Starting phenix.real_space_refine
on Mon Jul 28 09:15:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9of0_70416/07_2025/9of0_70416.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9of0_70416/07_2025/9of0_70416.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/9of0_70416/07_2025/9of0_70416.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9of0_70416/07_2025/9of0_70416.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9of0_70416/07_2025/9of0_70416.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9of0_70416/07_2025/9of0_70416.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=   0.044
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: 6
    Type Number    sf(0)   Gaussians
     P      40      5.49       5
     S      41      5.16       5
     C    3380      2.51       5
     N     988      2.21       5
     O    1123      1.98       5
     H    4664      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10236
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 5035
          Classifications: {'peptide': 314}
          Link IDs: {'PTRANS': 9, 'TRANS': 304}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4346
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 4346
          Classifications: {'peptide': 268}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 254}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 433
          Classifications: {'DNA': 21}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 20}
    Chain: "D"
      Number of atoms: 422
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 422
          Classifications: {'DNA': 21}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 20}
  Time building chain proxies: 6.79, per 1000 atoms: 0.66
  Number of scatterers: 10236
  At special positions: 0
  Unit cell: (76.804, 79.336, 130.82, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      41     16.00
     P      40     15.00
     O    1123      8.00
     N     988      7.00
     C    3380      6.00
     H    4664      1.00
    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: 3.11
  Conformation dependent library (CDL) restraints added in 618.8 milliseconds
  

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1118

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 5 sheets defined
      43.6% alpha, 29.4% beta
      14 base pairs and 28 stacking pairs defined.
    Time for finding SS restraints: 4.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 19
    Processing helix  chain 'A' and resid 21 through 40
      removed outlier: 3.813A  pdb=" N   TYR A  35 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   HIS A  39 " --> pdb=" O   TYR A  35 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   GLU A  40 " --> pdb=" O   GLU A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 52 through 74
      removed outlier: 3.587A  pdb=" N   SER A  72 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 94
      removed outlier: 4.346A  pdb=" N   LYS A  93 " --> pdb=" O   ASN A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 119
      removed outlier: 3.946A  pdb=" N   PHE A 118 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 127
    Processing helix  chain 'A' and resid 130 through 134
    Processing helix  chain 'A' and resid 136 through 138
      No H-bonds generated for 'chain 'A' and resid 136 through 138'
    Processing helix  chain 'A' and resid 139 through 148
    Processing helix  chain 'A' and resid 184 through 188
    Processing helix  chain 'A' and resid 260 through 265
    Processing helix  chain 'A' and resid 268 through 273
      removed outlier: 3.897A  pdb=" N   LEU A 272 " --> pdb=" O   HIS A 268 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU A 273 " --> pdb=" O   PRO A 269 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 268 through 273'
    Processing helix  chain 'A' and resid 282 through 284
      No H-bonds generated for 'chain 'A' and resid 282 through 284'
    Processing helix  chain 'A' and resid 285 through 300
    Processing helix  chain 'A' and resid 355 through 359
    Processing helix  chain 'B' and resid 93 through 116
    Processing helix  chain 'B' and resid 127 through 139
    Processing helix  chain 'B' and resid 160 through 173
    Processing helix  chain 'B' and resid 192 through 198
    Processing helix  chain 'B' and resid 200 through 205
      removed outlier: 3.815A  pdb=" N   TRP B 204 " --> pdb=" O   PRO B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 213
    Processing helix  chain 'B' and resid 214 through 216
      No H-bonds generated for 'chain 'B' and resid 214 through 216'
    Processing helix  chain 'B' and resid 217 through 226
    Processing helix  chain 'B' and resid 379 through 384
    Processing helix  chain 'B' and resid 387 through 392
      removed outlier: 3.742A  pdb=" N   LEU B 391 " --> pdb=" O   GLN B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 400
    Processing helix  chain 'B' and resid 401 through 403
      No H-bonds generated for 'chain 'B' and resid 401 through 403'
    Processing helix  chain 'B' and resid 404 through 419
      removed outlier: 3.761A  pdb=" N   VAL B 416 " --> pdb=" O   PHE B 412 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LYS B 417 " --> pdb=" O   GLN B 413 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111
      removed outlier: 6.562A  pdb=" N   MET A 108 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 7.034A  pdb=" N   THR A 103 " --> pdb=" O   MET A 108 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   PHE A 110 " --> pdb=" O   VAL A 101 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU A 219 " --> pdb=" O   TYR A 202 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 254 through 257
      removed outlier: 3.571A  pdb=" N   TYR A 256 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER A 246 " --> pdb=" O   CYS A 339 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   CYS A 336 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 254 through 257
      removed outlier: 3.571A  pdb=" N   TYR A 256 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER A 246 " --> pdb=" O   CYS A 339 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   CYS A 336 " --> pdb=" O   ILE A 326 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 186 through 189
      removed outlier: 6.481A  pdb=" N   ILE B 178 " --> pdb=" O   VAL B 187 " (cutoff:3.500A)
      removed outlier: 4.569A  pdb=" N   VAL B 189 " --> pdb=" O   LEU B 176 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   LEU B 176 " --> pdb=" O   VAL B 189 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LYS B 313 " --> pdb=" O   CYS B 336 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 373 through 376
      removed outlier: 4.321A  pdb=" N   PHE B 375 " --> pdb=" O   ARG B 366 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   TYR B 456 " --> pdb=" O   PHE B 446 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE B 458 " --> pdb=" O   PHE B 444 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   SER B 442 " --> pdb=" O   THR B 460 " (cutoff:3.500A)

    235 hydrogen bonds defined for protein.
    660 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      35 hydrogen bonds
      66 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      28 stacking parallelities
  Total time for adding SS restraints: 3.90

  Time building geometry restraints manager: 3.43 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 4644
        1.03 -     1.23: 33
        1.23 -     1.42: 2500
        1.42 -     1.61: 3194
        1.61 -     1.81: 62
  Bond restraints: 10433
  Sorted by residual:
  bond pdb=" CB  GLU B 403 "
       pdb=" CG  GLU B 403 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.35e+00
  bond pdb=" CB  PRO A 329 "
       pdb=" CG  PRO A 329 "
    ideal  model  delta    sigma   weight residual
    1.492  1.546 -0.054 5.00e-02 4.00e+02 1.17e+00
  bond pdb=" CG  LEU A  69 "
       pdb=" CD1 LEU A  69 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.46e-01
  bond pdb=" C   VAL B 187 "
       pdb=" O   VAL B 187 "
    ideal  model  delta    sigma   weight residual
    1.242  1.231  0.011 1.13e-02 7.83e+03 9.36e-01
  bond pdb=" O4'  DC C   6 "
       pdb=" C1'  DC C   6 "
    ideal  model  delta    sigma   weight residual
    1.414  1.396  0.018 2.00e-02 2.50e+03 7.78e-01
  ... (remaining 10428 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 18180
        1.55 -     3.09: 323
        3.09 -     4.64: 24
        4.64 -     6.18: 3
        6.18 -     7.73: 1
  Bond angle restraints: 18531
  Sorted by residual:
  angle pdb=" N   ASP A  21 "
        pdb=" CA  ASP A  21 "
        pdb=" C   ASP A  21 "
      ideal   model   delta    sigma   weight residual
     113.55  110.07    3.48 1.26e+00 6.30e-01 7.64e+00
  angle pdb=" N   MET B 115 "
        pdb=" CA  MET B 115 "
        pdb=" C   MET B 115 "
      ideal   model   delta    sigma   weight residual
     111.36  114.01   -2.65 1.09e+00 8.42e-01 5.91e+00
  angle pdb=" N   ILE B 369 "
        pdb=" CA  ILE B 369 "
        pdb=" C   ILE B 369 "
      ideal   model   delta    sigma   weight residual
     112.98  110.08    2.90 1.25e+00 6.40e-01 5.38e+00
  angle pdb=" CA  LEU A 332 "
        pdb=" CB  LEU A 332 "
        pdb=" CG  LEU A 332 "
      ideal   model   delta    sigma   weight residual
     116.30  124.03   -7.73 3.50e+00 8.16e-02 4.87e+00
  angle pdb=" N   LEU B 418 "
        pdb=" CA  LEU B 418 "
        pdb=" C   LEU B 418 "
      ideal   model   delta    sigma   weight residual
     111.71  109.43    2.28 1.15e+00 7.56e-01 3.94e+00
  ... (remaining 18526 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.29: 4637
       35.29 -    70.59: 252
       70.59 -   105.88: 12
      105.88 -   141.18: 1
      141.18 -   176.47: 1
  Dihedral angle restraints: 4903
    sinusoidal: 2871
      harmonic: 2032
  Sorted by residual:
  dihedral pdb=" C4'  DC C   3 "
           pdb=" C3'  DC C   3 "
           pdb=" O3'  DC C   3 "
           pdb=" P    DT C   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   43.53  176.47     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DC D   1 "
           pdb=" C3'  DC D   1 "
           pdb=" O3'  DC D   1 "
           pdb=" P    DA D   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00  -16.80 -123.20     1      3.50e+01 8.16e-04 1.21e+01
  dihedral pdb=" CA  LEU A 319 "
           pdb=" C   LEU A 319 "
           pdb=" N   GLU A 320 "
           pdb=" CA  GLU A 320 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.94   17.06     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 4900 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 527
       0.027 -    0.055: 259
       0.055 -    0.082: 50
       0.082 -    0.109: 30
       0.109 -    0.136: 24
  Chirality restraints: 890
  Sorted by residual:
  chirality pdb=" CA  ILE A 237 "
            pdb=" N   ILE A 237 "
            pdb=" C   ILE A 237 "
            pdb=" CB  ILE A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.65e-01
  chirality pdb=" CA  VAL A 340 "
            pdb=" N   VAL A 340 "
            pdb=" C   VAL A 340 "
            pdb=" CB  VAL A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  chirality pdb=" CA  ILE B 178 "
            pdb=" N   ILE B 178 "
            pdb=" C   ILE B 178 "
            pdb=" CB  ILE B 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.24e-01
  ... (remaining 887 not shown)

  Planarity restraints: 1416
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 328 "   -0.040 5.00e-02 4.00e+02   6.02e-02 5.80e+00
        pdb=" N   PRO A 329 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 329 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 329 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 316 "    0.021 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO B 317 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 317 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 317 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC D  18 "   -0.015 2.00e-02 2.50e+03   8.12e-03 1.48e+00
        pdb=" N1   DC D  18 "    0.018 2.00e-02 2.50e+03
        pdb=" C2   DC D  18 "    0.000 2.00e-02 2.50e+03
        pdb=" O2   DC D  18 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DC D  18 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC D  18 "   -0.004 2.00e-02 2.50e+03
        pdb=" N4   DC D  18 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5   DC D  18 "    0.002 2.00e-02 2.50e+03
        pdb=" C6   DC D  18 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1413 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.08: 144
        2.08 -     2.71: 15103
        2.71 -     3.34: 26644
        3.34 -     3.97: 34604
        3.97 -     4.60: 54249
  Nonbonded interactions: 130744
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B 403 "
            pdb=" H   GLU B 403 "
     model   vdw
     1.448 2.450
  nonbonded pdb=" HZ1 LYS B 220 "
            pdb=" O   ILE B 264 "
     model   vdw
     1.628 2.450
  nonbonded pdb="HH11 ARG A  58 "
            pdb=" O   THR A 127 "
     model   vdw
     1.648 2.450
  nonbonded pdb=" O   SER A 163 "
            pdb="HH12 ARG A 166 "
     model   vdw
     1.667 2.450
  nonbonded pdb=" H   GLN B 387 "
            pdb=" OE1 GLU B 390 "
     model   vdw
     1.679 2.450
  ... (remaining 130739 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:             3.730
  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:             0.180
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     30.710
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
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      :  0.004   0.054   5769  Z= 0.162
  Angle     :  0.591   7.728   7956  Z= 0.345
  Chirality :  0.039   0.136    890
  Planarity :  0.004   0.060    864
  Dihedral  : 20.146 176.472   2237
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.65 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.43 (0.37), residues: 560
  helix:  0.98 (0.42), residues: 192
  sheet: -0.59 (0.40), residues: 151
  loop :  0.59 (0.45), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 315 
 HIS   0.008   0.001   HIS B 401 
 PHE   0.009   0.001   PHE B 363 
 TYR   0.014   0.001   TYR A 202 
 ARG   0.005   0.001   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20695 (  257)
  hydrogen bonds       : angle       8.01804 (  726)
  covalent geometry    : bond        0.00352 ( 5769)
  covalent geometry    : angle       0.59084 ( 7956)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.4591
  time to fit residues: 39.6731
Evaluate side-chains
  61 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0980
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B  94 HIS ** 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 = 0.3841 r_free = 0.3841 target = 0.152517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.118299 restraints weight = 17146.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.122100 restraints weight = 9925.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.124589 restraints weight = 6860.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.1204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5769  Z= 0.153
  Angle     :  0.538   7.540   7956  Z= 0.302
  Chirality :  0.040   0.149    890
  Planarity :  0.004   0.034    864
  Dihedral  : 22.171 172.771   1062
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 11.46 %
    Favored  : 87.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.59 (0.37), residues: 560
  helix:  1.19 (0.41), residues: 193
  sheet: -0.62 (0.39), residues: 156
  loop :  0.72 (0.45), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 315 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.014   0.001   PHE B 363 
 TYR   0.013   0.001   TYR A 202 
 ARG   0.006   0.001   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05001 (  257)
  hydrogen bonds       : angle       5.08860 (  726)
  covalent geometry    : bond        0.00343 ( 5769)
  covalent geometry    : angle       0.53776 ( 7956)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 75
  average time/residue: 0.4334
  time to fit residues: 40.6882
Evaluate side-chains
  65 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 63
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain B residue  181 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B  94 HIS ** 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 = 0.3832 r_free = 0.3832 target = 0.151924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.117258 restraints weight = 17298.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.121016 restraints weight = 10065.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.123496 restraints weight = 7006.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   5769  Z= 0.155
  Angle     :  0.517   7.035   7956  Z= 0.289
  Chirality :  0.040   0.149    890
  Planarity :  0.004   0.037    864
  Dihedral  : 22.384 172.466   1062
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.28 %
    Favored  : 87.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 (0.37), residues: 560
  helix:  1.27 (0.41), residues: 193
  sheet: -0.60 (0.38), residues: 156
  loop :  0.74 (0.46), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 438 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.015   0.001   PHE A 244 
 TYR   0.013   0.001   TYR A 202 
 ARG   0.004   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04686 (  257)
  hydrogen bonds       : angle       4.83476 (  726)
  covalent geometry    : bond        0.00353 ( 5769)
  covalent geometry    : angle       0.51680 ( 7956)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.773 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8449 (tppp) cc_final: 0.7891 (ttpp)
  outliers start: 4
  outliers final: 3
  residues processed: 71
  average time/residue: 0.4115
  time to fit residues: 37.1344
Evaluate side-chains
  67 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 64
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain B residue  181 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 29 optimal weight:    0.4980
   chunk 56 optimal weight:    0.3980
   chunk 19 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 378 HIS ** 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 = 0.3851 r_free = 0.3851 target = 0.153993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.119122 restraints weight = 16619.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.122862 restraints weight = 9821.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.125074 restraints weight = 6845.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5769  Z= 0.148
  Angle     :  0.499   6.882   7956  Z= 0.277
  Chirality :  0.039   0.149    890
  Planarity :  0.004   0.039    864
  Dihedral  : 22.683 172.872   1062
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 12.01 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.37), residues: 560
  helix:  1.20 (0.40), residues: 200
  sheet: -0.55 (0.40), residues: 146
  loop :  0.58 (0.46), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 204 
 HIS   0.004   0.001   HIS B 367 
 PHE   0.012   0.001   PHE A 244 
 TYR   0.011   0.002   TYR A 202 
 ARG   0.007   0.000   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04417 (  257)
  hydrogen bonds       : angle       4.59648 (  726)
  covalent geometry    : bond        0.00335 ( 5769)
  covalent geometry    : angle       0.49859 ( 7956)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8448 (tppp) cc_final: 0.7958 (ttpp)
REVERT: A  172 MET cc_start: 0.8801 (ttt) cc_final: 0.8561 (ttt)
REVERT: B  394 LYS cc_start: 0.8599 (mttt) cc_final: 0.8249 (mttp)
REVERT: B  436 TRP cc_start: 0.8004 (m100) cc_final: 0.7698 (m100)
  outliers start: 4
  outliers final: 4
  residues processed: 71
  average time/residue: 0.4302
  time to fit residues: 38.6647
Evaluate side-chains
  68 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain B residue  181 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 11 optimal weight:    0.3980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 146 ASN
** B 378 HIS ** 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 = 0.3843 r_free = 0.3843 target = 0.153319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118465 restraints weight = 16737.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.122166 restraints weight = 9932.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.124177 restraints weight = 6933.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5769  Z= 0.159
  Angle     :  0.495   6.775   7956  Z= 0.275
  Chirality :  0.039   0.148    890
  Planarity :  0.004   0.040    864
  Dihedral  : 22.738 172.703   1062
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.01 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.56 (0.37), residues: 560
  helix:  1.18 (0.40), residues: 200
  sheet: -0.60 (0.39), residues: 146
  loop :  0.56 (0.46), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 204 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.013   0.001   PHE B 444 
 TYR   0.011   0.002   TYR A 202 
 ARG   0.004   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04478 (  257)
  hydrogen bonds       : angle       4.55713 (  726)
  covalent geometry    : bond        0.00364 ( 5769)
  covalent geometry    : angle       0.49519 ( 7956)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8489 (tppp) cc_final: 0.7890 (ttpp)
REVERT: A  172 MET cc_start: 0.8782 (ttt) cc_final: 0.8553 (ttt)
REVERT: B  394 LYS cc_start: 0.8664 (mttt) cc_final: 0.8305 (mttp)
REVERT: B  436 TRP cc_start: 0.8060 (m100) cc_final: 0.7637 (m100)
REVERT: B  452 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.7347 (m-30)
  outliers start: 7
  outliers final: 5
  residues processed: 73
  average time/residue: 0.4201
  time to fit residues: 38.9994
Evaluate side-chains
  71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain B residue  181 CYS
Chi-restraints excluded: chain B residue  452 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 39 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B 378 HIS ** 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 = 0.3835 r_free = 0.3835 target = 0.152625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.117568 restraints weight = 16972.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.121269 restraints weight = 9993.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 72)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.123735 restraints weight = 6979.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5769  Z= 0.169
  Angle     :  0.505   6.201   7956  Z= 0.281
  Chirality :  0.039   0.151    890
  Planarity :  0.004   0.039    864
  Dihedral  : 22.772 172.690   1062
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.38 %
    Favored  : 86.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.52 (0.37), residues: 560
  helix:  1.13 (0.40), residues: 200
  sheet: -0.49 (0.40), residues: 148
  loop :  0.46 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 204 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.013   0.001   PHE B 363 
 TYR   0.011   0.002   TYR A 202 
 ARG   0.004   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04607 (  257)
  hydrogen bonds       : angle       4.53179 (  726)
  covalent geometry    : bond        0.00388 ( 5769)
  covalent geometry    : angle       0.50521 ( 7956)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8460 (tppp) cc_final: 0.7847 (ttpp)
REVERT: A  172 MET cc_start: 0.8782 (ttt) cc_final: 0.8540 (ttt)
REVERT: B  394 LYS cc_start: 0.8649 (mttt) cc_final: 0.8326 (mttp)
REVERT: B  436 TRP cc_start: 0.8035 (m100) cc_final: 0.7644 (m100)
  outliers start: 7
  outliers final: 5
  residues processed: 73
  average time/residue: 0.4187
  time to fit residues: 38.9010
Evaluate side-chains
  70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain B residue  181 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0980
   chunk 36 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 14 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 59 optimal weight:    6.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 401 HIS ** 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 = 0.3839 r_free = 0.3839 target = 0.153110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.117912 restraints weight = 17169.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.121648 restraints weight = 10064.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.124149 restraints weight = 7002.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5769  Z= 0.145
  Angle     :  0.493   5.642   7956  Z= 0.275
  Chirality :  0.039   0.149    890
  Planarity :  0.004   0.038    864
  Dihedral  : 22.776 173.350   1062
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 12.75 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 (0.37), residues: 560
  helix:  1.30 (0.40), residues: 200
  sheet: -0.43 (0.40), residues: 148
  loop :  0.52 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 204 
 HIS   0.003   0.001   HIS B 401 
 PHE   0.015   0.001   PHE B 444 
 TYR   0.011   0.001   TYR A 202 
 ARG   0.003   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04284 (  257)
  hydrogen bonds       : angle       4.42927 (  726)
  covalent geometry    : bond        0.00329 ( 5769)
  covalent geometry    : angle       0.49344 ( 7956)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8432 (tppp) cc_final: 0.7835 (ttpp)
REVERT: A  172 MET cc_start: 0.8769 (ttt) cc_final: 0.8389 (ttt)
REVERT: B  394 LYS cc_start: 0.8620 (mttt) cc_final: 0.8331 (mttp)
  outliers start: 6
  outliers final: 5
  residues processed: 77
  average time/residue: 0.4072
  time to fit residues: 40.0527
Evaluate side-chains
  72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain B residue  181 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0870
   chunk 21 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** B 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 401 HIS ** 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 = 0.3832 r_free = 0.3832 target = 0.152518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.117306 restraints weight = 17065.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.120984 restraints weight = 10044.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.123468 restraints weight = 7018.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.2484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5769  Z= 0.153
  Angle     :  0.497   6.360   7956  Z= 0.276
  Chirality :  0.039   0.150    890
  Planarity :  0.004   0.039    864
  Dihedral  : 22.793 173.123   1062
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 13.31 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.66 (0.37), residues: 560
  helix:  1.28 (0.40), residues: 200
  sheet: -0.40 (0.40), residues: 148
  loop :  0.50 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 204 
 HIS   0.003   0.001   HIS B 367 
 PHE   0.012   0.001   PHE B 363 
 TYR   0.010   0.001   TYR A 202 
 ARG   0.004   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04353 (  257)
  hydrogen bonds       : angle       4.42683 (  726)
  covalent geometry    : bond        0.00348 ( 5769)
  covalent geometry    : angle       0.49703 ( 7956)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8465 (tppp) cc_final: 0.7863 (ttpp)
REVERT: B  394 LYS cc_start: 0.8624 (mttt) cc_final: 0.8340 (mttp)
  outliers start: 5
  outliers final: 5
  residues processed: 74
  average time/residue: 0.4125
  time to fit residues: 38.7000
Evaluate side-chains
  72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain B residue  181 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 49 optimal weight:    0.5980
   chunk 60 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0980
   chunk 19 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 401 HIS ** 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 = 0.3831 r_free = 0.3831 target = 0.152377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.117196 restraints weight = 17129.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.120808 restraints weight = 10061.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.123272 restraints weight = 7054.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5769  Z= 0.155
  Angle     :  0.503   5.979   7956  Z= 0.279
  Chirality :  0.039   0.150    890
  Planarity :  0.004   0.036    864
  Dihedral  : 22.832 173.122   1062
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 13.31 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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 (0.37), residues: 560
  helix:  1.29 (0.40), residues: 200
  sheet: -0.40 (0.40), residues: 148
  loop :  0.44 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 436 
 HIS   0.007   0.001   HIS B 401 
 PHE   0.019   0.001   PHE B 444 
 TYR   0.009   0.001   TYR A 202 
 ARG   0.003   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  257)
  hydrogen bonds       : angle       4.40472 (  726)
  covalent geometry    : bond        0.00352 ( 5769)
  covalent geometry    : angle       0.50255 ( 7956)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8408 (tppp) cc_final: 0.7939 (ttpp)
REVERT: B  394 LYS cc_start: 0.8608 (mttt) cc_final: 0.8339 (mttp)
  outliers start: 5
  outliers final: 5
  residues processed: 73
  average time/residue: 0.4206
  time to fit residues: 39.1303
Evaluate side-chains
  73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain B residue  181 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0670
   chunk 38 optimal weight:    0.2980
   chunk 58 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 11 optimal weight:    0.3980
   chunk 47 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.4718

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

Flipped N/Q/H residues before XYZ refinement:
** B 378 HIS ** 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 = 0.3850 r_free = 0.3850 target = 0.154205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.118862 restraints weight = 16950.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.122630 restraints weight = 10042.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.125081 restraints weight = 7012.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5769  Z= 0.132
  Angle     :  0.492   5.876   7956  Z= 0.271
  Chirality :  0.039   0.146    890
  Planarity :  0.004   0.057    864
  Dihedral  : 22.917 173.884   1062
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 13.68 %
    Favored  : 85.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.85 (0.38), residues: 560
  helix:  1.48 (0.40), residues: 200
  sheet: -0.30 (0.40), residues: 148
  loop :  0.54 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 438 
 HIS   0.003   0.001   HIS B 401 
 PHE   0.011   0.001   PHE A 244 
 TYR   0.009   0.001   TYR A 202 
 ARG   0.006   0.000   ARG A 179 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03872 (  257)
  hydrogen bonds       : angle       4.29401 (  726)
  covalent geometry    : bond        0.00299 ( 5769)
  covalent geometry    : angle       0.49231 ( 7956)

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

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8416 (tppp) cc_final: 0.7911 (ttpp)
REVERT: B  394 LYS cc_start: 0.8610 (mttt) cc_final: 0.8351 (mttp)
REVERT: B  401 HIS cc_start: 0.6774 (t-90) cc_final: 0.6437 (t-90)
  outliers start: 4
  outliers final: 4
  residues processed: 71
  average time/residue: 0.4289
  time to fit residues: 38.7061
Evaluate side-chains
  72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 68
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  235 MET
Chi-restraints excluded: chain A residue  355 SER
Chi-restraints excluded: chain B residue  181 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 54 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0570
   chunk 30 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 3 optimal weight:    0.2980
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
** B 378 HIS ** 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 = 0.3845 r_free = 0.3845 target = 0.153789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.118604 restraints weight = 16882.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.122276 restraints weight = 9931.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.124735 restraints weight = 6962.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5769  Z= 0.134
  Angle     :  0.495   6.541   7956  Z= 0.272
  Chirality :  0.038   0.146    890
  Planarity :  0.004   0.040    864
  Dihedral  : 22.935 173.704   1062
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 13.49 %
    Favored  : 85.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.84 (0.38), residues: 560
  helix:  1.46 (0.40), residues: 200
  sheet: -0.31 (0.40), residues: 148
  loop :  0.56 (0.48), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 438 
 HIS   0.003   0.001   HIS B 401 
 PHE   0.011   0.001   PHE A 244 
 TYR   0.009   0.001   TYR A 202 
 ARG   0.013   0.001   ARG A  14 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03916 (  257)
  hydrogen bonds       : angle       4.29049 (  726)
  covalent geometry    : bond        0.00304 ( 5769)
  covalent geometry    : angle       0.49453 ( 7956)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4137.09 seconds
wall clock time: 71 minutes 11.69 seconds (4271.69 seconds total)