Starting phenix.real_space_refine
on Wed Sep 17 14:15:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zn5_14801/09_2025/7zn5_14801.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zn5_14801/09_2025/7zn5_14801.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zn5_14801/09_2025/7zn5_14801.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zn5_14801/09_2025/7zn5_14801.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zn5_14801/09_2025/7zn5_14801.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zn5_14801/09_2025/7zn5_14801.map"
  }
  resolution = 3.7
  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=  -0.000 sd=   1.000
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
     P      97      5.49       5
     S      18      5.16       5
     C    5500      2.51       5
     N    1562      2.21       5
     O    1869      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9046
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3533
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 430, 3525
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 411}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
      Conformer: "B"
        Number of residues, atoms: 430, 3525
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 411}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
          bond proxies already assigned to first conformer: 3601
    Chain: "B"
      Number of atoms: 3566
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 435, 3566
          Classifications: {'peptide': 435}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 414}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 975
          Classifications: {'DNA': 48}
          Link IDs: {'rna3p': 47}
    Chain: "D"
      Number of atoms: 972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 972
          Classifications: {'DNA': 47}
          Link IDs: {'rna3p': 46}
  Time building chain proxies: 2.72, per 1000 atoms: 0.30
  Number of scatterers: 9046
  At special positions: 0
  Unit cell: (146.685, 98.679, 89.789, 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)
     S      18     16.00
     P      97     15.00
     O    1869      8.00
     N    1562      7.00
     C    5500      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: 0.96
  Conformation dependent library (CDL) restraints added in 408.1 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1636

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 7 sheets defined
      46.8% alpha, 9.6% beta
      13 base pairs and 63 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 31
      removed outlier: 4.267A  pdb=" N   TYR A  21 " --> pdb=" O   TYR A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 52 through 66
      removed outlier: 3.580A  pdb=" N   VAL A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU A  66 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.773A  pdb=" N   LYS A 126 " --> pdb=" O   GLU A 122 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   TYR A 127 " --> pdb=" O   GLN A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 163
    Processing helix  chain 'A' and resid 177 through 190
      removed outlier: 3.700A  pdb=" N   LEU A 181 " --> pdb=" O   GLY A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 212
      removed outlier: 4.153A  pdb=" N   HIS A 211 " --> pdb=" O   LYS A 207 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   TYR A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 233
    Processing helix  chain 'A' and resid 254 through 268
      removed outlier: 4.117A  pdb=" N   HIS A 268 " --> pdb=" O   TRP A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 296
    Processing helix  chain 'A' and resid 323 through 334
    Processing helix  chain 'A' and resid 342 through 356
      removed outlier: 3.927A  pdb=" N   GLN A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLY A 356 " --> pdb=" O   PHE A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 381
      removed outlier: 3.870A  pdb=" N   LYS A 360 " --> pdb=" O   GLY A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 418
    Processing helix  chain 'A' and resid 426 through 429
      removed outlier: 3.547A  pdb=" N   SER A 429 " --> pdb=" O   SER A 426 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 426 through 429'
    Processing helix  chain 'A' and resid 450 through 463
    Processing helix  chain 'B' and resid 15 through 31
      removed outlier: 4.349A  pdb=" N   TYR B  21 " --> pdb=" O   TYR B  17 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 49
    Processing helix  chain 'B' and resid 52 through 67
      removed outlier: 3.615A  pdb=" N   VAL B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 132
      removed outlier: 3.814A  pdb=" N   LYS B 126 " --> pdb=" O   GLU B 122 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   TYR B 127 " --> pdb=" O   GLN B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 164
      removed outlier: 3.659A  pdb=" N   GLY B 164 " --> pdb=" O   HIS B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 172
      removed outlier: 3.543A  pdb=" N   VAL B 172 " --> pdb=" O   PRO B 169 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 190
      removed outlier: 4.374A  pdb=" N   THR B 180 " --> pdb=" O   ALA B 176 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   LEU B 181 " --> pdb=" O   GLY B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 210
    Processing helix  chain 'B' and resid 227 through 233
    Processing helix  chain 'B' and resid 254 through 268
      removed outlier: 3.976A  pdb=" N   HIS B 268 " --> pdb=" O   TRP B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 296
    Processing helix  chain 'B' and resid 323 through 334
    Processing helix  chain 'B' and resid 342 through 355
      removed outlier: 3.693A  pdb=" N   GLN B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 382
      removed outlier: 3.789A  pdb=" N   LYS B 360 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ARG B 382 " --> pdb=" O   SER B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 418
    Processing helix  chain 'B' and resid 450 through 462
    Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71
    Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 109
      removed outlier: 3.822A  pdb=" N   PHE A 109 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   TYR A 423 " --> pdb=" O   PHE A 109 " (cutoff:3.500A)
      removed outlier: 10.285A  pdb=" N   LYS A 421 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   GLY A 442 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   TYR A 423 " --> pdb=" O   VAL A 440 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A 440 " --> pdb=" O   TYR A 423 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   VAL A 399 " --> pdb=" O   ILE A 390 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU A 388 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 175
      removed outlier: 6.698A  pdb=" N   VAL A 239 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   ASP A 276 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   THR A 241 " --> pdb=" O   ASP A 276 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   VAL A 194 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   TYR A 240 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   GLY A 196 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   TYR A 195 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   PHE A 219 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE A 197 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 222
      removed outlier: 3.552A  pdb=" N   GLY A 225 " --> pdb=" O   ASP A 222 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71
    Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 175
      removed outlier: 3.597A  pdb=" N   GLY B 175 " --> pdb=" O   SER B 318 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   VAL B 239 " --> pdb=" O   ILE B 274 " (cutoff:3.500A)
      removed outlier: 8.049A  pdb=" N   ASP B 276 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   THR B 241 " --> pdb=" O   ASP B 276 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   VAL B 194 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   TYR B 240 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   GLY B 196 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 387 through 389
      removed outlier: 3.874A  pdb=" N   LEU B 388 " --> pdb=" O   VAL B 401 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL B 440 " --> pdb=" O   TYR B 423 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   TYR B 423 " --> pdb=" O   VAL B 440 " (cutoff:3.500A)

    292 hydrogen bonds defined for protein.
    846 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      32 hydrogen bonds
      64 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      63 stacking parallelities
  Total time for adding SS restraints: 1.44

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2318
        1.34 -     1.45: 2259
        1.45 -     1.57: 4657
        1.57 -     1.69: 190
        1.69 -     1.81: 32
  Bond restraints: 9456
  Sorted by residual:
  bond pdb=" OP4 LLP A 309 "
       pdb=" P   LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.726  1.544  0.182 2.00e-02 2.50e+03 8.32e+01
  bond pdb=" OP4 LLP B 309 "
       pdb=" P   LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.726  1.545  0.181 2.00e-02 2.50e+03 8.18e+01
  bond pdb=" NZ  LLP B 309 "
       pdb=" C4' LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.273  1.432 -0.159 2.00e-02 2.50e+03 6.30e+01
  bond pdb=" NZ  LLP A 309 "
       pdb=" C4' LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.273  1.432 -0.159 2.00e-02 2.50e+03 6.29e+01
  bond pdb=" C4  LLP B 309 "
       pdb=" C4' LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.464  1.615 -0.151 2.00e-02 2.50e+03 5.72e+01
  ... (remaining 9451 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 13059
        2.23 -     4.45: 119
        4.45 -     6.68: 28
        6.68 -     8.90: 3
        8.90 -    11.13: 6
  Bond angle restraints: 13215
  Sorted by residual:
  angle pdb=" CA  ARG B 138 "
        pdb=" CB  ARG B 138 "
        pdb=" CG  ARG B 138 "
      ideal   model   delta    sigma   weight residual
     114.10  121.66   -7.56 2.00e+00 2.50e-01 1.43e+01
  angle pdb=" NZ  LLP A 309 "
        pdb=" C4' LLP A 309 "
        pdb=" C4  LLP A 309 "
      ideal   model   delta    sigma   weight residual
     120.09  108.96   11.13 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" NZ  LLP B 309 "
        pdb=" C4' LLP B 309 "
        pdb=" C4  LLP B 309 "
      ideal   model   delta    sigma   weight residual
     120.09  108.98   11.11 3.00e+00 1.11e-01 1.37e+01
  angle pdb=" CE  LLP A 309 "
        pdb=" NZ  LLP A 309 "
        pdb=" C4' LLP A 309 "
      ideal   model   delta    sigma   weight residual
     119.26  108.86   10.40 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" C   LEU A  49 "
        pdb=" N   LYS A  50 "
        pdb=" CA  LYS A  50 "
      ideal   model   delta    sigma   weight residual
     122.08  127.01   -4.93 1.47e+00 4.63e-01 1.12e+01
  ... (remaining 13210 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.21: 4923
       28.21 -    56.42: 464
       56.42 -    84.63: 30
       84.63 -   112.84: 2
      112.84 -   141.06: 1
  Dihedral angle restraints: 5420
    sinusoidal: 2863
      harmonic: 2557
  Sorted by residual:
  dihedral pdb=" CA  ARG A  74 "
           pdb=" C   ARG A  74 "
           pdb=" N   LYS A  75 "
           pdb=" CA  LYS A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.23  -20.77     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" C4'  DA D  33 "
           pdb=" C3'  DA D  33 "
           pdb=" O3'  DA D  33 "
           pdb=" P    DA D  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   78.94  141.06     1      3.50e+01 8.16e-04 1.39e+01
  dihedral pdb=" CA  PRO A  73 "
           pdb=" C   PRO A  73 "
           pdb=" N   ARG A  74 "
           pdb=" CA  ARG A  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.36   18.64     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 5417 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1046
       0.032 -    0.064: 257
       0.064 -    0.096: 92
       0.096 -    0.128: 49
       0.128 -    0.159: 6
  Chirality restraints: 1450
  Sorted by residual:
  chirality pdb=" CA  ARG B 138 "
            pdb=" N   ARG B 138 "
            pdb=" C   ARG B 138 "
            pdb=" CB  ARG B 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.36e-01
  chirality pdb=" CA  ILE A  72 "
            pdb=" N   ILE A  72 "
            pdb=" C   ILE A  72 "
            pdb=" CB  ILE A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CA  GLU B 154 "
            pdb=" N   GLU B 154 "
            pdb=" C   GLU B 154 "
            pdb=" CB  GLU B 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 1447 not shown)

  Planarity restraints: 1348
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP A 309 "   -0.156 2.00e-02 2.50e+03   2.55e-01 6.53e+02
        pdb=" NZ  LLP A 309 "    0.341 2.00e-02 2.50e+03
        pdb=" C4  LLP A 309 "    0.135 2.00e-02 2.50e+03
        pdb=" C4' LLP A 309 "   -0.320 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP B 309 "    0.089 2.00e-02 2.50e+03   8.51e-02 7.24e+01
        pdb=" NZ  LLP B 309 "   -0.091 2.00e-02 2.50e+03
        pdb=" C4  LLP B 309 "    0.081 2.00e-02 2.50e+03
        pdb=" C4' LLP B 309 "   -0.079 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 168 "   -0.032 5.00e-02 4.00e+02   4.78e-02 3.66e+00
        pdb=" N   PRO A 169 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 169 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 169 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1345 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 804
        2.74 -     3.28: 8566
        3.28 -     3.82: 15123
        3.82 -     4.36: 16992
        4.36 -     4.90: 27837
  Nonbonded interactions: 69322
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 254 "
            pdb=" OD1 ASN A 256 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" OG  SER A 162 "
            pdb=" OE2 GLU A 281 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" OE1 GLN B 184 "
            pdb=" OH  TYR B 330 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   HIS B 145 "
            pdb=" OG  SER B 339 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   THR B 131 "
            pdb=" ND2 ASN B 136 "
     model   vdw
     2.302 3.120
  ... (remaining 69317 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 15 through 442 or resid 444 through 464))
  selection = (chain 'B' and (resid 15 through 442 or resid 444 through 464))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.120
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.930
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.182   9456  Z= 0.271
  Angle     :  0.621  11.128  13215  Z= 0.319
  Chirality :  0.037   0.159   1450
  Planarity :  0.009   0.255   1348
  Dihedral  : 18.868 141.055   3784
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.52 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.18 (0.30), residues: 852
  helix:  1.18 (0.28), residues: 374
  sheet:  0.15 (0.52), residues: 106
  loop : -0.97 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 138 
 TYR   0.019   0.001   TYR A  82 
 PHE   0.011   0.001   PHE A 128 
 TRP   0.010   0.001   TRP A 264 
 HIS   0.003   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 ( 9456)
  covalent geometry    : angle       0.62082 (13215)
  hydrogen bonds       : bond        0.16656 (  324)
  hydrogen bonds       : angle       6.50322 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 ILE cc_start: 0.8787 (pt) cc_final: 0.8580 (mt)
REVERT: A  270 ASN cc_start: 0.7690 (t0) cc_final: 0.7392 (t0)
REVERT: B  270 ASN cc_start: 0.7313 (t0) cc_final: 0.6885 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1197
  time to fit residues: 16.2114
Evaluate side-chains
  66 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0770
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.7542

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 ASN
A 183 GLN
B  53 GLN
B 142 ASN
B 183 GLN
** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.130713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.094867 restraints weight = 16076.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.097839 restraints weight = 8565.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.099846 restraints weight = 5501.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.101212 restraints weight = 4030.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.102140 restraints weight = 3251.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3524
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3524 r_free = 0.3524    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3524 r_free = 0.3524    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3524
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9456  Z= 0.172
  Angle     :  0.627   8.560  13215  Z= 0.352
  Chirality :  0.042   0.152   1450
  Planarity :  0.005   0.049   1348
  Dihedral  : 20.528 139.102   2050
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  :  7.83 %
    Favored  : 90.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.04 (0.29), residues: 852
  helix:  1.01 (0.27), residues: 380
  sheet: -0.24 (0.48), residues: 117
  loop : -0.90 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  43 
 TYR   0.021   0.002   TYR B  21 
 PHE   0.013   0.002   PHE A 352 
 TRP   0.016   0.001   TRP B 264 
 HIS   0.006   0.001   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 9456)
  covalent geometry    : angle       0.62677 (13215)
  hydrogen bonds       : bond        0.04625 (  324)
  hydrogen bonds       : angle       4.09666 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   30 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7648 (pt0)
REVERT: A  237 ASP cc_start: 0.6136 (OUTLIER) cc_final: 0.5934 (m-30)
REVERT: A  270 ASN cc_start: 0.7775 (t0) cc_final: 0.7319 (t0)
REVERT: B   70 GLU cc_start: 0.8566 (tp30) cc_final: 0.8169 (pm20)
REVERT: B  268 HIS cc_start: 0.7452 (OUTLIER) cc_final: 0.7175 (t-90)
REVERT: B  270 ASN cc_start: 0.7437 (t0) cc_final: 0.6915 (t0)
  outliers start: 16
  outliers final: 10
  residues processed: 82
  average time/residue: 0.0973
  time to fit residues: 11.3350
Evaluate side-chains
  71 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  268 HIS
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 50 optimal weight:    8.9990
   chunk 21 optimal weight:    5.9990
   chunk 12 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 58 optimal weight:    0.6980
   chunk 91 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 142 ASN
B 183 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.130089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.096428 restraints weight = 17208.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.099129 restraints weight = 9737.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.100996 restraints weight = 6467.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.102250 restraints weight = 4841.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.102990 restraints weight = 3967.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3561
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3561 r_free = 0.3561    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3561
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9456  Z= 0.127
  Angle     :  0.560   5.888  13215  Z= 0.320
  Chirality :  0.040   0.145   1450
  Planarity :  0.005   0.057   1348
  Dihedral  : 20.697 143.344   2050
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  :  8.88 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.30 (0.30), residues: 852
  helix:  1.22 (0.27), residues: 378
  sheet:  0.07 (0.50), residues: 112
  loop : -0.81 (0.33), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  32 
 TYR   0.014   0.001   TYR B  17 
 PHE   0.008   0.001   PHE A 151 
 TRP   0.010   0.001   TRP B 264 
 HIS   0.006   0.001   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9456)
  covalent geometry    : angle       0.56026 (13215)
  hydrogen bonds       : bond        0.03598 (  324)
  hydrogen bonds       : angle       3.76199 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A   33 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7429 (tp)
REVERT: A  237 ASP cc_start: 0.5987 (OUTLIER) cc_final: 0.5736 (m-30)
REVERT: A  270 ASN cc_start: 0.7656 (t0) cc_final: 0.7160 (t0)
REVERT: B  270 ASN cc_start: 0.7452 (t0) cc_final: 0.6948 (t0)
  outliers start: 21
  outliers final: 12
  residues processed: 82
  average time/residue: 0.1226
  time to fit residues: 13.6246
Evaluate side-chains
  72 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 58
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 79 optimal weight:    9.9990
   chunk 57 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 ASN
B 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.132423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.095973 restraints weight = 16254.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.098957 restraints weight = 8698.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.101011 restraints weight = 5611.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.102376 restraints weight = 4122.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.103312 restraints weight = 3342.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3535
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3535 r_free = 0.3535    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3535
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7454
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9456  Z= 0.133
  Angle     :  0.559   6.272  13215  Z= 0.319
  Chirality :  0.040   0.140   1450
  Planarity :  0.005   0.049   1348
  Dihedral  : 20.882 144.222   2050
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 10.70 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.33 (0.30), residues: 852
  helix:  1.24 (0.27), residues: 379
  sheet:  0.11 (0.51), residues: 112
  loop : -0.81 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 343 
 TYR   0.021   0.001   TYR B  68 
 PHE   0.018   0.002   PHE B 119 
 TRP   0.006   0.001   TRP B 264 
 HIS   0.007   0.001   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9456)
  covalent geometry    : angle       0.55869 (13215)
  hydrogen bonds       : bond        0.03700 (  324)
  hydrogen bonds       : angle       3.68131 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 64
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A   33 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7347 (tp)
REVERT: A  270 ASN cc_start: 0.7747 (t0) cc_final: 0.7200 (t0)
REVERT: B  138 ARG cc_start: 0.7778 (pmt-80) cc_final: 0.7398 (pmt-80)
REVERT: B  270 ASN cc_start: 0.7541 (t0) cc_final: 0.7047 (t0)
  outliers start: 25
  outliers final: 16
  residues processed: 83
  average time/residue: 0.1085
  time to fit residues: 12.5737
Evaluate side-chains
  76 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 71 optimal weight:    0.4980
   chunk 50 optimal weight:    1.9990
   chunk 41 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0980
   chunk 61 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0670
   chunk 82 optimal weight:    9.9990
   chunk 5 optimal weight:    9.9990
   chunk 36 optimal weight:    7.9990
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 142 ASN
B 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.131226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.097013 restraints weight = 17099.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.099760 restraints weight = 9672.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.101635 restraints weight = 6426.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.102931 restraints weight = 4811.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.103810 restraints weight = 3942.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3574
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3574
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9456  Z= 0.122
  Angle     :  0.549   9.219  13215  Z= 0.311
  Chirality :  0.039   0.140   1450
  Planarity :  0.005   0.050   1348
  Dihedral  : 21.124 145.703   2050
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 12.79 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.52 (0.30), residues: 852
  helix:  1.45 (0.27), residues: 377
  sheet:  0.20 (0.51), residues: 112
  loop : -0.76 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 283 
 TYR   0.016   0.001   TYR B  68 
 PHE   0.010   0.001   PHE B 119 
 TRP   0.006   0.001   TRP A 264 
 HIS   0.008   0.001   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 9456)
  covalent geometry    : angle       0.54871 (13215)
  hydrogen bonds       : bond        0.03319 (  324)
  hydrogen bonds       : angle       3.56830 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  270 ASN cc_start: 0.7623 (t0) cc_final: 0.7168 (t0)
REVERT: B   32 ARG cc_start: 0.8014 (mmp-170) cc_final: 0.7776 (mmp-170)
REVERT: B   70 GLU cc_start: 0.8472 (tp30) cc_final: 0.8079 (pm20)
REVERT: B  270 ASN cc_start: 0.7478 (t0) cc_final: 0.6974 (t0)
  outliers start: 23
  outliers final: 19
  residues processed: 78
  average time/residue: 0.1033
  time to fit residues: 11.4921
Evaluate side-chains
  77 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 93 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 45 optimal weight:    8.9990
   chunk 90 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 15 optimal weight:    5.9990
   chunk 65 optimal weight:    7.9990
   chunk 79 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
B 142 ASN
B 361 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.126135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.089809 restraints weight = 16532.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.092501 restraints weight = 9104.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.094329 restraints weight = 6015.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.095600 restraints weight = 4507.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.096449 restraints weight = 3691.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3421
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3421
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   9456  Z= 0.267
  Angle     :  0.709   8.150  13215  Z= 0.394
  Chirality :  0.046   0.163   1450
  Planarity :  0.006   0.049   1348
  Dihedral  : 21.607 145.599   2050
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 13.05 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.41 (0.28), residues: 852
  helix:  0.53 (0.26), residues: 378
  sheet: -0.38 (0.48), residues: 116
  loop : -1.02 (0.33), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 245 
 TYR   0.025   0.002   TYR B  68 
 PHE   0.023   0.003   PHE A 352 
 TRP   0.010   0.002   TRP B 124 
 HIS   0.009   0.002   HIS A 145 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 9456)
  covalent geometry    : angle       0.70882 (13215)
  hydrogen bonds       : bond        0.05514 (  324)
  hydrogen bonds       : angle       4.14997 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 59
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  270 ASN cc_start: 0.7673 (t0) cc_final: 0.7130 (t0)
REVERT: B   17 TYR cc_start: 0.7305 (OUTLIER) cc_final: 0.6624 (t80)
REVERT: B   70 GLU cc_start: 0.8503 (tp30) cc_final: 0.7897 (pm20)
REVERT: B  270 ASN cc_start: 0.7656 (t0) cc_final: 0.7238 (t0)
  outliers start: 29
  outliers final: 22
  residues processed: 80
  average time/residue: 0.0937
  time to fit residues: 10.9842
Evaluate side-chains
  78 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   35 TYR
Chi-restraints excluded: chain A residue   66 GLU
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  116 THR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0870
   chunk 33 optimal weight:    0.5980
   chunk 45 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 41 optimal weight:    0.8980
   chunk 70 optimal weight:    3.9990
   overall best weight:    0.8960

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
B  23 HIS
B 142 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.130829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.094456 restraints weight = 16274.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.097359 restraints weight = 8782.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.099358 restraints weight = 5703.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.100702 restraints weight = 4209.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.101601 restraints weight = 3419.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3507
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3507 r_free = 0.3507    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3507
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7490
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9456  Z= 0.132
  Angle     :  0.571   7.874  13215  Z= 0.325
  Chirality :  0.040   0.152   1450
  Planarity :  0.005   0.052   1348
  Dihedral  : 21.559 145.937   2050
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 14.62 %
    Favored  : 82.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.12 (0.29), residues: 852
  helix:  1.06 (0.27), residues: 378
  sheet: -0.15 (0.50), residues: 113
  loop : -0.84 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 138 
 TYR   0.016   0.001   TYR B  68 
 PHE   0.011   0.001   PHE A 119 
 TRP   0.007   0.001   TRP A 124 
 HIS   0.011   0.001   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9456)
  covalent geometry    : angle       0.57115 (13215)
  hydrogen bonds       : bond        0.03639 (  324)
  hydrogen bonds       : angle       3.68930 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  270 ASN cc_start: 0.7607 (t0) cc_final: 0.7211 (t0)
REVERT: B   17 TYR cc_start: 0.7161 (OUTLIER) cc_final: 0.6557 (t80)
REVERT: B   32 ARG cc_start: 0.8028 (mmp-170) cc_final: 0.7803 (mmp-170)
REVERT: B   70 GLU cc_start: 0.8391 (tp30) cc_final: 0.7911 (pm20)
REVERT: B  270 ASN cc_start: 0.7602 (t0) cc_final: 0.7079 (t0)
REVERT: B  339 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.8084 (t)
  outliers start: 23
  outliers final: 15
  residues processed: 77
  average time/residue: 0.0962
  time to fit residues: 10.9213
Evaluate side-chains
  77 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   23 HIS
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 4 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0070
   chunk 53 optimal weight:   10.0000
   chunk 83 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.132173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.095942 restraints weight = 16146.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.098904 restraints weight = 8646.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.100905 restraints weight = 5586.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.102278 restraints weight = 4125.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.103204 restraints weight = 3349.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3532
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3532 r_free = 0.3532    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3532 r_free = 0.3532    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3532
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7462
moved from start:          0.2816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9456  Z= 0.126
  Angle     :  0.556   7.835  13215  Z= 0.316
  Chirality :  0.040   0.169   1450
  Planarity :  0.005   0.050   1348
  Dihedral  : 21.624 146.291   2050
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 15.01 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.34 (0.30), residues: 852
  helix:  1.27 (0.27), residues: 378
  sheet:  0.07 (0.51), residues: 112
  loop : -0.82 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 138 
 TYR   0.015   0.001   TYR B  68 
 PHE   0.011   0.001   PHE A 119 
 TRP   0.006   0.001   TRP B 264 
 HIS   0.023   0.001   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9456)
  covalent geometry    : angle       0.55551 (13215)
  hydrogen bonds       : bond        0.03444 (  324)
  hydrogen bonds       : angle       3.59853 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A  270 ASN cc_start: 0.7559 (t0) cc_final: 0.7159 (t0)
REVERT: B   17 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6546 (t80)
REVERT: B   32 ARG cc_start: 0.8079 (mmp-170) cc_final: 0.7817 (mmp-170)
REVERT: B   70 GLU cc_start: 0.8383 (tp30) cc_final: 0.7980 (pm20)
REVERT: B  270 ASN cc_start: 0.7595 (t0) cc_final: 0.7055 (t0)
REVERT: B  339 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8078 (t)
  outliers start: 21
  outliers final: 16
  residues processed: 77
  average time/residue: 0.0952
  time to fit residues: 10.6938
Evaluate side-chains
  80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 50 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 88 optimal weight:   10.0000
   chunk 71 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 36 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 91 optimal weight:    7.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
B  23 HIS
B 142 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.130451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.094346 restraints weight = 16331.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.097251 restraints weight = 8710.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.099139 restraints weight = 5630.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.100575 restraints weight = 4163.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.101367 restraints weight = 3364.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3503
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3503 r_free = 0.3503    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3503
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9456  Z= 0.151
  Angle     :  0.582   8.115  13215  Z= 0.328
  Chirality :  0.041   0.182   1450
  Planarity :  0.005   0.050   1348
  Dihedral  : 21.717 146.117   2050
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 15.80 %
    Favored  : 81.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.24 (0.30), residues: 852
  helix:  1.19 (0.27), residues: 378
  sheet:  0.07 (0.52), residues: 108
  loop : -0.87 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 245 
 TYR   0.016   0.001   TYR B  68 
 PHE   0.012   0.002   PHE A 352 
 TRP   0.004   0.001   TRP A 264 
 HIS   0.010   0.001   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9456)
  covalent geometry    : angle       0.58250 (13215)
  hydrogen bonds       : bond        0.03751 (  324)
  hydrogen bonds       : angle       3.63395 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 60
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  270 ASN cc_start: 0.7574 (t0) cc_final: 0.7147 (t0)
REVERT: B   17 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.6621 (t80)
REVERT: B   70 GLU cc_start: 0.8382 (tp30) cc_final: 0.7960 (pm20)
REVERT: B  270 ASN cc_start: 0.7627 (t0) cc_final: 0.7070 (t0)
REVERT: B  339 SER cc_start: 0.8343 (OUTLIER) cc_final: 0.8116 (t)
  outliers start: 24
  outliers final: 19
  residues processed: 78
  average time/residue: 0.1017
  time to fit residues: 11.2955
Evaluate side-chains
  80 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   23 HIS
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 85 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
B 142 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.128822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.092881 restraints weight = 16227.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.095691 restraints weight = 8801.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.097631 restraints weight = 5753.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.098948 restraints weight = 4262.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.099840 restraints weight = 3469.382|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3486
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3486 r_free = 0.3486    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3486
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.2962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9456  Z= 0.174
  Angle     :  0.595   7.209  13215  Z= 0.335
  Chirality :  0.042   0.162   1450
  Planarity :  0.005   0.050   1348
  Dihedral  : 21.778 145.964   2050
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 16.19 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.17 (0.29), residues: 852
  helix:  1.10 (0.27), residues: 378
  sheet: -0.08 (0.50), residues: 112
  loop : -0.84 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 245 
 TYR   0.018   0.001   TYR B  68 
 PHE   0.014   0.002   PHE B 352 
 TRP   0.003   0.001   TRP A 264 
 HIS   0.023   0.002   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 9456)
  covalent geometry    : angle       0.59530 (13215)
  hydrogen bonds       : bond        0.03949 (  324)
  hydrogen bonds       : angle       3.69898 (  910)

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

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

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1704 Ramachandran restraints generated.
    852 Oldfield, 0 Emsley, 852 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 60
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  270 ASN cc_start: 0.7555 (t0) cc_final: 0.7121 (t0)
REVERT: B   17 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6782 (t80)
REVERT: B   32 ARG cc_start: 0.8108 (mmp-170) cc_final: 0.7826 (mmp-170)
REVERT: B   70 GLU cc_start: 0.8423 (tp30) cc_final: 0.7984 (pm20)
REVERT: B  270 ASN cc_start: 0.7661 (t0) cc_final: 0.7194 (t0)
REVERT: B  339 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.8135 (t)
  outliers start: 23
  outliers final: 21
  residues processed: 76
  average time/residue: 0.0921
  time to fit residues: 10.1558
Evaluate side-chains
  82 residues out of total 764 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 59
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 THR
Chi-restraints excluded: chain A residue   33 ILE
Chi-restraints excluded: chain A residue   82 TYR
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain A residue  291 SER
Chi-restraints excluded: chain A residue  353 MET
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain B residue   17 TYR
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   50 LYS
Chi-restraints excluded: chain B residue   72 ILE
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  145 HIS
Chi-restraints excluded: chain B residue  173 VAL
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  320 MET
Chi-restraints excluded: chain B residue  339 SER
Chi-restraints excluded: chain B residue  340 THR
Chi-restraints excluded: chain B residue  349 LEU
Chi-restraints excluded: chain B residue  399 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 70 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0970
   chunk 44 optimal weight:   10.0000
   chunk 76 optimal weight:    2.9990
   chunk 90 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0370
   chunk 14 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.2260

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
B  23 HIS
B 142 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.129021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.093138 restraints weight = 16099.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.095973 restraints weight = 8759.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.097890 restraints weight = 5721.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.099196 restraints weight = 4244.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.100116 restraints weight = 3449.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3493
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3493 r_free = 0.3493    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3493
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.252   9456  Z= 0.280
  Angle     :  1.067  59.174  13215  Z= 0.679
  Chirality :  0.051   1.098   1450
  Planarity :  0.006   0.111   1348
  Dihedral  : 21.787 145.963   2050
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.41 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.93 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.19 (0.29), residues: 852
  helix:  1.21 (0.27), residues: 372
  sheet: -0.09 (0.50), residues: 112
  loop : -0.89 (0.34), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 245 
 TYR   0.016   0.001   TYR B  68 
 PHE   0.013   0.002   PHE A 352 
 TRP   0.004   0.001   TRP A 264 
 HIS   0.019   0.002   HIS B  23 

Details of bonding type rmsd
  covalent geometry    : bond        0.00556 ( 9456)
  covalent geometry    : angle       1.06671 (13215)
  hydrogen bonds       : bond        0.03906 (  324)
  hydrogen bonds       : angle       3.69493 (  910)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2165.07 seconds
wall clock time: 37 minutes 53.62 seconds (2273.62 seconds total)