints generated.
    862 Oldfield, 0 Emsley, 862 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 158
  time to evaluate  : 0.326 
Fit side-chains
REVERT: B  242 ASP cc_start: 0.7506 (m-30) cc_final: 0.7262 (m-30)
REVERT: B  364 ASN cc_start: 0.8781 (m-40) cc_final: 0.8464 (m-40)
REVERT: B  369 GLN cc_start: 0.7905 (mt0) cc_final: 0.7584 (mt0)
REVERT: B  405 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7342 (tt0)
  outliers start: 14
  outliers final: 9
  residues processed: 164
  average time/residue: 0.8949
  time to fit residues: 152.0040
Evaluate side-chains
  163 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 154
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  300 LYS
Chi-restraints excluded: chain A residue  343 GLN
Chi-restraints excluded: chain A residue  363 GLU
Chi-restraints excluded: chain A residue  394 LYS
Chi-restraints excluded: chain B residue  264 ASP
Chi-restraints excluded: chain B residue  300 LYS
Chi-restraints excluded: chain B residue  343 GLN
Chi-restraints excluded: chain B residue  363 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 52 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 5 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.111812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.101735 restraints weight = 8498.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3413 rms_B_bonded: 1.36
r_work: 0.3311 rms_B_bonded: 1.68 restraints_weight: 0.5000
r_work: 0.3176 rms_B_bonded: 3.04 restraints_weight: 0.2500
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.278   7032  Z= 0.441
  Angle     :  1.222  65.858   9584  Z= 0.740
  Chirality :  0.047   0.235   1048
  Planarity :  0.011   0.249   1260
  Dihedral  :  4.575  18.082    950
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 18.38 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.25 %
  Peptide Plane:
    Cis-proline     : 12.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.29), residues: 862
  helix:  2.08 (0.31), residues: 256
  sheet: -0.11 (0.43), residues: 154
  loop :  0.51 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 312 
 TYR   0.013   0.001   TYR A 144 
 PHE   0.014   0.001   PHE A 347 
 TRP   0.012   0.001   TRP B 198 
 HIS   0.003   0.001   HIS B 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00904 ( 7032)
  covalent geometry    : angle       1.22212 ( 9584)
  hydrogen bonds       : bond        0.03849 (  278)
  hydrogen bonds       : angle       4.94567 (  744)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3185.82 seconds
wall clock time: 54 minutes 42.90 seconds (3282.90 seconds total)