Starting phenix.real_space_refine
on Tue Feb 11 11:52:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cti_26991/02_2025/8cti_26991.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cti_26991/02_2025/8cti_26991.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cti_26991/02_2025/8cti_26991.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cti_26991/02_2025/8cti_26991.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cti_26991/02_2025/8cti_26991.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cti_26991/02_2025/8cti_26991.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      70      5.49       5
     S      19      5.16       5
     C    3114      2.51       5
     N     916      2.21       5
     O    1178      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5297
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1658
          Classifications: {'peptide': 202}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 187}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 271, 2131
          Classifications: {'peptide': 271}
          Link IDs: {'PTRANS': 8, 'TRANS': 262}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 1508
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 1508
          Classifications: {'RNA': 71}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 31}
          Link IDs: {'rna2p': 11, 'rna3p': 59}
  Time building chain proxies: 4.15, per 1000 atoms: 0.78
  Number of scatterers: 5297
  At special positions: 0
  Unit cell: (69.3, 89.1, 118.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P      70     15.00
     O    1178      8.00
     N     916      7.00
     C    3114      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 561.1 milliseconds
  

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  890

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 8 sheets defined
      19.2% alpha, 32.3% beta
      23 base pairs and 35 stacking pairs defined.
    Time for finding SS restraints: 2.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 44
    Processing helix  chain 'A' and resid 45 through 49
      removed outlier: 3.927A  pdb=" N   GLU A  48 " --> pdb=" O   ASP A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 95
      removed outlier: 3.641A  pdb=" N   VAL A  92 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLU A  93 " --> pdb=" O   GLY A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 125
    Processing helix  chain 'A' and resid 144 through 149
    Processing helix  chain 'A' and resid 168 through 174
      removed outlier: 4.012A  pdb=" N   LYS A 172 " --> pdb=" O   THR A 169 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG A 174 " --> pdb=" O   HIS A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 187
    Processing helix  chain 'A' and resid 200 through 214
      removed outlier: 3.775A  pdb=" N   HIS A 210 " --> pdb=" O   TRP A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 229 through 234
      removed outlier: 3.742A  pdb=" N   LEU A 234 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 248
    Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 138
      removed outlier: 8.288A  pdb=" N   LEU A 137 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   GLY A 105 " --> pdb=" O   LEU A 137 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   LEU A 102 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   GLU A  79 " --> pdb=" O   LYS A 156 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   PHE A 158 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   ALA A  81 " --> pdb=" O   PHE A 158 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   LEU A 160 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   ILE A  83 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   THR A 155 " --> pdb=" O   LEU A 193 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   TYR A 195 " --> pdb=" O   THR A 155 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   MET A 157 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 8.013A  pdb=" N   ILE A 197 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   PHE A 159 " --> pdb=" O   ILE A 197 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   GLY A 192 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   ILE A 255 " --> pdb=" O   VAL A 220 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 18
    Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 69
      removed outlier: 4.233A  pdb=" N   ALA B  66 " --> pdb=" O   THR B  79 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ARG B  84 " --> pdb=" O   ASP B  80 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   SER B  97 " --> pdb=" O   LEU B  87 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   ARG B  89 " --> pdb=" O   CYS B  95 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   CYS B  95 " --> pdb=" O   ARG B  89 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110
      removed outlier: 3.587A  pdb=" N   ALA B 107 " --> pdb=" O   ALA B 120 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   ASP B 125 " --> pdb=" O   ASP B 121 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LEU B 142 " --> pdb=" O   VAL B 126 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   SER B 128 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   LEU B 140 " --> pdb=" O   SER B 128 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 153
      removed outlier: 6.890A  pdb=" N   ALA B 163 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   VAL B 151 " --> pdb=" O   LEU B 161 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LEU B 161 " --> pdb=" O   VAL B 151 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   SER B 172 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
      removed outlier: 6.205A  pdb=" N   ILE B 169 " --> pdb=" O   PHE B 183 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   PHE B 183 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   VAL B 171 " --> pdb=" O   GLU B 181 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 196
      removed outlier: 3.595A  pdb=" N   SER B 208 " --> pdb=" O   THR B 212 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   THR B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   GLU B 217 " --> pdb=" O   GLN B 223 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   GLN B 223 " --> pdb=" O   GLU B 217 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 252
      removed outlier: 3.682A  pdb=" N   ARG B 248 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU B 261 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   CYS B 262 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
      removed outlier: 5.176A  pdb=" N   VAL B 267 " --> pdb=" O   CYS B 262 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL B 268 " --> pdb=" O   GLN B 285 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   GLN B 285 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   ILE B 270 " --> pdb=" O   ARG B 283 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 292 through 297
      removed outlier: 3.701A  pdb=" N   ASP B 294 " --> pdb=" O   LEU B 306 " (cutoff:3.500A)

    123 hydrogen bonds defined for protein.
    324 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      59 hydrogen bonds
      106 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      35 stacking parallelities
  Total time for adding SS restraints: 1.54

  Time building geometry restraints manager: 1.48 seconds

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

  Histogram of bond lengths:
        0.78 -     1.00: 1
        1.00 -     1.22: 8
        1.22 -     1.44: 2670
        1.44 -     1.66: 2861
        1.66 -     1.87: 25
  Bond restraints: 5565
  Sorted by residual:
  bond pdb=" CG  PRO B 134 "
       pdb=" CD  PRO B 134 "
    ideal  model  delta    sigma   weight residual
    1.503  0.783  0.720 3.40e-02 8.65e+02 4.49e+02
  bond pdb=" CB  PRO B 134 "
       pdb=" CG  PRO B 134 "
    ideal  model  delta    sigma   weight residual
    1.492  1.874 -0.382 5.00e-02 4.00e+02 5.83e+01
  bond pdb=" N   PRO B 134 "
       pdb=" CD  PRO B 134 "
    ideal  model  delta    sigma   weight residual
    1.473  1.561 -0.088 1.40e-02 5.10e+03 3.93e+01
  bond pdb=" CA  PRO B 134 "
       pdb=" CB  PRO B 134 "
    ideal  model  delta    sigma   weight residual
    1.534  1.482  0.051 1.49e-02 4.50e+03 1.19e+01
  bond pdb=" CB  ASP A  45 "
       pdb=" CG  ASP A  45 "
    ideal  model  delta    sigma   weight residual
    1.516  1.553 -0.037 2.50e-02 1.60e+03 2.24e+00
  ... (remaining 5560 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.21: 7869
        6.21 -    12.43: 11
       12.43 -    18.64: 1
       18.64 -    24.86: 1
       24.86 -    31.07: 1
  Bond angle restraints: 7883
  Sorted by residual:
  angle pdb=" N   PRO B 134 "
        pdb=" CD  PRO B 134 "
        pdb=" CG  PRO B 134 "
      ideal   model   delta    sigma   weight residual
     103.20   72.13   31.07 1.50e+00 4.44e-01 4.29e+02
  angle pdb=" CA  PRO B 134 "
        pdb=" CB  PRO B 134 "
        pdb=" CG  PRO B 134 "
      ideal   model   delta    sigma   weight residual
     104.50   85.59   18.91 1.90e+00 2.77e-01 9.91e+01
  angle pdb=" N   PRO B 134 "
        pdb=" CA  PRO B 134 "
        pdb=" CB  PRO B 134 "
      ideal   model   delta    sigma   weight residual
     103.33   94.12    9.21 1.10e+00 8.26e-01 7.01e+01
  angle pdb=" CA  PRO B 134 "
        pdb=" N   PRO B 134 "
        pdb=" CD  PRO B 134 "
      ideal   model   delta    sigma   weight residual
     112.00  105.45    6.55 1.40e+00 5.10e-01 2.19e+01
  angle pdb=" CB  PRO B 134 "
        pdb=" CG  PRO B 134 "
        pdb=" CD  PRO B 134 "
      ideal   model   delta    sigma   weight residual
     106.10   91.98   14.12 3.20e+00 9.77e-02 1.95e+01
  ... (remaining 7878 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.15: 2942
       22.15 -    44.30: 295
       44.30 -    66.45: 147
       66.45 -    88.60: 23
       88.60 -   110.75: 1
  Dihedral angle restraints: 3408
    sinusoidal: 2037
      harmonic: 1371
  Sorted by residual:
  dihedral pdb=" O4'   U C  19 "
           pdb=" C1'   U C  19 "
           pdb=" N1    U C  19 "
           pdb=" C2    U C  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   89.25  110.75     1      1.50e+01 4.44e-03 5.78e+01
  dihedral pdb=" O4'   C C  16 "
           pdb=" C1'   C C  16 "
           pdb=" N1    C C  16 "
           pdb=" C2    C C  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -55.71  -72.29     1      1.70e+01 3.46e-03 2.31e+01
  dihedral pdb=" O4'   A C   7 "
           pdb=" C1'   A C   7 "
           pdb=" N9    A C   7 "
           pdb=" C4    A C   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -170.80   64.80     1      1.70e+01 3.46e-03 1.91e+01
  ... (remaining 3405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 750
       0.043 -    0.085: 123
       0.085 -    0.128: 59
       0.128 -    0.170: 6
       0.170 -    0.213: 1
  Chirality restraints: 939
  Sorted by residual:
  chirality pdb=" CA  ASP A  45 "
            pdb=" N   ASP A  45 "
            pdb=" C   ASP A  45 "
            pdb=" CB  ASP A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.13e+00
  chirality pdb=" CA  GLN A 117 "
            pdb=" N   GLN A 117 "
            pdb=" C   GLN A 117 "
            pdb=" CB  GLN A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.01e-01
  chirality pdb=" CG  LEU B 149 "
            pdb=" CB  LEU B 149 "
            pdb=" CD1 LEU B 149 "
            pdb=" CD2 LEU B 149 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.44e-01
  ... (remaining 936 not shown)

  Planarity restraints: 740
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 133 "    0.053 5.00e-02 4.00e+02   7.51e-02 9.03e+00
        pdb=" N   PRO B 134 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B 134 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO B 134 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 118 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.89e+00
        pdb=" CG  ASP A 118 "   -0.042 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 118 "    0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 118 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 133 "   -0.010 2.00e-02 2.50e+03   2.01e-02 4.06e+00
        pdb=" C   GLU B 133 "    0.035 2.00e-02 2.50e+03
        pdb=" O   GLU B 133 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   PRO B 134 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 737 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 300
        2.71 -     3.26: 4875
        3.26 -     3.81: 9539
        3.81 -     4.35: 11728
        4.35 -     4.90: 17905
  Nonbonded interactions: 44347
  Sorted by model distance:
  nonbonded pdb=" O2'   G C  17 "
            pdb=" N2    G C  57 "
     model   vdw
     2.164 3.120
  nonbonded pdb=" O   GLY A  89 "
            pdb=" OG  SER A 237 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   LYS A 143 "
            pdb=" NZ  LYS B 168 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" NH1 ARG A 258 "
            pdb=" O   ILE A 259 "
     model   vdw
     2.274 3.120
  nonbonded pdb=" O   ASP A  45 "
            pdb=" OD1 ASP A  45 "
     model   vdw
     2.286 3.040
  ... (remaining 44342 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     17.530
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6117
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      :  0.011   0.720   5565  Z= 0.828
  Angle     :  0.792  31.069   7883  Z= 0.439
  Chirality :  0.040   0.213    939
  Planarity :  0.005   0.075    740
  Dihedral  : 20.285 110.750   2518
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 22.87 %
    Favored  : 76.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.38), residues: 459
  helix: -1.33 (0.55), residues: 69
  sheet: -0.36 (0.42), residues: 162
  loop : -1.28 (0.38), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 206 
 HIS   0.005   0.001   HIS B 187 
 PHE   0.016   0.002   PHE A 256 
 TYR   0.019   0.001   TYR B  38 
 ARG   0.002   0.000   ARG B  17 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 45
  time to evaluate  : 0.448 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 47
  average time/residue: 0.1323
  time to fit residues: 9.0892
Evaluate side-chains
  38 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  126 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    8.9990
   chunk 40 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    9.9990
   chunk 16 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.4726 r_free = 0.4726 target = 0.206703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.152160 restraints weight = 7649.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.152787 restraints weight = 5300.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.153929 restraints weight = 4279.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6453
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5565  Z= 0.252
  Angle     :  0.625   8.258   7883  Z= 0.319
  Chirality :  0.041   0.153    939
  Planarity :  0.004   0.037    740
  Dihedral  : 20.096 106.417   1631
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.19 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.96 (0.40), residues: 459
  helix: -0.29 (0.58), residues: 70
  sheet: -0.25 (0.40), residues: 179
  loop : -1.01 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 252 
 HIS   0.006   0.001   HIS B 187 
 PHE   0.018   0.002   PHE A 256 
 TYR   0.014   0.002   TYR B 218 
 ARG   0.003   0.000   ARG B 214 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A   79 GLU cc_start: 0.7854 (mp0) cc_final: 0.7499 (mp0)
REVERT: B   70 SER cc_start: 0.4956 (p) cc_final: 0.4706 (t)
REVERT: B  133 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7692 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 55
  average time/residue: 0.1242
  time to fit residues: 10.0088
Evaluate side-chains
  52 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  155 THR
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 21 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN
** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.204600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.156738 restraints weight = 7412.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.157123 restraints weight = 7761.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.158514 restraints weight = 7336.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.4192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6322
moved from start:          0.2477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5565  Z= 0.236
  Angle     :  0.575   8.680   7883  Z= 0.290
  Chirality :  0.039   0.147    939
  Planarity :  0.004   0.035    740
  Dihedral  : 19.798 100.876   1631
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 19.71 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.38), residues: 459
  helix: -0.04 (0.57), residues: 70
  sheet: -0.05 (0.41), residues: 166
  loop : -1.30 (0.40), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 206 
 HIS   0.005   0.001   HIS A 204 
 PHE   0.024   0.002   PHE B  36 
 TYR   0.010   0.001   TYR B 218 
 ARG   0.003   0.000   ARG B  17 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.460 
Fit side-chains
REVERT: A   79 GLU cc_start: 0.7984 (mp0) cc_final: 0.7699 (mp0)
REVERT: A  143 LYS cc_start: 0.7760 (ptpt) cc_final: 0.7512 (pttp)
REVERT: A  211 PHE cc_start: 0.5443 (OUTLIER) cc_final: 0.4272 (t80)
REVERT: B  133 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7582 (tm-30)
REVERT: B  187 HIS cc_start: 0.6272 (OUTLIER) cc_final: 0.5963 (m170)
  outliers start: 17
  outliers final: 8
  residues processed: 71
  average time/residue: 0.1493
  time to fit residues: 14.3090
Evaluate side-chains
  61 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  187 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 50 optimal weight:   20.0000
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0040
   chunk 39 optimal weight:    0.0270
   chunk 2 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 12 optimal weight:    0.0870
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.8232

-------------------------------------------------------------------------------
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 = 0.4704 r_free = 0.4704 target = 0.204011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.155935 restraints weight = 7606.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.156776 restraints weight = 8003.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.158434 restraints weight = 6752.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.4191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5565  Z= 0.212
  Angle     :  0.555   8.947   7883  Z= 0.279
  Chirality :  0.038   0.147    939
  Planarity :  0.004   0.039    740
  Dihedral  : 19.693  96.301   1631
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 22.38 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.39), residues: 459
  helix:  0.34 (0.58), residues: 70
  sheet: -0.06 (0.41), residues: 168
  loop : -1.17 (0.41), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 206 
 HIS   0.006   0.001   HIS B 187 
 PHE   0.017   0.002   PHE A 217 
 TYR   0.010   0.001   TYR B 218 
 ARG   0.003   0.000   ARG B 214 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.496 
Fit side-chains
REVERT: A   79 GLU cc_start: 0.7867 (mp0) cc_final: 0.7605 (mp0)
REVERT: A  137 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5959 (mt)
REVERT: A  211 PHE cc_start: 0.5343 (OUTLIER) cc_final: 0.4163 (t80)
REVERT: B  133 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7740 (tm-30)
REVERT: B  187 HIS cc_start: 0.6216 (OUTLIER) cc_final: 0.5906 (m170)
  outliers start: 20
  outliers final: 12
  residues processed: 68
  average time/residue: 0.1279
  time to fit residues: 12.3183
Evaluate side-chains
  65 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  187 HIS
Chi-restraints excluded: chain B residue  260 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 50 optimal weight:   20.0000
   chunk 37 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.202201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.150796 restraints weight = 7555.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.155850 restraints weight = 8707.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.156923 restraints weight = 5696.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.4157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6430
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5565  Z= 0.262
  Angle     :  0.596   9.166   7883  Z= 0.304
  Chirality :  0.040   0.150    939
  Planarity :  0.004   0.039    740
  Dihedral  : 19.692  90.522   1631
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  6.08 %
    Allowed  : 21.17 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.39), residues: 459
  helix:  0.54 (0.59), residues: 66
  sheet: -0.29 (0.41), residues: 173
  loop : -1.19 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 206 
 HIS   0.006   0.001   HIS B 187 
 PHE   0.017   0.002   PHE A 211 
 TYR   0.009   0.002   TYR B 218 
 ARG   0.003   0.000   ARG B  17 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 50
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A   79 GLU cc_start: 0.7831 (mp0) cc_final: 0.7593 (mp0)
REVERT: A  117 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8348 (pm20)
REVERT: A  137 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.5985 (mt)
REVERT: A  143 LYS cc_start: 0.7463 (ptpp) cc_final: 0.7202 (pttp)
REVERT: A  211 PHE cc_start: 0.5551 (OUTLIER) cc_final: 0.4152 (t80)
REVERT: B  133 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7792 (tm-30)
  outliers start: 25
  outliers final: 16
  residues processed: 70
  average time/residue: 0.1493
  time to fit residues: 14.3532
Evaluate side-chains
  66 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 47
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  117 GLN
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  173 TRP
Chi-restraints excluded: chain A residue  194 VAL
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  261 ASP
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  156 ASP
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  260 LEU
Chi-restraints excluded: chain B residue  297 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0770
   chunk 52 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 8 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.6942

-------------------------------------------------------------------------------
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 = 0.4712 r_free = 0.4712 target = 0.205323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.155484 restraints weight = 7540.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.159520 restraints weight = 7453.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.160943 restraints weight = 5111.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.4212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6338
moved from start:          0.4155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5565  Z= 0.185
  Angle     :  0.544   9.354   7883  Z= 0.277
  Chirality :  0.038   0.162    939
  Planarity :  0.004   0.036    740
  Dihedral  : 19.585  86.197   1631
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 23.84 %
    Favored  : 72.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.39), residues: 459
  helix:  0.82 (0.59), residues: 66
  sheet: -0.28 (0.40), residues: 182
  loop : -1.01 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 206 
 HIS   0.007   0.001   HIS B 187 
 PHE   0.015   0.002   PHE A 211 
 TYR   0.024   0.001   TYR A 115 
 ARG   0.002   0.000   ARG B 214 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.484 
Fit side-chains
REVERT: A   44 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.4948 (tpt)
REVERT: A   79 GLU cc_start: 0.7684 (mp0) cc_final: 0.7429 (mp0)
REVERT: A  211 PHE cc_start: 0.5467 (OUTLIER) cc_final: 0.4030 (t80)
REVERT: B  133 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7542 (tm-30)
  outliers start: 17
  outliers final: 12
  residues processed: 64
  average time/residue: 0.1492
  time to fit residues: 13.1784
Evaluate side-chains
  63 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   69 PHE
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  260 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    9.9990
   chunk 52 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 7 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.4691 r_free = 0.4691 target = 0.203072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.152838 restraints weight = 7491.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.155966 restraints weight = 7331.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.156979 restraints weight = 6143.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6408
moved from start:          0.4622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5565  Z= 0.212
  Angle     :  0.560   9.436   7883  Z= 0.282
  Chirality :  0.039   0.166    939
  Planarity :  0.004   0.035    740
  Dihedral  : 19.514  84.685   1631
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 23.84 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.70 (0.39), residues: 459
  helix:  0.99 (0.59), residues: 66
  sheet: -0.22 (0.41), residues: 171
  loop : -1.06 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 206 
 HIS   0.005   0.001   HIS B 187 
 PHE   0.015   0.002   PHE A 211 
 TYR   0.024   0.001   TYR A 115 
 ARG   0.003   0.000   ARG B  17 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.492 
Fit side-chains
REVERT: A  117 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8421 (pm20)
REVERT: A  137 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.5864 (mt)
REVERT: A  211 PHE cc_start: 0.5509 (OUTLIER) cc_final: 0.4005 (t80)
REVERT: B  133 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7590 (tm-30)
REVERT: B  226 CYS cc_start: 0.5685 (t) cc_final: 0.5345 (p)
REVERT: B  271 PHE cc_start: 0.6050 (m-10) cc_final: 0.5530 (m-80)
  outliers start: 18
  outliers final: 12
  residues processed: 67
  average time/residue: 0.1679
  time to fit residues: 15.4341
Evaluate side-chains
  65 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  117 GLN
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   69 PHE
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  260 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 18 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   chunk 32 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 16 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.4772 r_free = 0.4772 target = 0.210034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.157326 restraints weight = 7732.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.162485 restraints weight = 7647.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.163654 restraints weight = 5185.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.4405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6514
moved from start:          0.5135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5565  Z= 0.277
  Angle     :  0.621   9.414   7883  Z= 0.314
  Chirality :  0.040   0.182    939
  Planarity :  0.005   0.037    740
  Dihedral  : 19.607  84.345   1631
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 24.33 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.39), residues: 459
  helix:  0.77 (0.58), residues: 66
  sheet: -0.35 (0.41), residues: 170
  loop : -1.10 (0.41), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 206 
 HIS   0.005   0.001   HIS B 187 
 PHE   0.017   0.002   PHE A 211 
 TYR   0.008   0.002   TYR A 186 
 ARG   0.003   0.000   ARG B  17 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A  117 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8322 (pm20)
REVERT: A  137 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6114 (mt)
REVERT: A  211 PHE cc_start: 0.5596 (OUTLIER) cc_final: 0.4110 (t80)
REVERT: B  133 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7593 (tm-30)
REVERT: B  226 CYS cc_start: 0.5479 (t) cc_final: 0.5027 (p)
  outliers start: 18
  outliers final: 13
  residues processed: 66
  average time/residue: 0.1643
  time to fit residues: 14.2813
Evaluate side-chains
  64 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 48
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  117 GLN
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   69 PHE
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  260 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0870
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 278 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.205720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.154787 restraints weight = 7461.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.160077 restraints weight = 7643.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.160705 restraints weight = 5650.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.4235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6388
moved from start:          0.5424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5565  Z= 0.206
  Angle     :  0.576   9.297   7883  Z= 0.294
  Chirality :  0.038   0.176    939
  Planarity :  0.004   0.036    740
  Dihedral  : 19.522  84.430   1631
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 26.03 %
    Favored  : 70.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.39), residues: 459
  helix:  0.95 (0.59), residues: 66
  sheet: -0.26 (0.40), residues: 172
  loop : -0.96 (0.42), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 206 
 HIS   0.004   0.001   HIS B 187 
 PHE   0.017   0.002   PHE A 211 
 TYR   0.008   0.001   TYR A 150 
 ARG   0.002   0.000   ARG B  17 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.485 
Fit side-chains
REVERT: A  117 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8435 (pm20)
REVERT: A  137 LEU cc_start: 0.6339 (OUTLIER) cc_final: 0.5772 (mt)
REVERT: A  211 PHE cc_start: 0.5717 (OUTLIER) cc_final: 0.4142 (t80)
REVERT: B  133 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7522 (tm-30)
REVERT: B  164 ASP cc_start: 0.6972 (OUTLIER) cc_final: 0.6580 (p0)
REVERT: B  226 CYS cc_start: 0.5568 (t) cc_final: 0.5317 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 62
  average time/residue: 0.1570
  time to fit residues: 13.2130
Evaluate side-chains
  65 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 50
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  117 GLN
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   69 PHE
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  260 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 39 optimal weight:    0.0870
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.205989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.155873 restraints weight = 7342.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.157100 restraints weight = 6289.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.158697 restraints weight = 6225.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
moved from start:          0.5626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5565  Z= 0.188
  Angle     :  0.556   8.917   7883  Z= 0.284
  Chirality :  0.038   0.174    939
  Planarity :  0.005   0.062    740
  Dihedral  : 19.452  85.342   1631
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 25.79 %
    Favored  : 70.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.39), residues: 459
  helix:  1.14 (0.59), residues: 66
  sheet: -0.30 (0.39), residues: 181
  loop : -0.90 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 225 
 PHE   0.016   0.002   PHE A 211 
 TYR   0.008   0.001   TYR A 150 
 ARG   0.004   0.000   ARG B 277 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 0.550 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8437 (pm20)
REVERT: A  137 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.5919 (mt)
REVERT: A  211 PHE cc_start: 0.5664 (OUTLIER) cc_final: 0.4099 (t80)
REVERT: B  133 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7508 (tm-30)
REVERT: B  164 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6635 (p0)
  outliers start: 15
  outliers final: 11
  residues processed: 65
  average time/residue: 0.1982
  time to fit residues: 17.7526
Evaluate side-chains
  62 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 VAL
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  113 SER
Chi-restraints excluded: chain A residue  117 GLN
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  171 HIS
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   69 PHE
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  260 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 27 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 228 HIS
** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4697 r_free = 0.4697 target = 0.205334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.157901 restraints weight = 7183.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.161175 restraints weight = 6893.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.162766 restraints weight = 4908.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.4196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6469
moved from start:          0.5932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5565  Z= 0.281
  Angle     :  0.636   8.678   7883  Z= 0.329
  Chirality :  0.041   0.182    939
  Planarity :  0.005   0.063    740
  Dihedral  : 19.542  86.033   1631
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 25.30 %
    Favored  : 70.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.40), residues: 459
  helix:  0.76 (0.60), residues: 66
  sheet: -0.29 (0.40), residues: 170
  loop : -0.89 (0.43), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 206 
 HIS   0.006   0.002   HIS A 204 
 PHE   0.018   0.002   PHE A 211 
 TYR   0.008   0.001   TYR A 186 
 ARG   0.005   0.000   ARG B 277 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1948.68 seconds
wall clock time: 35 minutes 36.65 seconds (2136.65 seconds total)