Starting phenix.real_space_refine
on Wed Sep 17 17:53:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9of0_70416/09_2025/9of0_70416.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9of0_70416/09_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_70416/09_2025/9of0_70416.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9of0_70416/09_2025/9of0_70416.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9of0_70416/09_2025/9of0_70416.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9of0_70416/09_2025/9of0_70416.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.15, per 1000 atoms: 0.21
  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: 1.04
  Conformation dependent library (CDL) restraints added in 207.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 1.73
  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: 2.24

  Time building geometry restraints manager: 1.40 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:             4.740
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.060
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.900
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.270
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (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
 ARG   0.005   0.001   ARG A  14 
 TYR   0.014   0.001   TYR A 202 
 PHE   0.009   0.001   PHE B 363 
 TRP   0.003   0.001   TRP B 315 
 HIS   0.008   0.001   HIS B 401 

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

*********************** 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  : 0.360 
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: 0.2169
  time to fit residues: 18.4900
Evaluate side-chains
  60 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    0.2980
   chunk 56 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    0.2980
   chunk 58 optimal weight:    4.9990
   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  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 = 0.3845 r_free = 0.3845 target = 0.153369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.119323 restraints weight = 17239.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.123131 restraints weight = 10081.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.125690 restraints weight = 7016.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.127402 restraints weight = 5485.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.128404 restraints weight = 4653.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5769  Z= 0.163
  Angle     :  0.550   7.638   7956  Z= 0.309
  Chirality :  0.041   0.150    890
  Planarity :  0.004   0.033    864
  Dihedral  : 22.204 172.880   1062
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 11.46 %
    Favored  : 87.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.37), residues: 560
  helix:  1.13 (0.41), residues: 193
  sheet: -0.62 (0.39), residues: 156
  loop :  0.68 (0.45), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  14 
 TYR   0.015   0.001   TYR A 202 
 PHE   0.015   0.002   PHE B 363 
 TRP   0.004   0.001   TRP B 315 
 HIS   0.005   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 5769)
  covalent geometry    : angle       0.54964 ( 7956)
  hydrogen bonds       : bond        0.05025 (  257)
  hydrogen bonds       : angle       5.13252 (  726)

*********************** 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
  74 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 73
  average time/residue: 0.2076
  time to fit residues: 18.9362
Evaluate side-chains
  64 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
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 53 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 58 optimal weight:    4.9990
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 21 optimal weight:    0.0270
   chunk 46 optimal weight:    0.9990
   chunk 22 optimal weight:    0.2980
   overall best weight:    0.5438

-------------------------------------------------------------------------------
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 = 0.3839 r_free = 0.3839 target = 0.152591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.117759 restraints weight = 17262.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121544 restraints weight = 10038.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.124078 restraints weight = 6974.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.125777 restraints weight = 5474.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.126915 restraints weight = 4608.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5769  Z= 0.142
  Angle     :  0.509   6.980   7956  Z= 0.285
  Chirality :  0.040   0.148    890
  Planarity :  0.004   0.038    864
  Dihedral  : 22.417 172.749   1062
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.37), residues: 560
  helix:  1.32 (0.41), residues: 193
  sheet: -0.49 (0.39), residues: 148
  loop :  0.68 (0.45), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 428 
 TYR   0.013   0.001   TYR A 202 
 PHE   0.013   0.001   PHE A 244 
 TRP   0.013   0.001   TRP B 438 
 HIS   0.004   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5769)
  covalent geometry    : angle       0.50927 ( 7956)
  hydrogen bonds       : bond        0.04549 (  257)
  hydrogen bonds       : angle       4.76952 (  726)

*********************** 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
  71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 70
  average time/residue: 0.2062
  time to fit residues: 18.4572
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  : 0.278 
-------------------------------------------------------------------------------
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 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 19 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0980
   chunk 52 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3845 r_free = 0.3845 target = 0.153363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118406 restraints weight = 16978.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.122257 restraints weight = 10087.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.124680 restraints weight = 6983.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.126304 restraints weight = 5482.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.127395 restraints weight = 4647.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5769  Z= 0.163
  Angle     :  0.506   6.548   7956  Z= 0.282
  Chirality :  0.039   0.149    890
  Planarity :  0.004   0.044    864
  Dihedral  : 22.568 172.386   1062
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 11.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.37), residues: 560
  helix:  1.23 (0.41), residues: 194
  sheet: -0.49 (0.39), residues: 148
  loop :  0.62 (0.46), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  14 
 TYR   0.011   0.002   TYR A 202 
 PHE   0.013   0.001   PHE B 363 
 TRP   0.005   0.001   TRP B 204 
 HIS   0.004   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 5769)
  covalent geometry    : angle       0.50590 ( 7956)
  hydrogen bonds       : bond        0.04572 (  257)
  hydrogen bonds       : angle       4.68772 (  726)

*********************** 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
  73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8405 (tppp) cc_final: 0.7955 (ttpp)
REVERT: A  172 MET cc_start: 0.8793 (ttt) cc_final: 0.8581 (ttt)
REVERT: B  394 LYS cc_start: 0.8558 (mttt) cc_final: 0.8259 (mttp)
  outliers start: 5
  outliers final: 5
  residues processed: 72
  average time/residue: 0.1952
  time to fit residues: 17.6999
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  : 0.264 
-------------------------------------------------------------------------------
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3838 r_free = 0.3838 target = 0.152940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.118077 restraints weight = 16971.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121778 restraints weight = 9930.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.124224 restraints weight = 6944.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.125819 restraints weight = 5473.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.126738 restraints weight = 4648.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5769  Z= 0.165
  Angle     :  0.507   6.889   7956  Z= 0.283
  Chirality :  0.039   0.151    890
  Planarity :  0.004   0.042    864
  Dihedral  : 22.806 172.863   1062
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.37), residues: 560
  helix:  1.12 (0.40), residues: 200
  sheet: -0.60 (0.39), residues: 146
  loop :  0.44 (0.46), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  14 
 TYR   0.011   0.001   TYR A 202 
 PHE   0.014   0.001   PHE B 363 
 TRP   0.005   0.001   TRP B 204 
 HIS   0.004   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 5769)
  covalent geometry    : angle       0.50700 ( 7956)
  hydrogen bonds       : bond        0.04611 (  257)
  hydrogen bonds       : angle       4.61241 (  726)

*********************** 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
  75 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 69
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8459 (tppp) cc_final: 0.7868 (ttpp)
REVERT: B  394 LYS cc_start: 0.8572 (mttt) cc_final: 0.8304 (mttp)
  outliers start: 6
  outliers final: 5
  residues processed: 74
  average time/residue: 0.1802
  time to fit residues: 16.8997
Evaluate side-chains
  71 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 66
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 56 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   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**

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 = 0.152664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.117500 restraints weight = 17111.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.121260 restraints weight = 10054.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.123788 restraints weight = 7008.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.125312 restraints weight = 5491.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.126382 restraints weight = 4679.733|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.2328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5769  Z= 0.154
  Angle     :  0.504   6.531   7956  Z= 0.281
  Chirality :  0.039   0.150    890
  Planarity :  0.004   0.041    864
  Dihedral  : 22.825 173.147   1062
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 13.49 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.37), residues: 560
  helix:  1.28 (0.41), residues: 194
  sheet: -0.60 (0.39), residues: 146
  loop :  0.58 (0.45), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  14 
 TYR   0.012   0.001   TYR A 202 
 PHE   0.013   0.001   PHE B 363 
 TRP   0.005   0.001   TRP B 204 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 5769)
  covalent geometry    : angle       0.50437 ( 7956)
  hydrogen bonds       : bond        0.04521 (  257)
  hydrogen bonds       : angle       4.53331 (  726)

*********************** 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: 5
    poor density    : 69
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8443 (tppp) cc_final: 0.7843 (ttpp)
REVERT: B  394 LYS cc_start: 0.8586 (mttt) cc_final: 0.8323 (mttp)
  outliers start: 5
  outliers final: 4
  residues processed: 73
  average time/residue: 0.1982
  time to fit residues: 18.3017
Evaluate side-chains
  70 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 48 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0980
   chunk 59 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.3846 r_free = 0.3846 target = 0.153802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.118664 restraints weight = 16850.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.122426 restraints weight = 9916.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.124924 restraints weight = 6920.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.126583 restraints weight = 5419.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.127461 restraints weight = 4639.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2481

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= 0.132
  Angle     :  0.483   5.780   7956  Z= 0.269
  Chirality :  0.039   0.147    890
  Planarity :  0.003   0.038    864
  Dihedral  : 22.798 173.662   1062
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 14.05 %
    Favored  : 85.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.38), residues: 560
  helix:  1.36 (0.40), residues: 200
  sheet: -0.40 (0.40), residues: 148
  loop :  0.54 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 428 
 TYR   0.010   0.001   TYR A 202 
 PHE   0.018   0.001   PHE B 444 
 TRP   0.029   0.002   TRP B 438 
 HIS   0.003   0.001   HIS A 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5769)
  covalent geometry    : angle       0.48347 ( 7956)
  hydrogen bonds       : bond        0.04093 (  257)
  hydrogen bonds       : angle       4.41096 (  726)

*********************** 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
  74 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8461 (tppp) cc_final: 0.7837 (ttpp)
REVERT: B  394 LYS cc_start: 0.8572 (mttt) cc_final: 0.8328 (mttp)
  outliers start: 4
  outliers final: 4
  residues processed: 73
  average time/residue: 0.2026
  time to fit residues: 18.6971
Evaluate side-chains
  73 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 59 optimal weight:    6.9990
   chunk 56 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 46 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   chunk 28 optimal weight:    0.0870
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.153417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.118239 restraints weight = 16777.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.121956 restraints weight = 9963.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.124439 restraints weight = 6976.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.126033 restraints weight = 5486.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.127054 restraints weight = 4676.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2567

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= 0.136
  Angle     :  0.489   6.153   7956  Z= 0.271
  Chirality :  0.038   0.148    890
  Planarity :  0.004   0.037    864
  Dihedral  : 22.804 173.470   1062
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 13.86 %
    Favored  : 85.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.38), residues: 560
  helix:  1.39 (0.40), residues: 200
  sheet: -0.37 (0.40), residues: 148
  loop :  0.54 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 102 
 TYR   0.009   0.001   TYR A 202 
 PHE   0.012   0.001   PHE A 244 
 TRP   0.022   0.002   TRP B 436 
 HIS   0.002   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 5769)
  covalent geometry    : angle       0.48928 ( 7956)
  hydrogen bonds       : bond        0.04113 (  257)
  hydrogen bonds       : angle       4.38548 (  726)

*********************** 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
  76 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8438 (tppp) cc_final: 0.7903 (ttpp)
REVERT: B  394 LYS cc_start: 0.8568 (mttt) cc_final: 0.8323 (mttp)
  outliers start: 6
  outliers final: 6
  residues processed: 75
  average time/residue: 0.2019
  time to fit residues: 19.2265
Evaluate side-chains
  72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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  193 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 18 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3823 r_free = 0.3823 target = 0.151818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.116937 restraints weight = 17042.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.120528 restraints weight = 10041.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.122925 restraints weight = 7067.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.124393 restraints weight = 5557.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.125187 restraints weight = 4775.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5769  Z= 0.179
  Angle     :  0.511   6.075   7956  Z= 0.284
  Chirality :  0.039   0.149    890
  Planarity :  0.004   0.037    864
  Dihedral  : 22.851 173.144   1062
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.23 %
    Favored  : 84.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.38), residues: 560
  helix:  1.27 (0.40), residues: 200
  sheet: -0.39 (0.40), residues: 148
  loop :  0.42 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 102 
 TYR   0.009   0.002   TYR A 316 
 PHE   0.014   0.002   PHE B 444 
 TRP   0.015   0.002   TRP B 438 
 HIS   0.003   0.001   HIS A 136 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 5769)
  covalent geometry    : angle       0.51126 ( 7956)
  hydrogen bonds       : bond        0.04429 (  257)
  hydrogen bonds       : angle       4.43857 (  726)

*********************** 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: 6
    poor density    : 68
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8513 (tppp) cc_final: 0.7893 (ttpp)
REVERT: B  394 LYS cc_start: 0.8602 (mttt) cc_final: 0.8373 (mttp)
  outliers start: 6
  outliers final: 6
  residues processed: 73
  average time/residue: 0.1960
  time to fit residues: 18.0997
Evaluate side-chains
  72 residues out of total 541 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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  193 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 25 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0060
   chunk 29 optimal weight:    0.9990
   chunk 19 optimal weight:    0.1980
   chunk 23 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.3596

-------------------------------------------------------------------------------
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 = 0.3859 r_free = 0.3859 target = 0.155246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.120266 restraints weight = 16761.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.123978 restraints weight = 9790.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.126384 restraints weight = 6841.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.128015 restraints weight = 5379.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.129112 restraints weight = 4554.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5769  Z= 0.120
  Angle     :  0.476   5.786   7956  Z= 0.263
  Chirality :  0.038   0.147    890
  Planarity :  0.003   0.030    864
  Dihedral  : 22.908 174.392   1062
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  : 14.60 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.90 (0.38), residues: 560
  helix:  1.52 (0.41), residues: 200
  sheet: -0.38 (0.40), residues: 151
  loop :  0.69 (0.48), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 102 
 TYR   0.008   0.001   TYR A 202 
 PHE   0.011   0.001   PHE A 244 
 TRP   0.017   0.001   TRP B 438 
 HIS   0.003   0.001   HIS A 194 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 5769)
  covalent geometry    : angle       0.47612 ( 7956)
  hydrogen bonds       : bond        0.03561 (  257)
  hydrogen bonds       : angle       4.23754 (  726)

********************** 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: 3
    poor density    : 69
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 LYS cc_start: 0.8365 (tppp) cc_final: 0.7827 (ttpp)
REVERT: A   88 ASP cc_start: 0.7479 (m-30) cc_final: 0.7150 (t0)
REVERT: B  394 LYS cc_start: 0.8570 (mttt) cc_final: 0.8345 (mttm)
  outliers start: 3
  outliers final: 3
  residues processed: 71
  average time/residue: 0.1817
  time to fit residues: 16.3844
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  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  175 THR
Chi-restraints excluded: chain A residue  235 MET
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 60 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 7 optimal weight:    0.4980
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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**
** 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 = 0.4080 r_free = 0.4080 target = 0.169445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.134939 restraints weight = 17485.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.138934 restraints weight = 10103.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.141548 restraints weight = 7030.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.143269 restraints weight = 5496.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.144136 restraints weight = 4682.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   5769  Z= 0.217
  Angle     :  0.556   6.958   7956  Z= 0.309
  Chirality :  0.041   0.157    890
  Planarity :  0.004   0.033    864
  Dihedral  : 23.126 171.714   1062
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 14.60 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.37), residues: 560
  helix:  1.16 (0.40), residues: 200
  sheet: -0.51 (0.40), residues: 148
  loop :  0.29 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  14 
 TYR   0.013   0.002   TYR A 278 
 PHE   0.017   0.002   PHE B 363 
 TRP   0.012   0.002   TRP B 438 
 HIS   0.004   0.001   HIS B 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 5769)
  covalent geometry    : angle       0.55596 ( 7956)
  hydrogen bonds       : bond        0.04965 (  257)
  hydrogen bonds       : angle       4.49282 (  726)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2225.08 seconds
wall clock time: 38 minutes 34.28 seconds (2314.28 seconds total)