Starting phenix.real_space_refine
on Thu Mar  6 08:31:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cti_26991/03_2025/8cti_26991.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cti_26991/03_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_26991/03_2025/8cti_26991.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cti_26991/03_2025/8cti_26991.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cti_26991/03_2025/8cti_26991.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cti_26991/03_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-5624/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: 4.08, per 1000 atoms: 0.77
  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: 1.35
  Conformation dependent library (CDL) restraints added in 596.5 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: 2.01
  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: 1.58

  Time building geometry restraints manager: 1.61 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:             2.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.000
  Find NCS groups from input model:        0.050
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.360
-------------------------------------------------------------------------------
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  : 0.405 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 47
  average time/residue: 0.1278
  time to fit residues: 8.7652
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  : 0.429 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4742 r_free = 0.4742 target = 0.208401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.148764 restraints weight = 7615.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.153474 restraints weight = 4744.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.156544 restraints weight = 3556.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.4164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6402
moved from start:          0.1391

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= 0.219
  Angle     :  0.606   8.214   7883  Z= 0.308
  Chirality :  0.040   0.153    939
  Planarity :  0.004   0.038    740
  Dihedral  : 20.057 106.701   1631
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 20.68 %
    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: -1.03 (0.39), residues: 459
  helix: -0.31 (0.58), residues: 70
  sheet: -0.37 (0.39), residues: 187
  loop : -0.99 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 216 
 HIS   0.006   0.001   HIS B 187 
 PHE   0.017   0.002   PHE A 256 
 TYR   0.012   0.001   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
  51 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.496 
Fit side-chains
REVERT: B   70 SER cc_start: 0.5012 (p) cc_final: 0.4763 (t)
REVERT: B  133 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7673 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 50
  average time/residue: 0.1143
  time to fit residues: 8.5945
Evaluate side-chains
  48 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 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:    0.5980
   chunk 21 optimal weight:    7.9990
   chunk 44 optimal weight:    7.9990
   chunk 30 optimal weight:    0.6980
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A  77 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4713 r_free = 0.4713 target = 0.205232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.156414 restraints weight = 7456.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.163431 restraints weight = 6493.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.163984 restraints weight = 4061.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.4269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6162
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5565  Z= 0.205
  Angle     :  0.547   8.659   7883  Z= 0.276
  Chirality :  0.038   0.141    939
  Planarity :  0.004   0.040    740
  Dihedral  : 19.724 100.687   1631
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 19.95 %
    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: -0.92 (0.39), residues: 459
  helix: -0.03 (0.57), residues: 70
  sheet: -0.15 (0.40), residues: 178
  loop : -1.15 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A  46 
 HIS   0.005   0.001   HIS B 187 
 PHE   0.016   0.002   PHE A 211 
 TYR   0.011   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
  68 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A   79 GLU cc_start: 0.8076 (mp0) cc_final: 0.7641 (mp0)
REVERT: A  173 TRP cc_start: 0.6057 (OUTLIER) cc_final: 0.5606 (m-10)
REVERT: A  211 PHE cc_start: 0.5461 (OUTLIER) cc_final: 0.4367 (t80)
REVERT: B  133 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7578 (tm-30)
REVERT: B  187 HIS cc_start: 0.6010 (OUTLIER) cc_final: 0.5724 (m170)
  outliers start: 16
  outliers final: 8
  residues processed: 63
  average time/residue: 0.1233
  time to fit residues: 11.0368
Evaluate side-chains
  57 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
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  173 TRP
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:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 50 optimal weight:   20.0000
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 12 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 256 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4646 r_free = 0.4646 target = 0.197583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.149111 restraints weight = 7801.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.152824 restraints weight = 8301.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.153515 restraints weight = 6974.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.4108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6525
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   5565  Z= 0.401
  Angle     :  0.736   9.010   7883  Z= 0.376
  Chirality :  0.044   0.173    939
  Planarity :  0.006   0.042    740
  Dihedral  : 20.002  93.755   1631
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 17.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 19.22 %
    Favored  : 74.94 %
  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: -1.27 (0.38), residues: 459
  helix: -0.21 (0.58), residues: 66
  sheet: -0.29 (0.42), residues: 172
  loop : -1.46 (0.39), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 173 
 HIS   0.008   0.002   HIS B 178 
 PHE   0.029   0.003   PHE B 190 
 TYR   0.014   0.002   TYR A 186 
 ARG   0.006   0.001   ARG B  17 

*********************** 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
  83 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A   79 GLU cc_start: 0.7917 (mp0) cc_final: 0.7677 (mp0)
REVERT: A  137 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6016 (mt)
REVERT: A  211 PHE cc_start: 0.5650 (OUTLIER) cc_final: 0.4127 (t80)
REVERT: B  133 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7954 (tm-30)
REVERT: B  164 ASP cc_start: 0.7175 (OUTLIER) cc_final: 0.6607 (p0)
REVERT: B  187 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.7202 (m170)
REVERT: B  295 VAL cc_start: 0.6394 (p) cc_final: 0.6160 (t)
  outliers start: 24
  outliers final: 12
  residues processed: 78
  average time/residue: 0.1468
  time to fit residues: 15.5223
Evaluate side-chains
  66 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 50
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
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  106 THR
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  187 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0070
   chunk 22 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 50 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 48 optimal weight:    8.9990
   overall best weight:    0.7598

-------------------------------------------------------------------------------
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 = 0.4676 r_free = 0.4676 target = 0.202163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.151266 restraints weight = 7398.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.153051 restraints weight = 6481.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.154440 restraints weight = 5917.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6414
moved from start:          0.4251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5565  Z= 0.196
  Angle     :  0.566   9.219   7883  Z= 0.290
  Chirality :  0.039   0.157    939
  Planarity :  0.004   0.036    740
  Dihedral  : 19.767  90.568   1631
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 23.11 %
    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: -0.99 (0.39), residues: 459
  helix:  0.32 (0.60), residues: 66
  sheet: -0.37 (0.40), residues: 181
  loop : -1.16 (0.41), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 206 
 HIS   0.007   0.001   HIS A 144 
 PHE   0.018   0.002   PHE A 211 
 TYR   0.017   0.002   TYR A  37 
 ARG   0.003   0.000   ARG B 214 

*********************** 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
  72 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 51
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A   79 GLU cc_start: 0.7732 (mp0) cc_final: 0.7515 (mp0)
REVERT: A  132 GLN cc_start: 0.2430 (OUTLIER) cc_final: 0.1934 (mm-40)
REVERT: A  171 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.6863 (p90)
REVERT: A  211 PHE cc_start: 0.5751 (OUTLIER) cc_final: 0.4101 (t80)
REVERT: B  133 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7565 (tm-30)
REVERT: B  277 ARG cc_start: 0.8255 (tpt170) cc_final: 0.8045 (tpp80)
  outliers start: 21
  outliers final: 9
  residues processed: 69
  average time/residue: 0.1570
  time to fit residues: 14.5345
Evaluate side-chains
  61 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
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  132 GLN
Chi-restraints excluded: chain A residue  171 HIS
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   69 PHE
Chi-restraints excluded: chain B residue   86 ILE
Chi-restraints excluded: chain B residue  126 VAL
Chi-restraints excluded: chain B residue  164 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:   10.0000
   chunk 52 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 43 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   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 = 0.4640 r_free = 0.4640 target = 0.198446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4106 r_free = 0.4106 target = 0.147336 restraints weight = 7378.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.149465 restraints weight = 6472.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.150362 restraints weight = 6377.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6500
moved from start:          0.4838

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     :  0.607   9.392   7883  Z= 0.308
  Chirality :  0.040   0.164    939
  Planarity :  0.005   0.039    740
  Dihedral  : 19.699  85.530   1631
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  6.57 %
    Allowed  : 20.92 %
    Favored  : 72.51 %
  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: -1.00 (0.39), residues: 459
  helix:  0.39 (0.59), residues: 66
  sheet: -0.37 (0.42), residues: 175
  loop : -1.19 (0.41), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 206 
 HIS   0.006   0.001   HIS B 187 
 PHE   0.016   0.002   PHE A 211 
 TYR   0.014   0.002   TYR A 115 
 ARG   0.007   0.001   ARG A 138 

*********************** 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
  79 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 52
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 MET cc_start: 0.5888 (OUTLIER) cc_final: 0.5249 (tpt)
REVERT: A   50 TYR cc_start: 0.5197 (OUTLIER) cc_final: 0.2862 (m-80)
REVERT: A   79 GLU cc_start: 0.7747 (mp0) cc_final: 0.7530 (mp0)
REVERT: A  132 GLN cc_start: 0.2478 (OUTLIER) cc_final: 0.1911 (mm-40)
REVERT: A  137 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6150 (mt)
REVERT: A  211 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.4204 (t80)
REVERT: B  133 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7598 (tm-30)
  outliers start: 27
  outliers final: 19
  residues processed: 74
  average time/residue: 0.1408
  time to fit residues: 14.3122
Evaluate side-chains
  74 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 50
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 MET
Chi-restraints excluded: chain A residue   50 TYR
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  123 LEU
Chi-restraints excluded: chain A residue  132 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 A residue  244 VAL
Chi-restraints excluded: chain A residue  261 ASP
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  146 SER
Chi-restraints excluded: chain B residue  151 VAL
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  199 THR
Chi-restraints excluded: chain B residue  228 HIS
Chi-restraints excluded: chain B residue  316 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:    7.9990
   chunk 52 optimal weight:    4.9990
   chunk 49 optimal weight:    9.9990
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
** B 307 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 = 0.4961 r_free = 0.4961 target = 0.226726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.184944 restraints weight = 7848.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.188153 restraints weight = 11688.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.189721 restraints weight = 9542.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.4492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6325
moved from start:          0.4977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5565  Z= 0.197
  Angle     :  0.553   9.457   7883  Z= 0.281
  Chirality :  0.038   0.168    939
  Planarity :  0.004   0.038    740
  Dihedral  : 19.601  85.714   1631
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.84 %
    Allowed  : 22.63 %
    Favored  : 71.53 %
  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: -0.88 (0.39), residues: 459
  helix:  0.71 (0.59), residues: 66
  sheet: -0.51 (0.40), residues: 184
  loop : -0.98 (0.42), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 206 
 HIS   0.004   0.001   HIS B 187 
 PHE   0.017   0.002   PHE A 211 
 TYR   0.021   0.002   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
  79 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 55
  time to evaluate  : 0.453 
Fit side-chains
REVERT: A  132 GLN cc_start: 0.2303 (OUTLIER) cc_final: 0.1726 (mm-40)
REVERT: A  137 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6375 (mt)
REVERT: A  211 PHE cc_start: 0.5502 (OUTLIER) cc_final: 0.3931 (t80)
REVERT: B  133 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7492 (tm-30)
REVERT: B  277 ARG cc_start: 0.7018 (tpp-160) cc_final: 0.6778 (tpp-160)
  outliers start: 24
  outliers final: 14
  residues processed: 72
  average time/residue: 0.1491
  time to fit residues: 14.5227
Evaluate side-chains
  67 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 50
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
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  132 GLN
Chi-restraints excluded: chain A residue  137 LEU
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  261 ASP
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  199 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    8.9990
   chunk 18 optimal weight:    5.9990
   chunk 17 optimal weight:    0.7980
   chunk 51 optimal weight:    9.9990
   chunk 32 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0050
   chunk 5 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0050
   chunk 7 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.4208

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

Flipped N/Q/H residues before XYZ refinement:
B 278 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.205688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.156480 restraints weight = 7376.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.161996 restraints weight = 7153.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.163249 restraints weight = 4734.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.4230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6322
moved from start:          0.5275

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= 0.157
  Angle     :  0.550  10.588   7883  Z= 0.282
  Chirality :  0.037   0.144    939
  Planarity :  0.004   0.037    740
  Dihedral  : 19.461  85.016   1631
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 26.03 %
    Favored  : 71.05 %
  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: -0.64 (0.39), residues: 459
  helix:  0.90 (0.57), residues: 69
  sheet: -0.14 (0.41), residues: 167
  loop : -1.02 (0.41), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 206 
 HIS   0.003   0.001   HIS B 187 
 PHE   0.017   0.001   PHE A 211 
 TYR   0.008   0.001   TYR A  37 
 ARG   0.002   0.000   ARG A 121 

*********************** 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
  67 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
REVERT: A  132 GLN cc_start: 0.2285 (OUTLIER) cc_final: 0.1731 (mm-40)
REVERT: A  211 PHE cc_start: 0.5762 (OUTLIER) cc_final: 0.4071 (t80)
REVERT: B  133 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7486 (tm-30)
REVERT: B  164 ASP cc_start: 0.6833 (OUTLIER) cc_final: 0.6451 (p0)
REVERT: B  271 PHE cc_start: 0.6092 (m-80) cc_final: 0.5663 (m-80)
  outliers start: 12
  outliers final: 6
  residues processed: 66
  average time/residue: 0.1529
  time to fit residues: 13.7889
Evaluate side-chains
  59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  132 GLN
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  126 VAL
Chi-restraints excluded: chain B residue  164 ASP
Chi-restraints excluded: chain B residue  199 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0870
   chunk 19 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   chunk 24 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0370
   overall best weight:    0.3236

-------------------------------------------------------------------------------
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 = 0.4700 r_free = 0.4700 target = 0.206808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.157666 restraints weight = 7281.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.161753 restraints weight = 7106.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.163035 restraints weight = 5310.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6333
moved from start:          0.5411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   5565  Z= 0.153
  Angle     :  0.554   9.952   7883  Z= 0.287
  Chirality :  0.038   0.175    939
  Planarity :  0.004   0.036    740
  Dihedral  : 19.371  84.670   1631
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 26.03 %
    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: -0.57 (0.39), residues: 459
  helix:  0.93 (0.60), residues: 66
  sheet: -0.13 (0.39), residues: 176
  loop : -0.94 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 293 
 HIS   0.007   0.001   HIS A 171 
 PHE   0.015   0.001   PHE A 211 
 TYR   0.026   0.001   TYR A 115 
 ARG   0.002   0.000   ARG B  89 

*********************** 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: 14
    poor density    : 51
  time to evaluate  : 0.432 
Fit side-chains
REVERT: A  132 GLN cc_start: 0.2170 (OUTLIER) cc_final: 0.1612 (mm-40)
REVERT: A  211 PHE cc_start: 0.5694 (OUTLIER) cc_final: 0.4042 (t80)
REVERT: B  133 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7459 (tm-30)
  outliers start: 14
  outliers final: 9
  residues processed: 64
  average time/residue: 0.1413
  time to fit residues: 12.4762
Evaluate side-chains
  57 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 46
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
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  132 GLN
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  199 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 53 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 228 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.203402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.153563 restraints weight = 7352.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.156174 restraints weight = 7178.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.158502 restraints weight = 5247.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6431
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   0.035   5565  Z= 0.207
  Angle     :  0.583   9.823   7883  Z= 0.301
  Chirality :  0.038   0.175    939
  Planarity :  0.004   0.036    740
  Dihedral  : 19.388  85.418   1631
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 27.01 %
    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: -0.57 (0.39), residues: 459
  helix:  0.74 (0.58), residues: 70
  sheet: -0.01 (0.41), residues: 167
  loop : -0.99 (0.41), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 293 
 HIS   0.004   0.001   HIS B 225 
 PHE   0.017   0.001   PHE A 211 
 TYR   0.030   0.002   TYR A 115 
 ARG   0.009   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
  63 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.472 
Fit side-chains
REVERT: A  211 PHE cc_start: 0.5767 (OUTLIER) cc_final: 0.4094 (t80)
  outliers start: 11
  outliers final: 9
  residues processed: 61
  average time/residue: 0.1587
  time to fit residues: 13.7718
Evaluate side-chains
  59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
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  211 PHE
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  145 LEU
Chi-restraints excluded: chain B residue  228 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 228 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.202544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.152133 restraints weight = 7223.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.155529 restraints weight = 7133.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.156952 restraints weight = 5772.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.4159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6456
moved from start:          0.5772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5565  Z= 0.227
  Angle     :  0.602   9.670   7883  Z= 0.310
  Chirality :  0.039   0.182    939
  Planarity :  0.004   0.036    740
  Dihedral  : 19.408  85.584   1631
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 27.01 %
    Favored  : 70.07 %
  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: -0.65 (0.39), residues: 459
  helix:  0.70 (0.59), residues: 70
  sheet:  0.04 (0.41), residues: 163
  loop : -1.12 (0.41), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 252 
 HIS   0.009   0.001   HIS B 225 
 PHE   0.017   0.002   PHE A 211 
 TYR   0.028   0.002   TYR A 115 
 ARG   0.004   0.000   ARG B 277 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2026.93 seconds
wall clock time: 35 minutes 54.24 seconds (2154.24 seconds total)