Starting phenix.real_space_refine
on Tue Feb  3 15:35:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hiu_52201/02_2026/9hiu_52201.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hiu_52201/02_2026/9hiu_52201.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hiu_52201/02_2026/9hiu_52201.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hiu_52201/02_2026/9hiu_52201.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hiu_52201/02_2026/9hiu_52201.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hiu_52201/02_2026/9hiu_52201.cif"
  }
  resolution = 3.2
  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=   0.005
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: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    2883      2.51       5
     N     741      2.21       5
     O     798      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4441
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2062
          Classifications: {'peptide': 255}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 241}
    Chain: "B"
      Number of atoms: 2293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2293
          Classifications: {'peptide': 285}
          Link IDs: {'PTRANS': 19, 'TRANS': 265}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 86
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
  Time building chain proxies: 1.13, per 1000 atoms: 0.25
  Number of scatterers: 4441
  At special positions: 0
  Unit cell: (77.18, 85.125, 70.37, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O     798      8.00
     N     741      7.00
     C    2883      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 163.1 milliseconds
  

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1054

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 4 sheets defined
      55.0% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 178 through 193
      removed outlier: 4.035A  pdb=" N   VAL A 191 " --> pdb=" O   ARG A 187 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   LYS A 192 " --> pdb=" O   GLU A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 225
    Processing helix  chain 'A' and resid 228 through 246
    Processing helix  chain 'A' and resid 251 through 269
      removed outlier: 4.386A  pdb=" N   LEU A 255 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 282
    Processing helix  chain 'A' and resid 287 through 303
    Processing helix  chain 'A' and resid 310 through 321
      removed outlier: 3.588A  pdb=" N   PHE A 314 " --> pdb=" O   THR A 310 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   GLN A 317 " --> pdb=" O   GLN A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 340
    Processing helix  chain 'A' and resid 351 through 368
    Processing helix  chain 'A' and resid 373 through 381
    Processing helix  chain 'A' and resid 387 through 400
    Processing helix  chain 'A' and resid 407 through 413
    Processing helix  chain 'A' and resid 415 through 419
    Processing helix  chain 'A' and resid 420 through 424
    Processing helix  chain 'B' and resid 45 through 56
    Processing helix  chain 'B' and resid 87 through 94
    Processing helix  chain 'B' and resid 100 through 121
    Processing helix  chain 'B' and resid 145 through 149
      removed outlier: 4.273A  pdb=" N   LEU B 148 " --> pdb=" O   ASP B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 175
    Processing helix  chain 'B' and resid 182 through 198
      removed outlier: 3.503A  pdb=" N   ILE B 186 " --> pdb=" O   THR B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 220
    Processing helix  chain 'B' and resid 247 through 252
    Processing helix  chain 'B' and resid 256 through 267
    Processing helix  chain 'B' and resid 276 through 281
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 6.066A  pdb=" N   PHE B 285 " --> pdb=" O   ALA B 282 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 12
      removed outlier: 4.192A  pdb=" N   GLU C  10 " --> pdb=" O   ASN C   6 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ALA C  12 " --> pdb=" O   SER C   8 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 11
      removed outlier: 5.639A  pdb=" N   LYS B   6 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   ARG B  22 " --> pdb=" O   LYS B   6 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   VAL B  18 " --> pdb=" O   ILE B  10 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   TYR B  19 " --> pdb=" O   LEU B  32 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASP B  68 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   GLU B  81 " --> pdb=" O   LEU B  66 " (cutoff:3.500A)
      removed outlier: 7.425A  pdb=" N   LEU B  66 " --> pdb=" O   GLU B  81 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 86
    Processing sheet with id=AA3, first strand: chain 'B' and resid 123 through 124
    Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 157
      removed outlier: 4.600A  pdb=" N   VAL B 156 " --> pdb=" O   TYR B 180 " (cutoff:3.500A)

    215 hydrogen bonds defined for protein.
    618 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.43

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1400
        1.34 -     1.46: 920
        1.46 -     1.58: 2195
        1.58 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 4547
  Sorted by residual:
  bond pdb=" CB  GLU A 385 "
       pdb=" CG  GLU A 385 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 6.02e-01
  bond pdb=" CB  PRO A 346 "
       pdb=" CG  PRO A 346 "
    ideal  model  delta    sigma   weight residual
    1.506  1.535 -0.029 3.90e-02 6.57e+02 5.62e-01
  bond pdb=" CB  GLN B 287 "
       pdb=" CG  GLN B 287 "
    ideal  model  delta    sigma   weight residual
    1.520  1.541 -0.021 3.00e-02 1.11e+03 4.81e-01
  bond pdb=" CG  GLN B 287 "
       pdb=" CD  GLN B 287 "
    ideal  model  delta    sigma   weight residual
    1.516  1.533 -0.017 2.50e-02 1.60e+03 4.44e-01
  bond pdb=" C   TRP B 227 "
       pdb=" O   TRP B 227 "
    ideal  model  delta    sigma   weight residual
    1.244  1.238  0.005 9.30e-03 1.16e+04 3.47e-01
  ... (remaining 4542 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 6021
        1.23 -     2.46: 103
        2.46 -     3.70: 32
        3.70 -     4.93: 5
        4.93 -     6.16: 2
  Bond angle restraints: 6163
  Sorted by residual:
  angle pdb=" N   GLU B  42 "
        pdb=" CA  GLU B  42 "
        pdb=" C   GLU B  42 "
      ideal   model   delta    sigma   weight residual
     114.56  110.69    3.87 1.27e+00 6.20e-01 9.30e+00
  angle pdb=" N   VAL B   7 "
        pdb=" CA  VAL B   7 "
        pdb=" C   VAL B   7 "
      ideal   model   delta    sigma   weight residual
     111.58  109.28    2.30 1.06e+00 8.90e-01 4.70e+00
  angle pdb=" CA  GLU B  42 "
        pdb=" C   GLU B  42 "
        pdb=" N   GLY B  43 "
      ideal   model   delta    sigma   weight residual
     119.26  116.88    2.38 1.14e+00 7.69e-01 4.35e+00
  angle pdb=" N   SER B 239 "
        pdb=" CA  SER B 239 "
        pdb=" C   SER B 239 "
      ideal   model   delta    sigma   weight residual
     110.68  108.04    2.64 1.39e+00 5.18e-01 3.59e+00
  angle pdb=" CB  GLN B 287 "
        pdb=" CG  GLN B 287 "
        pdb=" CD  GLN B 287 "
      ideal   model   delta    sigma   weight residual
     112.60  115.68   -3.08 1.70e+00 3.46e-01 3.28e+00
  ... (remaining 6158 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.97: 2283
       15.97 -    31.94: 343
       31.94 -    47.90: 94
       47.90 -    63.87: 25
       63.87 -    79.84: 6
  Dihedral angle restraints: 2751
    sinusoidal: 1126
      harmonic: 1625
  Sorted by residual:
  dihedral pdb=" CA  GLY B 153 "
           pdb=" C   GLY B 153 "
           pdb=" N   VAL B 154 "
           pdb=" CA  VAL B 154 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.20   15.80     0      5.00e+00 4.00e-02 9.99e+00
  dihedral pdb=" CG  ARG B 217 "
           pdb=" CD  ARG B 217 "
           pdb=" NE  ARG B 217 "
           pdb=" CZ  ARG B 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  132.33  -42.33     2      1.50e+01 4.44e-03 9.67e+00
  dihedral pdb=" CA  ASP B 206 "
           pdb=" CB  ASP B 206 "
           pdb=" CG  ASP B 206 "
           pdb=" OD1 ASP B 206 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.26   53.26     1      2.00e+01 2.50e-03 9.64e+00
  ... (remaining 2748 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 448
       0.029 -    0.058: 164
       0.058 -    0.086: 55
       0.086 -    0.115: 26
       0.115 -    0.144: 4
  Chirality restraints: 697
  Sorted by residual:
  chirality pdb=" CA  ILE B  99 "
            pdb=" N   ILE B  99 "
            pdb=" C   ILE B  99 "
            pdb=" CB  ILE B  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  VAL B 154 "
            pdb=" N   VAL B 154 "
            pdb=" C   VAL B 154 "
            pdb=" CB  VAL B 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.67e-01
  chirality pdb=" CA  ILE B  63 "
            pdb=" N   ILE B  63 "
            pdb=" C   ILE B  63 "
            pdb=" CB  ILE B  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 694 not shown)

  Planarity restraints: 775
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 252 "    0.023 5.00e-02 4.00e+02   3.56e-02 2.02e+00
        pdb=" N   PRO B 253 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO B 253 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 253 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 345 "   -0.021 5.00e-02 4.00e+02   3.19e-02 1.63e+00
        pdb=" N   PRO A 346 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 346 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 346 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B  60 "   -0.020 5.00e-02 4.00e+02   2.99e-02 1.43e+00
        pdb=" N   PRO B  61 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B  61 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B  61 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 772 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1116
        2.80 -     3.32: 4226
        3.32 -     3.85: 7821
        3.85 -     4.37: 9310
        4.37 -     4.90: 15689
  Nonbonded interactions: 38162
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 251 "
            pdb=" OH  TYR A 286 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OE1 GLU A 220 "
            pdb=" NH1 ARG C   5 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OD1 ASP A 216 "
            pdb=" OG  SER A 408 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR A 238 "
            pdb=" O   LEU A 306 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OD1 ASP B 223 "
            pdb=" N   GLU B 224 "
     model   vdw
     2.300 3.120
  ... (remaining 38157 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.480
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  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:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
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      :  0.002   0.029   4547  Z= 0.093
  Angle     :  0.457   6.159   6163  Z= 0.241
  Chirality :  0.037   0.144    697
  Planarity :  0.004   0.036    775
  Dihedral  : 16.793  79.839   1697
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 21.47 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.38), residues: 539
  helix:  1.92 (0.33), residues: 280
  sheet: -1.13 (0.95), residues: 24
  loop : -0.38 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  36 
 TYR   0.005   0.001   TYR A 413 
 PHE   0.013   0.001   PHE B 152 
 TRP   0.009   0.001   TRP A 372 
 HIS   0.006   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 4547)
  covalent geometry    : angle       0.45690 ( 6163)
  hydrogen bonds       : bond        0.13309 (  215)
  hydrogen bonds       : angle       6.04361 (  618)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  188 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7487 (tt0)
REVERT: A  202 LYS cc_start: 0.8249 (mmtm) cc_final: 0.7750 (mttt)
REVERT: A  293 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7346 (mtp-110)
REVERT: A  326 ASN cc_start: 0.8015 (t0) cc_final: 0.7534 (t0)
REVERT: A  334 MET cc_start: 0.7964 (tpp) cc_final: 0.7655 (mmm)
REVERT: A  400 LYS cc_start: 0.8414 (mttt) cc_final: 0.7896 (mtmt)
REVERT: B   22 ARG cc_start: 0.7966 (mtp-110) cc_final: 0.7736 (mtm110)
REVERT: B   29 VAL cc_start: 0.8450 (t) cc_final: 0.8169 (p)
REVERT: B   42 GLU cc_start: 0.7259 (mm-30) cc_final: 0.6715 (mm-30)
REVERT: B  148 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8375 (tp)
REVERT: B  278 LYS cc_start: 0.8082 (ttmp) cc_final: 0.7492 (tttt)
  outliers start: 6
  outliers final: 4
  residues processed: 93
  average time/residue: 0.1019
  time to fit residues: 11.2253
Evaluate side-chains
  90 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  178 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.123027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.103432 restraints weight = 5264.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.51
r_work: 0.2878 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.0971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   4547  Z= 0.170
  Angle     :  0.530   5.922   6163  Z= 0.268
  Chirality :  0.040   0.148    697
  Planarity :  0.004   0.035    775
  Dihedral  :  5.665  56.349    607
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.06 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.12 (0.38), residues: 539
  helix:  1.75 (0.32), residues: 292
  sheet: -1.11 (0.94), residues: 24
  loop : -0.36 (0.43), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  36 
 TYR   0.011   0.001   TYR A 347 
 PHE   0.017   0.002   PHE B 152 
 TRP   0.012   0.001   TRP A 372 
 HIS   0.006   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 ( 4547)
  covalent geometry    : angle       0.52980 ( 6163)
  hydrogen bonds       : bond        0.03769 (  215)
  hydrogen bonds       : angle       4.67485 (  618)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A  188 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7460 (tt0)
REVERT: A  202 LYS cc_start: 0.8334 (mmtm) cc_final: 0.7765 (mttt)
REVERT: A  370 GLN cc_start: 0.7756 (mt0) cc_final: 0.6823 (mm-40)
REVERT: A  400 LYS cc_start: 0.8496 (mttt) cc_final: 0.8055 (mtmt)
REVERT: B   29 VAL cc_start: 0.8443 (t) cc_final: 0.8176 (p)
REVERT: B  131 GLN cc_start: 0.8116 (mt0) cc_final: 0.7628 (mp10)
REVERT: B  148 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8389 (tp)
REVERT: B  178 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7449 (mmtt)
REVERT: B  278 LYS cc_start: 0.8040 (ttmp) cc_final: 0.7509 (ttpt)
  outliers start: 11
  outliers final: 8
  residues processed: 92
  average time/residue: 0.0926
  time to fit residues: 10.2536
Evaluate side-chains
  88 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  252 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0770
   chunk 31 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7538

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.124397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.106272 restraints weight = 5204.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.40
r_work: 0.2935 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.0978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4547  Z= 0.105
  Angle     :  0.461   5.998   6163  Z= 0.235
  Chirality :  0.039   0.146    697
  Planarity :  0.004   0.036    775
  Dihedral  :  4.399  49.434    597
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 21.47 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.38), residues: 539
  helix:  1.99 (0.32), residues: 288
  sheet: -0.91 (0.92), residues: 24
  loop : -0.31 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  36 
 TYR   0.008   0.001   TYR A 347 
 PHE   0.014   0.001   PHE B 152 
 TRP   0.009   0.001   TRP A 372 
 HIS   0.006   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 4547)
  covalent geometry    : angle       0.46149 ( 6163)
  hydrogen bonds       : bond        0.03149 (  215)
  hydrogen bonds       : angle       4.45441 (  618)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A  188 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7518 (tt0)
REVERT: A  202 LYS cc_start: 0.8297 (mmtm) cc_final: 0.7774 (mttt)
REVERT: A  370 GLN cc_start: 0.7748 (mt0) cc_final: 0.6861 (mm-40)
REVERT: A  400 LYS cc_start: 0.8482 (mttt) cc_final: 0.8039 (mtmt)
REVERT: B   22 ARG cc_start: 0.8013 (mtp-110) cc_final: 0.7517 (mtm110)
REVERT: B   29 VAL cc_start: 0.8419 (t) cc_final: 0.8165 (p)
REVERT: B  131 GLN cc_start: 0.8131 (mt0) cc_final: 0.7655 (mp10)
REVERT: B  178 LYS cc_start: 0.8191 (mmmt) cc_final: 0.7460 (mmtt)
REVERT: B  268 HIS cc_start: 0.8562 (OUTLIER) cc_final: 0.7822 (m-70)
REVERT: B  278 LYS cc_start: 0.7979 (ttmp) cc_final: 0.7420 (ttpt)
  outliers start: 15
  outliers final: 10
  residues processed: 99
  average time/residue: 0.0964
  time to fit residues: 11.5514
Evaluate side-chains
  93 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  268 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 40 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 395 HIS
B 265 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.120520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.101557 restraints weight = 5264.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 1.49
r_work: 0.2867 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2722 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4547  Z= 0.184
  Angle     :  0.534   5.860   6163  Z= 0.269
  Chirality :  0.041   0.152    697
  Planarity :  0.004   0.039    775
  Dihedral  :  4.249  19.593    595
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 21.06 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.37), residues: 539
  helix:  1.76 (0.32), residues: 287
  sheet: -0.89 (0.92), residues: 24
  loop : -0.35 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 126 
 TYR   0.012   0.001   TYR A 347 
 PHE   0.018   0.002   PHE B 152 
 TRP   0.013   0.001   TRP A 372 
 HIS   0.005   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 4547)
  covalent geometry    : angle       0.53430 ( 6163)
  hydrogen bonds       : bond        0.03588 (  215)
  hydrogen bonds       : angle       4.62637 (  618)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.174 
Fit side-chains
REVERT: A  188 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7405 (tt0)
REVERT: A  202 LYS cc_start: 0.8340 (mmtm) cc_final: 0.7700 (mttt)
REVERT: A  250 ARG cc_start: 0.8297 (ttm170) cc_final: 0.7867 (ttm170)
REVERT: A  370 GLN cc_start: 0.7627 (mt0) cc_final: 0.6731 (mm-40)
REVERT: A  400 LYS cc_start: 0.8495 (mttt) cc_final: 0.8045 (mtmt)
REVERT: B    2 GLU cc_start: 0.6297 (mp0) cc_final: 0.5807 (mp0)
REVERT: B   29 VAL cc_start: 0.8444 (t) cc_final: 0.8170 (p)
REVERT: B   84 HIS cc_start: 0.7274 (t70) cc_final: 0.7035 (t-170)
REVERT: B   86 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8176 (p0)
REVERT: B  131 GLN cc_start: 0.8144 (mt0) cc_final: 0.7554 (mp10)
REVERT: B  148 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8271 (tp)
REVERT: B  278 LYS cc_start: 0.7997 (ttmp) cc_final: 0.7455 (ttpt)
  outliers start: 16
  outliers final: 12
  residues processed: 101
  average time/residue: 0.0961
  time to fit residues: 11.6653
Evaluate side-chains
  95 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  252 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 395 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 = 0.3242 r_free = 0.3242 target = 0.120396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.101464 restraints weight = 5291.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.49
r_work: 0.2865 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   4547  Z= 0.185
  Angle     :  0.537   5.881   6163  Z= 0.271
  Chirality :  0.041   0.151    697
  Planarity :  0.004   0.041    775
  Dihedral  :  4.319  19.826    595
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 21.06 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.37), residues: 539
  helix:  1.67 (0.31), residues: 287
  sheet: -0.84 (0.95), residues: 24
  loop : -0.46 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  22 
 TYR   0.012   0.001   TYR A 347 
 PHE   0.018   0.002   PHE B 152 
 TRP   0.014   0.001   TRP A 372 
 HIS   0.005   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 ( 4547)
  covalent geometry    : angle       0.53660 ( 6163)
  hydrogen bonds       : bond        0.03561 (  215)
  hydrogen bonds       : angle       4.64355 (  618)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.159 
Fit side-chains
REVERT: A  188 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7486 (tt0)
REVERT: A  200 MET cc_start: 0.8448 (mmt) cc_final: 0.8048 (mmt)
REVERT: A  202 LYS cc_start: 0.8353 (mmtm) cc_final: 0.7771 (mttt)
REVERT: A  370 GLN cc_start: 0.7653 (mt0) cc_final: 0.6793 (mm-40)
REVERT: A  400 LYS cc_start: 0.8518 (mttt) cc_final: 0.8071 (mtmt)
REVERT: B    2 GLU cc_start: 0.6386 (mp0) cc_final: 0.5920 (mp0)
REVERT: B   29 VAL cc_start: 0.8438 (t) cc_final: 0.8167 (p)
REVERT: B   84 HIS cc_start: 0.7289 (t70) cc_final: 0.7061 (t-170)
REVERT: B   86 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8187 (p0)
REVERT: B  148 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8273 (tp)
REVERT: B  278 LYS cc_start: 0.7978 (ttmp) cc_final: 0.7449 (ttpt)
  outliers start: 18
  outliers final: 12
  residues processed: 106
  average time/residue: 0.1040
  time to fit residues: 13.1402
Evaluate side-chains
  99 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  178 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 1 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0060
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   overall best weight:    1.0800

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 395 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.122184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.103310 restraints weight = 5346.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 1.50
r_work: 0.2893 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2749 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4547  Z= 0.126
  Angle     :  0.492   5.983   6163  Z= 0.249
  Chirality :  0.039   0.149    697
  Planarity :  0.005   0.083    775
  Dihedral  :  4.154  20.042    595
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 20.86 %
    Favored  : 74.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.37), residues: 539
  helix:  1.99 (0.32), residues: 280
  sheet: -0.78 (0.94), residues: 24
  loop : -0.56 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 122 
 TYR   0.010   0.001   TYR A 347 
 PHE   0.015   0.001   PHE B 152 
 TRP   0.013   0.001   TRP A 372 
 HIS   0.006   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4547)
  covalent geometry    : angle       0.49172 ( 6163)
  hydrogen bonds       : bond        0.03229 (  215)
  hydrogen bonds       : angle       4.50249 (  618)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  188 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7468 (tt0)
REVERT: A  200 MET cc_start: 0.8457 (mmt) cc_final: 0.8042 (mmt)
REVERT: A  202 LYS cc_start: 0.8331 (mmtm) cc_final: 0.7691 (mttt)
REVERT: A  218 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8474 (mt)
REVERT: A  370 GLN cc_start: 0.7623 (mt0) cc_final: 0.6849 (mm-40)
REVERT: A  400 LYS cc_start: 0.8513 (mttt) cc_final: 0.8065 (mtmt)
REVERT: B    2 GLU cc_start: 0.6294 (mp0) cc_final: 0.5804 (mp0)
REVERT: B   22 ARG cc_start: 0.8033 (mtp-110) cc_final: 0.7473 (mtm110)
REVERT: B   29 VAL cc_start: 0.8440 (t) cc_final: 0.8177 (p)
REVERT: B   84 HIS cc_start: 0.7265 (t70) cc_final: 0.7016 (t-170)
REVERT: B   86 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8141 (p0)
REVERT: B  131 GLN cc_start: 0.8128 (mt0) cc_final: 0.7569 (mp10)
REVERT: B  148 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8320 (tp)
REVERT: B  278 LYS cc_start: 0.7914 (ttmp) cc_final: 0.7394 (ttpt)
  outliers start: 21
  outliers final: 15
  residues processed: 110
  average time/residue: 0.1000
  time to fit residues: 13.2812
Evaluate side-chains
  101 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  252 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 35 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 395 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 = 0.3297 r_free = 0.3297 target = 0.124885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.106369 restraints weight = 5268.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 1.41
r_work: 0.2920 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2775 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4547  Z= 0.109
  Angle     :  0.475   6.024   6163  Z= 0.241
  Chirality :  0.039   0.147    697
  Planarity :  0.005   0.081    775
  Dihedral  :  4.033  19.744    595
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.86 %
    Favored  : 75.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.37), residues: 539
  helix:  2.13 (0.32), residues: 280
  sheet: -0.73 (0.93), residues: 24
  loop : -0.53 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 122 
 TYR   0.008   0.001   TYR A 347 
 PHE   0.014   0.001   PHE B 152 
 TRP   0.011   0.001   TRP A 372 
 HIS   0.006   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 4547)
  covalent geometry    : angle       0.47482 ( 6163)
  hydrogen bonds       : bond        0.03031 (  215)
  hydrogen bonds       : angle       4.40058 (  618)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  188 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7594 (tt0)
REVERT: A  202 LYS cc_start: 0.8319 (mmtm) cc_final: 0.7728 (mttt)
REVERT: A  218 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8446 (mt)
REVERT: A  334 MET cc_start: 0.8242 (tpp) cc_final: 0.7995 (mmm)
REVERT: A  370 GLN cc_start: 0.7709 (mt0) cc_final: 0.6985 (mm-40)
REVERT: A  400 LYS cc_start: 0.8577 (mttt) cc_final: 0.8170 (mtmt)
REVERT: B    2 GLU cc_start: 0.6269 (mp0) cc_final: 0.5781 (mp0)
REVERT: B   22 ARG cc_start: 0.8095 (mtp-110) cc_final: 0.7603 (mtm110)
REVERT: B   29 VAL cc_start: 0.8438 (t) cc_final: 0.8210 (p)
REVERT: B   86 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8202 (p0)
REVERT: B  131 GLN cc_start: 0.8161 (mt0) cc_final: 0.7674 (mp10)
REVERT: B  148 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8331 (tp)
REVERT: B  278 LYS cc_start: 0.7997 (ttmp) cc_final: 0.7479 (ttpt)
  outliers start: 18
  outliers final: 14
  residues processed: 103
  average time/residue: 0.0986
  time to fit residues: 12.2511
Evaluate side-chains
  102 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  252 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 395 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 = 0.3286 r_free = 0.3286 target = 0.123979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.104613 restraints weight = 5240.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 1.49
r_work: 0.2899 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4547  Z= 0.130
  Angle     :  0.494   5.950   6163  Z= 0.250
  Chirality :  0.039   0.148    697
  Planarity :  0.005   0.081    775
  Dihedral  :  4.069  19.436    595
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 20.86 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.25 (0.37), residues: 539
  helix:  2.02 (0.32), residues: 282
  sheet: -0.73 (0.94), residues: 24
  loop : -0.48 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 122 
 TYR   0.010   0.001   TYR A 347 
 PHE   0.016   0.001   PHE B 152 
 TRP   0.012   0.001   TRP A 372 
 HIS   0.006   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4547)
  covalent geometry    : angle       0.49396 ( 6163)
  hydrogen bonds       : bond        0.03174 (  215)
  hydrogen bonds       : angle       4.42846 (  618)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  188 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7553 (tt0)
REVERT: A  202 LYS cc_start: 0.8327 (mmtm) cc_final: 0.7712 (mttt)
REVERT: A  370 GLN cc_start: 0.7653 (mt0) cc_final: 0.6863 (mm-40)
REVERT: A  400 LYS cc_start: 0.8518 (mttt) cc_final: 0.8077 (mtmt)
REVERT: B    2 GLU cc_start: 0.6424 (mp0) cc_final: 0.5931 (mp0)
REVERT: B   29 VAL cc_start: 0.8442 (t) cc_final: 0.8186 (p)
REVERT: B   86 ASP cc_start: 0.8520 (OUTLIER) cc_final: 0.8118 (p0)
REVERT: B  131 GLN cc_start: 0.8172 (mt0) cc_final: 0.7615 (mp10)
REVERT: B  148 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8306 (tp)
REVERT: B  278 LYS cc_start: 0.7939 (ttmp) cc_final: 0.7388 (ttpt)
  outliers start: 17
  outliers final: 15
  residues processed: 100
  average time/residue: 0.1017
  time to fit residues: 12.1905
Evaluate side-chains
  103 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue   94 SER
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  252 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 34 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0270
   chunk 2 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0970
   chunk 24 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 395 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 = 0.3313 r_free = 0.3313 target = 0.125970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.107281 restraints weight = 5235.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3079 rms_B_bonded: 1.48
r_work: 0.2949 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4547  Z= 0.096
  Angle     :  0.464   6.058   6163  Z= 0.236
  Chirality :  0.038   0.146    697
  Planarity :  0.005   0.073    775
  Dihedral  :  3.872  18.541    595
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.27 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.37), residues: 539
  helix:  2.21 (0.32), residues: 280
  sheet: -0.69 (0.92), residues: 24
  loop : -0.49 (0.41), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 122 
 TYR   0.006   0.001   TYR A 347 
 PHE   0.014   0.001   PHE B 152 
 TRP   0.010   0.001   TRP A 372 
 HIS   0.006   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 4547)
  covalent geometry    : angle       0.46434 ( 6163)
  hydrogen bonds       : bond        0.02863 (  215)
  hydrogen bonds       : angle       4.27356 (  618)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.189 
Fit side-chains
REVERT: A  188 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7466 (tt0)
REVERT: A  202 LYS cc_start: 0.8361 (mmtm) cc_final: 0.7835 (mttt)
REVERT: A  218 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8362 (mt)
REVERT: A  300 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7967 (ttmm)
REVERT: A  334 MET cc_start: 0.8089 (tpp) cc_final: 0.7861 (mmm)
REVERT: A  370 GLN cc_start: 0.7623 (mt0) cc_final: 0.6827 (mm-40)
REVERT: A  400 LYS cc_start: 0.8466 (mttt) cc_final: 0.8016 (mtmt)
REVERT: B    2 GLU cc_start: 0.6436 (mp0) cc_final: 0.5934 (mp0)
REVERT: B   22 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7549 (mtm110)
REVERT: B   29 VAL cc_start: 0.8488 (t) cc_final: 0.8225 (p)
REVERT: B   86 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8022 (p0)
REVERT: B  131 GLN cc_start: 0.8145 (mt0) cc_final: 0.7588 (mp10)
REVERT: B  148 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8299 (tp)
REVERT: B  278 LYS cc_start: 0.7917 (ttmp) cc_final: 0.7410 (ttpt)
  outliers start: 17
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1005
  time to fit residues: 12.2173
Evaluate side-chains
  104 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  397 THR
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  252 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    6.9990
   chunk 6 optimal weight:    0.8980
   chunk 47 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0970
   chunk 52 optimal weight:    0.2980
   chunk 13 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.127374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.108800 restraints weight = 5226.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 1.47
r_work: 0.2971 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4547  Z= 0.091
  Angle     :  0.461   6.068   6163  Z= 0.233
  Chirality :  0.038   0.145    697
  Planarity :  0.005   0.070    775
  Dihedral  :  3.764  17.961    595
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 21.68 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.38), residues: 539
  helix:  2.25 (0.32), residues: 282
  sheet: -0.63 (0.92), residues: 24
  loop : -0.38 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 378 
 TYR   0.005   0.001   TYR A 413 
 PHE   0.014   0.001   PHE B 152 
 TRP   0.010   0.001   TRP A 372 
 HIS   0.006   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 4547)
  covalent geometry    : angle       0.46072 ( 6163)
  hydrogen bonds       : bond        0.02744 (  215)
  hydrogen bonds       : angle       4.20350 (  618)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A  188 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7413 (tt0)
REVERT: A  202 LYS cc_start: 0.8339 (mmtm) cc_final: 0.7828 (mttt)
REVERT: A  218 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8355 (mt)
REVERT: A  293 ARG cc_start: 0.7770 (ttm110) cc_final: 0.7382 (mtp-110)
REVERT: A  300 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7910 (ttmm)
REVERT: A  347 TYR cc_start: 0.8621 (m-80) cc_final: 0.7651 (m-80)
REVERT: A  370 GLN cc_start: 0.7580 (mt0) cc_final: 0.6788 (mm-40)
REVERT: A  400 LYS cc_start: 0.8446 (mttt) cc_final: 0.8006 (mtmt)
REVERT: A  424 LEU cc_start: 0.8142 (mt) cc_final: 0.7845 (mt)
REVERT: B    2 GLU cc_start: 0.6447 (mp0) cc_final: 0.5920 (mp0)
REVERT: B   22 ARG cc_start: 0.8038 (mtp-110) cc_final: 0.7519 (mtm110)
REVERT: B   29 VAL cc_start: 0.8520 (t) cc_final: 0.8269 (p)
REVERT: B   86 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7971 (p0)
REVERT: B  131 GLN cc_start: 0.8081 (mt0) cc_final: 0.7558 (mp10)
REVERT: B  148 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8345 (tp)
REVERT: B  278 LYS cc_start: 0.7891 (ttmp) cc_final: 0.7357 (ttpt)
  outliers start: 15
  outliers final: 12
  residues processed: 103
  average time/residue: 0.0892
  time to fit residues: 11.1544
Evaluate side-chains
  105 residues out of total 489 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  274 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  422 SER
Chi-restraints excluded: chain B residue    1 MET
Chi-restraints excluded: chain B residue   18 VAL
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain B residue   49 ILE
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue   86 ASP
Chi-restraints excluded: chain B residue  148 LEU
Chi-restraints excluded: chain B residue  178 LYS
Chi-restraints excluded: chain B residue  252 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0870
   chunk 19 optimal weight:    0.0270
   chunk 36 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.5816

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

Flipped N/Q/H residues before XYZ refinement:
** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 395 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 = 0.3322 r_free = 0.3322 target = 0.126790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.108124 restraints weight = 5250.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 1.48
r_work: 0.2962 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   4547  Z= 0.098
  Angle     :  0.483   8.211   6163  Z= 0.241
  Chirality :  0.038   0.146    697
  Planarity :  0.005   0.070    775
  Dihedral  :  3.785  17.816    595
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 21.27 %
    Favored  : 75.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.37), residues: 539
  helix:  2.25 (0.32), residues: 282
  sheet: -0.68 (0.92), residues: 24
  loop : -0.35 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 378 
 TYR   0.005   0.001   TYR A 413 
 PHE   0.014   0.001   PHE B 152 
 TRP   0.011   0.001   TRP A 372 
 HIS   0.006   0.001   HIS A 296 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 4547)
  covalent geometry    : angle       0.48273 ( 6163)
  hydrogen bonds       : bond        0.02833 (  215)
  hydrogen bonds       : angle       4.15728 (  618)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1253.94 seconds
wall clock time: 22 minutes 13.41 seconds (1333.41 seconds total)