Starting phenix.real_space_refine
on Tue Mar  3 13:11:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kue_23036/03_2026/7kue_23036.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kue_23036/03_2026/7kue_23036.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kue_23036/03_2026/7kue_23036.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kue_23036/03_2026/7kue_23036.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kue_23036/03_2026/7kue_23036.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kue_23036/03_2026/7kue_23036.map"
  }
  resolution = 3.5
  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=   0.002 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 96 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P       3      5.49       5
     S      24      5.16       5
     C    3049      2.51       5
     N     780      2.21       5
     O     866      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4726
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 499
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 499
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 3, 'TRANS': 58}
    Chain: "A"
      Number of atoms: 2342
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2342
          Classifications: {'peptide': 290}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 269}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 1854
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 225, 1854
          Classifications: {'peptide': 225}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 218}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 31
          Unusual residues: {'ADP': 1, 'AF3': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.31, per 1000 atoms: 0.28
  Number of scatterers: 4726
  At special positions: 0
  Unit cell: (76.36, 83.83, 89.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      24     16.00
     P       3     15.00
     Al      1     13.00
     F       3      9.00
     O     866      8.00
     N     780      7.00
     C    3049      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: 0.41
  Conformation dependent library (CDL) restraints added in 291.6 milliseconds
  

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1114

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 2 sheets defined
      49.9% alpha, 1.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'C' and resid 284 through 287
      removed outlier: 3.523A  pdb=" N   HIS C 287 " --> pdb=" O   ASP C 284 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 284 through 287'
    Processing helix  chain 'C' and resid 288 through 293
      removed outlier: 4.093A  pdb=" N   ILE C 292 " --> pdb=" O   ARG C 288 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA C 293 " --> pdb=" O   LYS C 289 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 288 through 293'
    Processing helix  chain 'C' and resid 297 through 309
      removed outlier: 3.787A  pdb=" N   ALA C 301 " --> pdb=" O   ASN C 297 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   THR C 307 " --> pdb=" O   GLU C 303 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLU C 308 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 56
      removed outlier: 3.988A  pdb=" N   ILE A  52 " --> pdb=" O   ASP A  48 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   GLU A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 95
      removed outlier: 3.775A  pdb=" N   VAL A  92 " --> pdb=" O   THR A  88 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   LYS A  95 " --> pdb=" O   GLU A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 123
      removed outlier: 3.547A  pdb=" N   ALA A 108 " --> pdb=" O   ALA A 104 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   TRP A 109 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   MET A 110 " --> pdb=" O   ILE A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 171
      removed outlier: 3.771A  pdb=" N   ARG A 171 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 178
    Processing helix  chain 'A' and resid 185 through 201
      removed outlier: 3.916A  pdb=" N   TRP A 189 " --> pdb=" O   ALA A 185 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   SER A 190 " --> pdb=" O   ILE A 186 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   VAL A 191 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 221
      removed outlier: 4.105A  pdb=" N   GLU A 215 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 252
      removed outlier: 3.507A  pdb=" N   GLU A 251 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU A 252 " --> pdb=" O   ARG A 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 248 through 252'
    Processing helix  chain 'A' and resid 262 through 271
      removed outlier: 3.731A  pdb=" N   PHE A 266 " --> pdb=" O   TYR A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 284
    Processing helix  chain 'B' and resid 52 through 57
      removed outlier: 3.772A  pdb=" N   MET B  57 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 73
    Processing helix  chain 'B' and resid 111 through 131
      removed outlier: 4.147A  pdb=" N   ASP B 115 " --> pdb=" O   GLU B 111 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU B 131 " --> pdb=" O   ILE B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 152
      removed outlier: 4.109A  pdb=" N   GLU B 151 " --> pdb=" O   ARG B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 174
      removed outlier: 3.972A  pdb=" N   ILE B 162 " --> pdb=" O   ASP B 158 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   VAL B 163 " --> pdb=" O   PRO B 159 " (cutoff:3.500A)
      removed outlier: 5.318A  pdb=" N   HIS B 164 " --> pdb=" O   LYS B 160 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   ILE B 167 " --> pdb=" O   VAL B 163 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE B 168 " --> pdb=" O   HIS B 164 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 186
    Processing helix  chain 'B' and resid 198 through 206
    Processing helix  chain 'B' and resid 214 through 222
    Processing helix  chain 'B' and resid 223 through 229
      removed outlier: 3.594A  pdb=" N   VAL B 228 " --> pdb=" O   ASP B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 240
    Processing helix  chain 'B' and resid 244 through 255
    Processing helix  chain 'B' and resid 262 through 271
    Processing helix  chain 'B' and resid 272 through 275
      removed outlier: 3.619A  pdb=" N   ASP B 275 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 272 through 275'
    Processing helix  chain 'B' and resid 278 through 287
      removed outlier: 3.932A  pdb=" N   THR B 285 " --> pdb=" O   ARG B 281 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   PHE B 287 " --> pdb=" O   LEU B 283 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 328 through 344
      removed outlier: 4.070A  pdb=" N   LEU B 332 " --> pdb=" O   ASP B 328 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21
      removed outlier: 3.883A  pdb=" N   VAL A  20 " --> pdb=" O   GLU A  37 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLU A  37 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU A  79 " --> pdb=" O   ILE A  38 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 136

    148 hydrogen bonds defined for protein.
    432 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.59

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 764
        1.31 -     1.44: 1302
        1.44 -     1.56: 2719
        1.56 -     1.69: 10
        1.69 -     1.81: 43
  Bond restraints: 4838
  Sorted by residual:
  bond pdb=" C1' ADP A 401 "
       pdb=" C2' ADP A 401 "
    ideal  model  delta    sigma   weight residual
    1.524  1.302  0.222 2.00e-02 2.50e+03 1.24e+02
  bond pdb=" C1' ADP A 401 "
       pdb=" O4' ADP A 401 "
    ideal  model  delta    sigma   weight residual
    1.426  1.628 -0.202 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C4  ADP A 401 "
       pdb=" C5  ADP A 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.342  0.148 2.00e-02 2.50e+03 5.50e+01
  bond pdb=" N   ASN B 175 "
       pdb=" CA  ASN B 175 "
    ideal  model  delta    sigma   weight residual
    1.462  1.373  0.089 1.46e-02 4.69e+03 3.70e+01
  bond pdb=" C5  ADP A 401 "
       pdb=" C6  ADP A 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.370  0.120 2.00e-02 2.50e+03 3.61e+01
  ... (remaining 4833 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.04: 6504
        7.04 -    14.07: 39
       14.07 -    21.11: 4
       21.11 -    28.15: 3
       28.15 -    35.18: 3
  Bond angle restraints: 6553
  Sorted by residual:
  angle pdb=" N   ASP A 228 "
        pdb=" CA  ASP A 228 "
        pdb=" C   ASP A 228 "
      ideal   model   delta    sigma   weight residual
     112.04  143.10  -31.06 1.44e+00 4.82e-01 4.65e+02
  angle pdb=" N   PHE B 177 "
        pdb=" CA  PHE B 177 "
        pdb=" C   PHE B 177 "
      ideal   model   delta    sigma   weight residual
     111.92  128.85  -16.93 1.34e+00 5.57e-01 1.60e+02
  angle pdb=" C   ASP A 228 "
        pdb=" CA  ASP A 228 "
        pdb=" CB  ASP A 228 "
      ideal   model   delta    sigma   weight residual
     110.56   88.28   22.28 1.83e+00 2.99e-01 1.48e+02
  angle pdb=" O2P TPO A 162 "
        pdb=" P   TPO A 162 "
        pdb=" O3P TPO A 162 "
      ideal   model   delta    sigma   weight residual
     113.68   78.50   35.18 3.00e+00 1.11e-01 1.38e+02
  angle pdb=" O1P TPO A 162 "
        pdb=" P   TPO A 162 "
        pdb=" O3P TPO A 162 "
      ideal   model   delta    sigma   weight residual
     115.11   80.11   35.00 3.00e+00 1.11e-01 1.36e+02
  ... (remaining 6548 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.62: 2830
       32.62 -    65.24: 77
       65.24 -    97.86: 4
       97.86 -   130.47: 0
      130.47 -   163.09: 1
  Dihedral angle restraints: 2912
    sinusoidal: 1200
      harmonic: 1712
  Sorted by residual:
  dihedral pdb=" N   PHE B 177 "
           pdb=" C   PHE B 177 "
           pdb=" CA  PHE B 177 "
           pdb=" CB  PHE B 177 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  167.36  -44.56     0      2.50e+00 1.60e-01 3.18e+02
  dihedral pdb=" C   PHE B 177 "
           pdb=" N   PHE B 177 "
           pdb=" CA  PHE B 177 "
           pdb=" CB  PHE B 177 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -166.19   43.59     0      2.50e+00 1.60e-01 3.04e+02
  dihedral pdb=" C5' ADP A 401 "
           pdb=" O5' ADP A 401 "
           pdb=" PA  ADP A 401 "
           pdb=" O2A ADP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  136.91  163.09     1      2.00e+01 2.50e-03 4.70e+01
  ... (remaining 2909 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.402: 724
       0.402 -    0.805: 4
       0.805 -    1.207: 0
       1.207 -    1.609: 0
       1.609 -    2.012: 1
  Chirality restraints: 729
  Sorted by residual:
  chirality pdb=" CA  PHE B 177 "
            pdb=" N   PHE B 177 "
            pdb=" C   PHE B 177 "
            pdb=" CB  PHE B 177 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    0.50    2.01 2.00e-01 2.50e+01 1.01e+02
  chirality pdb=" CA  ASP A 228 "
            pdb=" N   ASP A 228 "
            pdb=" C   ASP A 228 "
            pdb=" CB  ASP A 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.72    0.79 2.00e-01 2.50e+01 1.54e+01
  chirality pdb=" CB  ILE A  72 "
            pdb=" CA  ILE A  72 "
            pdb=" CG1 ILE A  72 "
            pdb=" CG2 ILE A  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.13    0.52 2.00e-01 2.50e+01 6.67e+00
  ... (remaining 726 not shown)

  Planarity restraints: 821
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  58 "   -0.039 2.00e-02 2.50e+03   4.07e-02 4.15e+01
        pdb=" CG  TRP B  58 "    0.105 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  58 "   -0.061 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  58 "    0.007 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  58 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  58 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  58 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  58 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  58 "   -0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  58 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 223 "   -0.019 2.00e-02 2.50e+03   4.00e-02 1.60e+01
        pdb=" C   THR A 223 "    0.069 2.00e-02 2.50e+03
        pdb=" O   THR A 223 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   PRO A 224 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 102 "    0.063 5.00e-02 4.00e+02   9.52e-02 1.45e+01
        pdb=" N   PRO A 103 "   -0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO A 103 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO A 103 "    0.053 5.00e-02 4.00e+02
  ... (remaining 818 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 417
        2.74 -     3.28: 4349
        3.28 -     3.82: 7737
        3.82 -     4.36: 8930
        4.36 -     4.90: 15068
  Nonbonded interactions: 36501
  Sorted by model distance:
  nonbonded pdb=" CG  PRO A 224 "
            pdb=" SD  MET A 273 "
     model   vdw
     2.205 3.800
  nonbonded pdb=" O   SER A 287 "
            pdb=" OG  SER A 287 "
     model   vdw
     2.328 3.040
  nonbonded pdb=" OG1 THR A  88 "
            pdb=" O   LEU A 135 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OG  SER B 153 "
            pdb=" OE1 GLN B 156 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" OD2 ASP B 224 "
            pdb=" OH  TYR B 282 "
     model   vdw
     2.358 3.040
  ... (remaining 36496 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.77 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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.220
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
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      :  0.010   0.222   4838  Z= 0.497
  Angle     :  1.620  35.182   6553  Z= 0.815
  Chirality :  0.110   2.012    729
  Planarity :  0.010   0.095    821
  Dihedral  : 15.459 163.093   1798
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  1.36 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.54 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -4.55 (0.28), residues: 560
  helix: -3.26 (0.22), residues: 258
  sheet: -3.17 (0.78), residues: 35
  loop : -2.66 (0.33), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  50 
 TYR   0.055   0.003   TYR A  57 
 PHE   0.027   0.003   PHE B 177 
 TRP   0.105   0.006   TRP B  58 
 HIS   0.008   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00973 ( 4838)
  covalent geometry    : angle       1.61951 ( 6553)
  hydrogen bonds       : bond        0.17122 (  148)
  hydrogen bonds       : angle       7.16704 (  432)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 141
  time to evaluate  : 0.194 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 ILE cc_start: 0.8250 (mm) cc_final: 0.8025 (mm)
REVERT: A   49 MET cc_start: 0.7567 (tpt) cc_final: 0.7328 (tpt)
REVERT: A   62 GLN cc_start: 0.6934 (mp10) cc_final: 0.6594 (mp10)
REVERT: A   91 GLU cc_start: 0.7155 (pp20) cc_final: 0.6933 (pp20)
REVERT: A  131 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6998 (mtmt)
REVERT: A  154 ILE cc_start: 0.7867 (mt) cc_final: 0.7608 (mt)
REVERT: A  184 SER cc_start: 0.8464 (t) cc_final: 0.8216 (t)
REVERT: A  272 THR cc_start: 0.8194 (p) cc_final: 0.7828 (p)
REVERT: B   50 ARG cc_start: 0.7770 (mtt90) cc_final: 0.7515 (mpp-170)
REVERT: B  186 LYS cc_start: 0.7224 (ttmm) cc_final: 0.6990 (ttmm)
REVERT: B  246 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7946 (ttmm)
REVERT: B  270 THR cc_start: 0.7898 (p) cc_final: 0.7684 (p)
  outliers start: 4
  outliers final: 3
  residues processed: 145
  average time/residue: 0.0814
  time to fit residues: 14.4813
Evaluate side-chains
  137 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 134
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 TRP
Chi-restraints excluded: chain B residue  178 ILE
Chi-restraints excluded: chain B residue  179 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 213 GLN
B 132 ASN
B 152 ASN
B 164 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.151092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.134878 restraints weight = 7762.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.139159 restraints weight = 3854.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.141927 restraints weight = 2289.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.143783 restraints weight = 1543.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.145075 restraints weight = 1128.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3879
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3879 r_free = 0.3879    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3879
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6862
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4838  Z= 0.167
  Angle     :  0.738   9.050   6553  Z= 0.377
  Chirality :  0.049   0.228    729
  Planarity :  0.008   0.075    821
  Dihedral  :  9.760 163.088    643
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.66 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -3.33 (0.32), residues: 560
  helix: -1.83 (0.28), residues: 266
  sheet: -2.99 (0.81), residues: 34
  loop : -2.45 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 147 
 TYR   0.020   0.002   TYR B 237 
 PHE   0.017   0.002   PHE B 177 
 TRP   0.056   0.003   TRP B  58 
 HIS   0.005   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 ( 4838)
  covalent geometry    : angle       0.73789 ( 6553)
  hydrogen bonds       : bond        0.04269 (  148)
  hydrogen bonds       : angle       4.99179 (  432)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 141
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 MET cc_start: 0.7586 (tpt) cc_final: 0.7313 (tpt)
REVERT: A   57 TYR cc_start: 0.7765 (m-80) cc_final: 0.7216 (m-80)
REVERT: A   62 GLN cc_start: 0.7232 (mp10) cc_final: 0.6936 (mp10)
REVERT: A   91 GLU cc_start: 0.7297 (pp20) cc_final: 0.6964 (pp20)
REVERT: A  154 ILE cc_start: 0.8316 (mt) cc_final: 0.8094 (mt)
REVERT: A  233 SER cc_start: 0.7678 (p) cc_final: 0.7213 (m)
REVERT: A  236 MET cc_start: 0.5757 (tmm) cc_final: 0.5225 (tmm)
REVERT: A  272 THR cc_start: 0.8385 (p) cc_final: 0.8050 (p)
REVERT: B   50 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7463 (mpp-170)
REVERT: B  186 LYS cc_start: 0.7392 (ttmm) cc_final: 0.7152 (ttmm)
REVERT: B  246 LYS cc_start: 0.8298 (ttmm) cc_final: 0.7980 (ttmm)
  outliers start: 9
  outliers final: 4
  residues processed: 144
  average time/residue: 0.0844
  time to fit residues: 15.0556
Evaluate side-chains
  138 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  229 TRP
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue  333 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 37 optimal weight:    0.0970
   chunk 40 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0870
   chunk 32 optimal weight:    0.2980
   chunk 42 optimal weight:    0.2980
   chunk 56 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.2756

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

Flipped N/Q/H residues before XYZ refinement:
B 164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.153016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.136578 restraints weight = 7712.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.140891 restraints weight = 3847.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.143709 restraints weight = 2299.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.145477 restraints weight = 1547.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.146771 restraints weight = 1145.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3901
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3901 r_free = 0.3901    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3899 r_free = 0.3899    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3899
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6836
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4838  Z= 0.117
  Angle     :  0.656   7.258   6553  Z= 0.333
  Chirality :  0.047   0.225    729
  Planarity :  0.007   0.072    821
  Dihedral  :  8.916 151.751    640
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.09 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -2.83 (0.33), residues: 560
  helix: -1.33 (0.30), residues: 274
  sheet: -2.83 (1.00), residues: 24
  loop : -2.36 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 152 
 TYR   0.013   0.001   TYR B  60 
 PHE   0.028   0.001   PHE B 145 
 TRP   0.044   0.002   TRP B  58 
 HIS   0.007   0.001   HIS A 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 4838)
  covalent geometry    : angle       0.65591 ( 6553)
  hydrogen bonds       : bond        0.03838 (  148)
  hydrogen bonds       : angle       4.67659 (  432)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 139
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8025 (pptt) cc_final: 0.7595 (pptt)
REVERT: A   38 ILE cc_start: 0.8075 (mm) cc_final: 0.7864 (mm)
REVERT: A   49 MET cc_start: 0.7523 (tpt) cc_final: 0.7238 (tpt)
REVERT: A   57 TYR cc_start: 0.7769 (m-80) cc_final: 0.7225 (m-80)
REVERT: A   91 GLU cc_start: 0.7284 (pp20) cc_final: 0.6977 (pp20)
REVERT: A  154 ILE cc_start: 0.8300 (mt) cc_final: 0.8058 (mt)
REVERT: A  236 MET cc_start: 0.5731 (tmm) cc_final: 0.5205 (tmm)
REVERT: A  272 THR cc_start: 0.8491 (p) cc_final: 0.8060 (p)
REVERT: B   50 ARG cc_start: 0.7928 (mtt90) cc_final: 0.7488 (mpp-170)
REVERT: B  186 LYS cc_start: 0.7402 (ttmm) cc_final: 0.7135 (ttmm)
REVERT: B  246 LYS cc_start: 0.8284 (ttmm) cc_final: 0.7988 (ttmm)
  outliers start: 10
  outliers final: 6
  residues processed: 143
  average time/residue: 0.0811
  time to fit residues: 14.1975
Evaluate side-chains
  141 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 135
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  229 TRP
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  333 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 164 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.141390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.125995 restraints weight = 7684.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.130032 restraints weight = 3805.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.132590 restraints weight = 2269.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.134341 restraints weight = 1529.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.135461 restraints weight = 1114.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3742 r_free = 0.3742    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3742 r_free = 0.3742    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.3348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   4838  Z= 0.332
  Angle     :  0.841   8.199   6553  Z= 0.441
  Chirality :  0.056   0.199    729
  Planarity :  0.008   0.083    821
  Dihedral  :  8.811 135.498    640
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 15.50 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -2.78 (0.33), residues: 560
  helix: -1.13 (0.30), residues: 272
  sheet: -3.83 (0.91), residues: 21
  loop : -2.43 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 147 
 TYR   0.017   0.002   TYR C 300 
 PHE   0.021   0.002   PHE A 266 
 TRP   0.012   0.003   TRP B  58 
 HIS   0.013   0.002   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00714 ( 4838)
  covalent geometry    : angle       0.84102 ( 6553)
  hydrogen bonds       : bond        0.04983 (  148)
  hydrogen bonds       : angle       4.95440 (  432)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  307 THR cc_start: 0.8655 (p) cc_final: 0.8388 (t)
REVERT: A    6 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6714 (tt0)
REVERT: A   12 LYS cc_start: 0.8165 (pptt) cc_final: 0.7769 (pptt)
REVERT: A   49 MET cc_start: 0.7397 (tpt) cc_final: 0.7132 (tpt)
REVERT: A  106 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7985 (tp)
REVERT: A  128 ARG cc_start: 0.8238 (mtm180) cc_final: 0.7598 (mtm180)
REVERT: A  233 SER cc_start: 0.8282 (p) cc_final: 0.7885 (m)
REVERT: A  236 MET cc_start: 0.5707 (tmm) cc_final: 0.5316 (tmm)
REVERT: B   50 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7497 (mpp-170)
REVERT: B  123 LYS cc_start: 0.7822 (mmmt) cc_final: 0.7270 (mmmt)
REVERT: B  223 LEU cc_start: 0.8345 (mt) cc_final: 0.8142 (mt)
REVERT: B  246 LYS cc_start: 0.8378 (ttmm) cc_final: 0.8020 (ttmm)
  outliers start: 26
  outliers final: 15
  residues processed: 166
  average time/residue: 0.0910
  time to fit residues: 18.3104
Evaluate side-chains
  167 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  176 LEU
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  187 ASP
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  229 TRP
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  327 ILE
Chi-restraints excluded: chain B residue  333 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.145650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.129785 restraints weight = 7773.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.133906 restraints weight = 3814.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.136594 restraints weight = 2252.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.138355 restraints weight = 1510.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.139251 restraints weight = 1105.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3792
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3792 r_free = 0.3792    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3792 r_free = 0.3792    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3792
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4838  Z= 0.154
  Angle     :  0.701   7.215   6553  Z= 0.355
  Chirality :  0.049   0.209    729
  Planarity :  0.007   0.081    821
  Dihedral  :  8.188 123.996    640
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 19.96 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -2.53 (0.34), residues: 560
  helix: -0.92 (0.30), residues: 273
  sheet: -3.68 (1.02), residues: 17
  loop : -2.35 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 168 
 TYR   0.015   0.002   TYR B  60 
 PHE   0.017   0.001   PHE A 266 
 TRP   0.015   0.002   TRP B  58 
 HIS   0.008   0.001   HIS A 127 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 4838)
  covalent geometry    : angle       0.70139 ( 6553)
  hydrogen bonds       : bond        0.04140 (  148)
  hydrogen bonds       : angle       4.66310 (  432)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6626 (tt0)
REVERT: A   12 LYS cc_start: 0.8141 (pptt) cc_final: 0.7720 (pptt)
REVERT: A   37 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6575 (mt-10)
REVERT: A   49 MET cc_start: 0.7403 (tpt) cc_final: 0.7146 (tpt)
REVERT: A   57 TYR cc_start: 0.7824 (m-80) cc_final: 0.7344 (m-80)
REVERT: A  148 PHE cc_start: 0.8375 (m-80) cc_final: 0.8030 (m-80)
REVERT: A  233 SER cc_start: 0.8287 (p) cc_final: 0.7806 (m)
REVERT: A  236 MET cc_start: 0.5706 (tmm) cc_final: 0.5182 (tmm)
REVERT: B   50 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7486 (mpp-170)
REVERT: B  246 LYS cc_start: 0.8382 (ttmm) cc_final: 0.8018 (ttmm)
  outliers start: 21
  outliers final: 14
  residues processed: 152
  average time/residue: 0.0883
  time to fit residues: 16.3738
Evaluate side-chains
  155 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  299 ASN
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  229 TRP
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 14 optimal weight:    0.0870
   chunk 39 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0060
   chunk 5 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
B 118 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.146790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.130795 restraints weight = 7883.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.134877 restraints weight = 3895.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.137487 restraints weight = 2324.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.139341 restraints weight = 1567.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.140336 restraints weight = 1144.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.3506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4838  Z= 0.138
  Angle     :  0.686   6.433   6553  Z= 0.347
  Chirality :  0.048   0.185    729
  Planarity :  0.006   0.080    821
  Dihedral  :  7.662 110.324    640
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 21.90 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -2.36 (0.35), residues: 560
  helix: -0.74 (0.31), residues: 274
  sheet: -3.61 (1.06), residues: 17
  loop : -2.33 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 168 
 TYR   0.029   0.002   TYR B 237 
 PHE   0.027   0.001   PHE A 266 
 TRP   0.017   0.002   TRP B  58 
 HIS   0.008   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4838)
  covalent geometry    : angle       0.68647 ( 6553)
  hydrogen bonds       : bond        0.03901 (  148)
  hydrogen bonds       : angle       4.55289 (  432)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8155 (pptt) cc_final: 0.7749 (pptt)
REVERT: A   37 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6811 (mt-10)
REVERT: A   49 MET cc_start: 0.7405 (tpt) cc_final: 0.7142 (tpt)
REVERT: A   57 TYR cc_start: 0.7777 (m-80) cc_final: 0.7268 (m-80)
REVERT: A   62 GLN cc_start: 0.7341 (mp10) cc_final: 0.7055 (mt0)
REVERT: A  148 PHE cc_start: 0.8339 (m-80) cc_final: 0.8050 (m-80)
REVERT: A  233 SER cc_start: 0.8280 (p) cc_final: 0.7787 (m)
REVERT: A  236 MET cc_start: 0.5693 (tmm) cc_final: 0.5186 (tmm)
REVERT: B   50 ARG cc_start: 0.8005 (mtt90) cc_final: 0.7508 (mpp-170)
REVERT: B   65 LEU cc_start: 0.8270 (tp) cc_final: 0.7979 (tt)
REVERT: B  114 LEU cc_start: 0.7935 (pp) cc_final: 0.7725 (mt)
REVERT: B  122 LYS cc_start: 0.7895 (tptt) cc_final: 0.7531 (tptt)
REVERT: B  216 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7702 (mttt)
REVERT: B  246 LYS cc_start: 0.8366 (ttmm) cc_final: 0.7988 (ttmm)
  outliers start: 24
  outliers final: 15
  residues processed: 146
  average time/residue: 0.0916
  time to fit residues: 16.3085
Evaluate side-chains
  155 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 139
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  299 ASN
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  229 TRP
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   58 TRP
Chi-restraints excluded: chain B residue   60 TYR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  130 HIS
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0970
   chunk 17 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.6778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.145695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.129797 restraints weight = 7724.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.133822 restraints weight = 3853.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.136349 restraints weight = 2312.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.138126 restraints weight = 1574.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.139051 restraints weight = 1162.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7001
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4838  Z= 0.151
  Angle     :  0.697   6.932   6553  Z= 0.352
  Chirality :  0.049   0.212    729
  Planarity :  0.006   0.079    821
  Dihedral  :  7.318  97.792    640
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.71 %
    Favored  : 74.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -2.22 (0.35), residues: 560
  helix: -0.56 (0.31), residues: 273
  sheet: -3.62 (1.08), residues: 17
  loop : -2.33 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 201 
 TYR   0.028   0.002   TYR B 237 
 PHE   0.043   0.001   PHE A 266 
 TRP   0.018   0.002   TRP B  58 
 HIS   0.008   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4838)
  covalent geometry    : angle       0.69737 ( 6553)
  hydrogen bonds       : bond        0.03937 (  148)
  hydrogen bonds       : angle       4.59950 (  432)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 145
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6616 (tt0)
REVERT: A   12 LYS cc_start: 0.8181 (pptt) cc_final: 0.7764 (pptt)
REVERT: A   49 MET cc_start: 0.7398 (tpt) cc_final: 0.7113 (tpt)
REVERT: A   57 TYR cc_start: 0.7767 (m-80) cc_final: 0.7325 (m-80)
REVERT: A   62 GLN cc_start: 0.7374 (mp10) cc_final: 0.7112 (mt0)
REVERT: A  128 ARG cc_start: 0.8152 (mtm180) cc_final: 0.7311 (mtm180)
REVERT: A  148 PHE cc_start: 0.8319 (m-80) cc_final: 0.8035 (m-80)
REVERT: A  170 TYR cc_start: 0.7837 (m-80) cc_final: 0.7492 (m-80)
REVERT: A  216 VAL cc_start: 0.8092 (p) cc_final: 0.7858 (p)
REVERT: A  233 SER cc_start: 0.8343 (p) cc_final: 0.7864 (m)
REVERT: A  236 MET cc_start: 0.5729 (tmm) cc_final: 0.5254 (tmm)
REVERT: B   50 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7519 (mpp-170)
REVERT: B  114 LEU cc_start: 0.7960 (pp) cc_final: 0.7751 (mt)
REVERT: B  122 LYS cc_start: 0.7935 (tptt) cc_final: 0.7575 (tptt)
REVERT: B  216 LYS cc_start: 0.8052 (mppt) cc_final: 0.7718 (mttt)
REVERT: B  246 LYS cc_start: 0.8355 (ttmm) cc_final: 0.7973 (ttmm)
  outliers start: 22
  outliers final: 17
  residues processed: 152
  average time/residue: 0.0931
  time to fit residues: 17.2096
Evaluate side-chains
  153 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 LEU
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  229 TRP
Chi-restraints excluded: chain A residue  266 PHE
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   58 TRP
Chi-restraints excluded: chain B residue   60 TYR
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  245 CYS
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0770
   chunk 42 optimal weight:    0.0470
   chunk 1 optimal weight:    0.0040
   chunk 51 optimal weight:    0.0980
   overall best weight:    0.1848

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.148959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.133087 restraints weight = 7880.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.137200 restraints weight = 3876.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.139875 restraints weight = 2298.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.141559 restraints weight = 1535.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.142827 restraints weight = 1140.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.3696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4838  Z= 0.122
  Angle     :  0.688   8.723   6553  Z= 0.342
  Chirality :  0.047   0.190    729
  Planarity :  0.006   0.078    821
  Dihedral  :  7.015  84.023    640
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 23.84 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -2.07 (0.35), residues: 560
  helix: -0.35 (0.32), residues: 266
  sheet: -3.64 (1.12), residues: 17
  loop : -2.30 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 168 
 TYR   0.021   0.001   TYR B 237 
 PHE   0.032   0.001   PHE A 266 
 TRP   0.018   0.001   TRP B  58 
 HIS   0.005   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 4838)
  covalent geometry    : angle       0.68821 ( 6553)
  hydrogen bonds       : bond        0.03637 (  148)
  hydrogen bonds       : angle       4.57242 (  432)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 136
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6489 (tt0)
REVERT: A   12 LYS cc_start: 0.8213 (pptt) cc_final: 0.7799 (pptt)
REVERT: A   49 MET cc_start: 0.7415 (tpt) cc_final: 0.7125 (tpt)
REVERT: A   57 TYR cc_start: 0.7662 (m-80) cc_final: 0.6992 (m-80)
REVERT: A  148 PHE cc_start: 0.8300 (m-80) cc_final: 0.8009 (m-80)
REVERT: A  150 LEU cc_start: 0.8221 (mp) cc_final: 0.8000 (mt)
REVERT: A  233 SER cc_start: 0.8286 (p) cc_final: 0.7821 (m)
REVERT: A  236 MET cc_start: 0.5741 (tmm) cc_final: 0.5255 (tmm)
REVERT: B   50 ARG cc_start: 0.7999 (mtt90) cc_final: 0.7511 (mpp-170)
REVERT: B  122 LYS cc_start: 0.7886 (tptt) cc_final: 0.7515 (tptt)
REVERT: B  216 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7709 (mttt)
REVERT: B  246 LYS cc_start: 0.8336 (ttmm) cc_final: 0.7948 (ttmm)
  outliers start: 21
  outliers final: 14
  residues processed: 143
  average time/residue: 0.0855
  time to fit residues: 15.0511
Evaluate side-chains
  148 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 133
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  229 TRP
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   58 TRP
Chi-restraints excluded: chain B residue   60 TYR
Chi-restraints excluded: chain B residue   66 GLN
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  216 LYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  245 CYS
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 37 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.147204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.131454 restraints weight = 7746.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.135526 restraints weight = 3811.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.138145 restraints weight = 2262.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.139970 restraints weight = 1527.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.141168 restraints weight = 1113.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.3866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4838  Z= 0.149
  Angle     :  0.701   8.331   6553  Z= 0.352
  Chirality :  0.049   0.200    729
  Planarity :  0.006   0.078    821
  Dihedral  :  6.912  74.091    640
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 25.39 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -2.04 (0.36), residues: 560
  helix: -0.35 (0.32), residues: 273
  sheet: -3.71 (1.11), residues: 17
  loop : -2.29 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 171 
 TYR   0.019   0.002   TYR B 237 
 PHE   0.045   0.001   PHE A 266 
 TRP   0.018   0.002   TRP B  58 
 HIS   0.008   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4838)
  covalent geometry    : angle       0.70143 ( 6553)
  hydrogen bonds       : bond        0.03862 (  148)
  hydrogen bonds       : angle       4.58980 (  432)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A    6 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6571 (tt0)
REVERT: A   12 LYS cc_start: 0.8267 (pptt) cc_final: 0.7856 (pptt)
REVERT: A   49 MET cc_start: 0.7381 (tpt) cc_final: 0.7083 (tpt)
REVERT: A   57 TYR cc_start: 0.7664 (m-80) cc_final: 0.7069 (m-80)
REVERT: A   62 GLN cc_start: 0.7365 (mp10) cc_final: 0.7069 (mt0)
REVERT: A   86 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6945 (mt)
REVERT: A  128 ARG cc_start: 0.8105 (mtm180) cc_final: 0.7534 (mtm180)
REVERT: A  148 PHE cc_start: 0.8313 (m-80) cc_final: 0.8027 (m-80)
REVERT: A  233 SER cc_start: 0.8350 (p) cc_final: 0.7901 (m)
REVERT: A  236 MET cc_start: 0.5755 (tmm) cc_final: 0.5270 (tmm)
REVERT: B   50 ARG cc_start: 0.7996 (mtt90) cc_final: 0.7488 (mpp-170)
REVERT: B  122 LYS cc_start: 0.7922 (tptt) cc_final: 0.7568 (tptt)
REVERT: B  216 LYS cc_start: 0.8061 (mppt) cc_final: 0.7720 (mttt)
REVERT: B  246 LYS cc_start: 0.8337 (ttmm) cc_final: 0.7947 (ttmm)
  outliers start: 20
  outliers final: 15
  residues processed: 141
  average time/residue: 0.0872
  time to fit residues: 15.0420
Evaluate side-chains
  153 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  299 ASN
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  229 TRP
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   58 TRP
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   66 GLN
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  245 CYS
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0970
   chunk 20 optimal weight:    0.0870
   chunk 30 optimal weight:    0.3980
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.4756

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.148303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.132233 restraints weight = 7777.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.136373 restraints weight = 3812.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.139072 restraints weight = 2265.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.140850 restraints weight = 1520.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.142118 restraints weight = 1119.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4838  Z= 0.134
  Angle     :  0.713   7.958   6553  Z= 0.357
  Chirality :  0.048   0.203    729
  Planarity :  0.006   0.077    821
  Dihedral  :  6.327  56.226    640
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 24.81 %
    Favored  : 71.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -2.04 (0.36), residues: 560
  helix: -0.31 (0.32), residues: 272
  sheet: -3.72 (1.12), residues: 17
  loop : -2.34 (0.38), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 168 
 TYR   0.020   0.001   TYR B 237 
 PHE   0.024   0.001   PHE A 266 
 TRP   0.017   0.002   TRP B  58 
 HIS   0.007   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4838)
  covalent geometry    : angle       0.71294 ( 6553)
  hydrogen bonds       : bond        0.03747 (  148)
  hydrogen bonds       : angle       4.78822 (  432)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 144
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 LYS cc_start: 0.8296 (pptt) cc_final: 0.7884 (pptt)
REVERT: A   49 MET cc_start: 0.7388 (tpt) cc_final: 0.7098 (tpt)
REVERT: A   62 GLN cc_start: 0.7302 (mp10) cc_final: 0.7001 (mt0)
REVERT: A   86 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6952 (mt)
REVERT: A  131 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7666 (mtmm)
REVERT: A  148 PHE cc_start: 0.8308 (m-80) cc_final: 0.8027 (m-80)
REVERT: A  233 SER cc_start: 0.8379 (p) cc_final: 0.7939 (m)
REVERT: A  236 MET cc_start: 0.5749 (OUTLIER) cc_final: 0.5261 (tmm)
REVERT: B   50 ARG cc_start: 0.7994 (mtt90) cc_final: 0.7489 (mpp-170)
REVERT: B  122 LYS cc_start: 0.7910 (tptt) cc_final: 0.7562 (tptt)
REVERT: B  216 LYS cc_start: 0.8056 (mppt) cc_final: 0.7727 (mttt)
REVERT: B  246 LYS cc_start: 0.8325 (ttmm) cc_final: 0.7980 (ttmm)
  outliers start: 21
  outliers final: 16
  residues processed: 150
  average time/residue: 0.0843
  time to fit residues: 15.7449
Evaluate side-chains
  160 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 142
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  299 ASN
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  191 VAL
Chi-restraints excluded: chain A residue  198 LEU
Chi-restraints excluded: chain A residue  229 TRP
Chi-restraints excluded: chain A residue  236 MET
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain B residue   58 TRP
Chi-restraints excluded: chain B residue   59 SER
Chi-restraints excluded: chain B residue   60 TYR
Chi-restraints excluded: chain B residue   66 GLN
Chi-restraints excluded: chain B residue  174 GLU
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  254 LEU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  333 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0870
   chunk 2 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** A  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.146480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.130396 restraints weight = 7899.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.134578 restraints weight = 3884.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.137291 restraints weight = 2305.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.138930 restraints weight = 1547.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.140252 restraints weight = 1157.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.4072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   4838  Z= 0.154
  Angle     :  0.730   8.016   6553  Z= 0.368
  Chirality :  0.051   0.230    729
  Planarity :  0.006   0.077    821
  Dihedral  :  5.796  53.039    640
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 10.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 25.78 %
    Favored  : 70.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 are not related in a simple way.
  whole: -2.12 (0.36), residues: 560
  helix: -0.45 (0.32), residues: 273
  sheet: -3.74 (1.12), residues: 17
  loop : -2.29 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 248 
 TYR   0.020   0.002   TYR B 237 
 PHE   0.028   0.001   PHE A 266 
 TRP   0.018   0.002   TRP B  58 
 HIS   0.008   0.001   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 4838)
  covalent geometry    : angle       0.73002 ( 6553)
  hydrogen bonds       : bond        0.03872 (  148)
  hydrogen bonds       : angle       4.82789 (  432)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 987.49 seconds
wall clock time: 17 minutes 37.99 seconds (1057.99 seconds total)