Starting phenix.real_space_refine
on Tue Feb 11 07:44:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8efp_28087/02_2025/8efp_28087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8efp_28087/02_2025/8efp_28087.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8efp_28087/02_2025/8efp_28087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8efp_28087/02_2025/8efp_28087.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8efp_28087/02_2025/8efp_28087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8efp_28087/02_2025/8efp_28087.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
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      13      5.16       5
     C    2977      2.51       5
     N     808      2.21       5
     O     907      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 4705
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 1976
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1976
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 18, 'TRANS': 224}
    Chain: "C"
      Number of atoms: 2729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2729
          Classifications: {'peptide': 351}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 11, 'TRANS': 339}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 105
          Unresolved non-hydrogen angles: 127
          Unresolved non-hydrogen dihedrals: 85
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 59
  Time building chain proxies: 3.27, per 1000 atoms: 0.70
  Number of scatterers: 4705
  At special positions: 0
  Unit cell: (76.176, 74.52, 113.436, 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      13     16.00
     O     907      8.00
     N     808      7.00
     C    2977      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 531.6 milliseconds
  

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1150

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 3 sheets defined
      40.2% alpha, 6.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'B' and resid 22 through 37
    Processing helix  chain 'B' and resid 43 through 56
    Processing helix  chain 'B' and resid 217 through 222
      removed outlier: 3.524A  pdb=" N   PHE B 220 " --> pdb=" O   PRO B 217 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   SER B 221 " --> pdb=" O   GLU B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 249
    Processing helix  chain 'C' and resid 4 through 18
      removed outlier: 3.527A  pdb=" N   ALA C  18 " --> pdb=" O   LYS C  14 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 57 through 62
    Processing helix  chain 'C' and resid 68 through 77
      removed outlier: 4.179A  pdb=" N   ASP C  74 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 126 through 136
    Processing helix  chain 'C' and resid 143 through 150
      removed outlier: 3.660A  pdb=" N   ARG C 147 " --> pdb=" O   PRO C 143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 180 through 186
      removed outlier: 4.258A  pdb=" N   HIS C 186 " --> pdb=" O   ILE C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 262
    Processing helix  chain 'C' and resid 264 through 279
    Processing helix  chain 'C' and resid 281 through 299
    Processing helix  chain 'C' and resid 307 through 315
    Processing helix  chain 'C' and resid 322 through 339
    Processing helix  chain 'C' and resid 342 through 353
    Processing helix  chain 'C' and resid 354 through 369
    Processing helix  chain 'C' and resid 371 through 376
    Processing helix  chain 'C' and resid 383 through 404
    Processing sheet with id=AA1, first strand: chain 'B' and resid 82 through 83
      removed outlier: 6.594A  pdb=" N   LEU B  82 " --> pdb=" O   ASN B 103 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   LEU B 102 " --> pdb=" O   SER B 123 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 161 through 163
      removed outlier: 3.521A  pdb=" N   CYS B 183 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
      removed outlier: 5.824A  pdb=" N   LYS B 204 " --> pdb=" O   ARG B 228 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   ASN B 230 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   TYR B 206 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 22 through 24
      removed outlier: 3.853A  pdb=" N   SER C 206 " --> pdb=" O   LEU C 162 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   GLU C 160 " --> pdb=" O   ARG C 208 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   LYS C 210 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 5.414A  pdb=" N   VAL C 158 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)

    177 hydrogen bonds defined for protein.
    522 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: 1.17

  Time building geometry restraints manager: 1.36 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 959
        1.33 -     1.45: 1038
        1.45 -     1.57: 2773
        1.57 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 4790
  Sorted by residual:
  bond pdb=" N   LEU C 263 "
       pdb=" CA  LEU C 263 "
    ideal  model  delta    sigma   weight residual
    1.456  1.499 -0.043 1.14e-02 7.69e+03 1.42e+01
  bond pdb=" N   ASP C 173 "
       pdb=" CA  ASP C 173 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.029 9.70e-03 1.06e+04 9.06e+00
  bond pdb=" N   LYS C 177 "
       pdb=" CA  LYS C 177 "
    ideal  model  delta    sigma   weight residual
    1.453  1.490 -0.037 1.26e-02 6.30e+03 8.83e+00
  bond pdb=" CA  LYS C 177 "
       pdb=" C   LYS C 177 "
    ideal  model  delta    sigma   weight residual
    1.519  1.534 -0.016 5.30e-03 3.56e+04 8.82e+00
  bond pdb=" N   THR C 264 "
       pdb=" CA  THR C 264 "
    ideal  model  delta    sigma   weight residual
    1.454  1.494 -0.039 1.33e-02 5.65e+03 8.68e+00
  ... (remaining 4785 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.02: 6360
        4.02 -     8.05: 109
        8.05 -    12.07: 15
       12.07 -    16.09: 5
       16.09 -    20.12: 6
  Bond angle restraints: 6495
  Sorted by residual:
  angle pdb=" C   PHE B  98 "
        pdb=" CA  PHE B  98 "
        pdb=" CB  PHE B  98 "
      ideal   model   delta    sigma   weight residual
     113.37   93.25   20.12 1.61e+00 3.86e-01 1.56e+02
  angle pdb=" N   SER C 180 "
        pdb=" CA  SER C 180 "
        pdb=" C   SER C 180 "
      ideal   model   delta    sigma   weight residual
     112.94   95.36   17.58 1.41e+00 5.03e-01 1.56e+02
  angle pdb=" N   PRO C 215 "
        pdb=" CA  PRO C 215 "
        pdb=" C   PRO C 215 "
      ideal   model   delta    sigma   weight residual
     111.19   94.15   17.04 1.57e+00 4.06e-01 1.18e+02
  angle pdb=" N   GLN C 194 "
        pdb=" CA  GLN C 194 "
        pdb=" C   GLN C 194 "
      ideal   model   delta    sigma   weight residual
     108.23   89.70   18.53 1.72e+00 3.38e-01 1.16e+02
  angle pdb=" N   ARG C 195 "
        pdb=" CA  ARG C 195 "
        pdb=" C   ARG C 195 "
      ideal   model   delta    sigma   weight residual
     108.76   93.60   15.16 1.69e+00 3.50e-01 8.05e+01
  ... (remaining 6490 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.18: 2474
       18.18 -    36.37: 360
       36.37 -    54.55: 101
       54.55 -    72.73: 11
       72.73 -    90.91: 8
  Dihedral angle restraints: 2954
    sinusoidal: 1197
      harmonic: 1757
  Sorted by residual:
  dihedral pdb=" C   PHE B  98 "
           pdb=" N   PHE B  98 "
           pdb=" CA  PHE B  98 "
           pdb=" CB  PHE B  98 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -97.68  -24.92     0      2.50e+00 1.60e-01 9.94e+01
  dihedral pdb=" C   VAL C 213 "
           pdb=" N   VAL C 213 "
           pdb=" CA  VAL C 213 "
           pdb=" CB  VAL C 213 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -103.01  -18.99     0      2.50e+00 1.60e-01 5.77e+01
  dihedral pdb=" C   GLN C 194 "
           pdb=" N   GLN C 194 "
           pdb=" CA  GLN C 194 "
           pdb=" CB  GLN C 194 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -104.35  -18.25     0      2.50e+00 1.60e-01 5.33e+01
  ... (remaining 2951 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.147: 709
       0.147 -    0.293: 30
       0.293 -    0.440: 3
       0.440 -    0.586: 0
       0.586 -    0.733: 5
  Chirality restraints: 747
  Sorted by residual:
  chirality pdb=" CA  VAL C 213 "
            pdb=" N   VAL C 213 "
            pdb=" C   VAL C 213 "
            pdb=" CB  VAL C 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    3.17   -0.73 2.00e-01 2.50e+01 1.34e+01
  chirality pdb=" CA  TYR C 176 "
            pdb=" N   TYR C 176 "
            pdb=" C   TYR C 176 "
            pdb=" CB  TYR C 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.82    0.69 2.00e-01 2.50e+01 1.18e+01
  chirality pdb=" CA  TRP C 179 "
            pdb=" N   TRP C 179 "
            pdb=" C   TRP C 179 "
            pdb=" CB  TRP C 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    3.13   -0.62 2.00e-01 2.50e+01 9.68e+00
  ... (remaining 744 not shown)

  Planarity restraints: 848
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B  95 "   -0.024 2.00e-02 2.50e+03   4.63e-02 2.14e+01
        pdb=" C   LEU B  95 "    0.080 2.00e-02 2.50e+03
        pdb=" O   LEU B  95 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   PRO B  96 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  37 "   -0.013 2.00e-02 2.50e+03   2.68e-02 7.18e+00
        pdb=" C   ASN B  37 "    0.046 2.00e-02 2.50e+03
        pdb=" O   ASN B  37 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   SER B  38 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE C 398 "   -0.011 2.00e-02 2.50e+03   2.19e-02 4.80e+00
        pdb=" C   ILE C 398 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ILE C 398 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU C 399 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 845 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 64
        2.51 -     3.10: 3894
        3.10 -     3.70: 7797
        3.70 -     4.30: 10845
        4.30 -     4.90: 16554
  Nonbonded interactions: 39154
  Sorted by model distance:
  nonbonded pdb=" O   TRP C 179 "
            pdb=" CG  TRP C 179 "
     model   vdw
     1.908 3.260
  nonbonded pdb=" O   TRP C 179 "
            pdb=" CD2 TRP C 179 "
     model   vdw
     2.113 3.260
  nonbonded pdb=" N   VAL C 213 "
            pdb=" O   VAL C 213 "
     model   vdw
     2.191 2.496
  nonbonded pdb=" OG1 THR C 151 "
            pdb=" NH1 ARG C 152 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" O   LYS C 359 "
            pdb=" N   VAL C 362 "
     model   vdw
     2.258 3.120
  ... (remaining 39149 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     14.880
  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:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6341
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      :  0.006   0.052   4790  Z= 0.385
  Angle     :  1.460  20.115   6495  Z= 0.886
  Chirality :  0.085   0.733    747
  Planarity :  0.007   0.067    848
  Dihedral  : 18.607  90.911   1804
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 33.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.31 %
    Favored  : 86.69 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 31.03 %
    Favored  : 65.90 %
  Cbeta Deviations :  1.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.26 (0.29), residues: 586
  helix: -2.31 (0.31), residues: 203
  sheet: -3.30 (0.61), residues: 49
  loop : -3.21 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP B  34 
 HIS   0.006   0.001   HIS B  26 
 PHE   0.021   0.003   PHE B  98 
 TYR   0.027   0.002   TYR C 129 
 ARG   0.008   0.001   ARG C 124 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  207 TYR cc_start: 0.7911 (m-10) cc_final: 0.7477 (m-10)
REVERT: C  275 LEU cc_start: 0.8243 (pp) cc_final: 0.7875 (pp)
  outliers start: 16
  outliers final: 4
  residues processed: 77
  average time/residue: 0.1897
  time to fit residues: 18.4524
Evaluate side-chains
  50 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  105 ASP
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain C residue   86 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 44 optimal weight:   20.0000
   chunk 24 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 23 optimal weight:    0.0270
   chunk 46 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 34 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.9040

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

Flipped N/Q/H residues before XYZ refinement:
B  78 HIS
B  87 ASN
** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 ASN
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 257 GLN
C 186 HIS
** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.083076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.065257 restraints weight = 28669.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.066504 restraints weight = 20151.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.067621 restraints weight = 15743.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   4790  Z= 0.263
  Angle     :  0.888  11.610   6495  Z= 0.446
  Chirality :  0.047   0.162    747
  Planarity :  0.006   0.067    848
  Dihedral  :  7.617  59.333    647
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 22.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.92 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 29.69 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.89 (0.30), residues: 586
  helix: -1.86 (0.31), residues: 212
  sheet: -3.48 (0.56), residues: 54
  loop : -3.01 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP C 179 
 HIS   0.005   0.001   HIS C  51 
 PHE   0.017   0.002   PHE C  34 
 TYR   0.018   0.001   TYR B  27 
 ARG   0.011   0.001   ARG C  33 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 LEU cc_start: 0.8605 (pp) cc_final: 0.8089 (mt)
REVERT: B  108 ARG cc_start: 0.6518 (OUTLIER) cc_final: 0.5362 (pmt-80)
REVERT: C  122 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8277 (pp20)
REVERT: C  275 LEU cc_start: 0.8564 (pp) cc_final: 0.8316 (pp)
  outliers start: 17
  outliers final: 10
  residues processed: 67
  average time/residue: 0.1739
  time to fit residues: 14.9997
Evaluate side-chains
  57 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  244 LEU
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  122 GLU
Chi-restraints excluded: chain C residue  285 ARG
Chi-restraints excluded: chain C residue  332 PHE
Chi-restraints excluded: chain C residue  394 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 18 optimal weight:    0.3980
   chunk 42 optimal weight:    9.9990
   chunk 41 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 52 optimal weight:    0.2980
   chunk 43 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:
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.081367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.063490 restraints weight = 29175.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.064928 restraints weight = 20152.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.065971 restraints weight = 15415.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4790  Z= 0.261
  Angle     :  0.814  11.795   6495  Z= 0.406
  Chirality :  0.043   0.134    747
  Planarity :  0.005   0.070    848
  Dihedral  :  6.988  55.309    645
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 23.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.09 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 29.12 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.65 (0.31), residues: 586
  helix: -1.50 (0.31), residues: 222
  sheet: -3.45 (0.49), residues: 72
  loop : -2.91 (0.34), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  34 
 HIS   0.007   0.001   HIS C 186 
 PHE   0.011   0.002   PHE B 192 
 TYR   0.012   0.001   TYR B  27 
 ARG   0.005   0.001   ARG B  44 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 49
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 LEU cc_start: 0.8754 (pp) cc_final: 0.8189 (mt)
REVERT: B  108 ARG cc_start: 0.6643 (OUTLIER) cc_final: 0.5239 (pmt-80)
REVERT: C   15 GLU cc_start: 0.9067 (tp30) cc_final: 0.8126 (mp0)
REVERT: C   62 LEU cc_start: 0.9470 (tt) cc_final: 0.9231 (mm)
  outliers start: 22
  outliers final: 9
  residues processed: 67
  average time/residue: 0.1656
  time to fit residues: 14.5177
Evaluate side-chains
  53 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  156 TYR
Chi-restraints excluded: chain C residue  285 ARG
Chi-restraints excluded: chain C residue  332 PHE
Chi-restraints excluded: chain C residue  379 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 44 optimal weight:    7.9990
   chunk 45 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 38 optimal weight:    0.0270
   chunk 27 optimal weight:    0.0970
   overall best weight:    1.1640

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

Flipped N/Q/H residues before XYZ refinement:
** B  26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  53 GLN
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 ASN
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.081776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.063919 restraints weight = 29114.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.065349 restraints weight = 20163.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.066405 restraints weight = 15466.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start:          0.3472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4790  Z= 0.228
  Angle     :  0.795  11.192   6495  Z= 0.393
  Chirality :  0.043   0.126    747
  Planarity :  0.005   0.062    848
  Dihedral  :  6.433  28.773    643
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 20.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.75 %
    Favored  : 89.25 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 28.16 %
    Favored  : 68.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.40 (0.32), residues: 586
  helix: -1.33 (0.31), residues: 224
  sheet: -3.18 (0.52), residues: 66
  loop : -2.80 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  34 
 HIS   0.005   0.001   HIS C 186 
 PHE   0.011   0.001   PHE B 192 
 TYR   0.013   0.001   TYR C 393 
 ARG   0.003   0.001   ARG C 285 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 51
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ILE cc_start: 0.9502 (tp) cc_final: 0.9202 (pt)
REVERT: B   75 LEU cc_start: 0.8800 (pp) cc_final: 0.8386 (mt)
REVERT: B  108 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.5383 (pmt-80)
REVERT: C   15 GLU cc_start: 0.9057 (tp30) cc_final: 0.8082 (mp0)
REVERT: C   62 LEU cc_start: 0.9458 (tt) cc_final: 0.9214 (mm)
REVERT: C  147 ARG cc_start: 0.9242 (ptp-170) cc_final: 0.9035 (ptp-170)
REVERT: C  275 LEU cc_start: 0.8518 (pp) cc_final: 0.8256 (pp)
  outliers start: 16
  outliers final: 13
  residues processed: 62
  average time/residue: 0.1708
  time to fit residues: 13.7644
Evaluate side-chains
  61 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  216 LEU
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain C residue   40 VAL
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  156 TYR
Chi-restraints excluded: chain C residue  285 ARG
Chi-restraints excluded: chain C residue  320 VAL
Chi-restraints excluded: chain C residue  332 PHE
Chi-restraints excluded: chain C residue  379 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 40 optimal weight:   20.0000
   chunk 36 optimal weight:    7.9990
   chunk 58 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** B  26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 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 = 0.4253 r_free = 0.4253 target = 0.080178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.062315 restraints weight = 29607.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.063652 restraints weight = 20852.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.064643 restraints weight = 16200.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7353
moved from start:          0.4066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   4790  Z= 0.249
  Angle     :  0.772  10.459   6495  Z= 0.382
  Chirality :  0.043   0.162    747
  Planarity :  0.005   0.061    848
  Dihedral  :  6.261  29.857    643
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 22.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.92 %
    Favored  : 89.08 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 28.54 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.04 (0.33), residues: 586
  helix: -1.02 (0.32), residues: 219
  sheet: -3.03 (0.55), residues: 66
  loop : -2.57 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  34 
 HIS   0.005   0.001   HIS C 186 
 PHE   0.011   0.002   PHE B 192 
 TYR   0.010   0.001   TYR B 227 
 ARG   0.004   0.001   ARG C 285 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 51
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ILE cc_start: 0.9467 (tp) cc_final: 0.9206 (pt)
REVERT: B   75 LEU cc_start: 0.8846 (pp) cc_final: 0.8385 (mt)
REVERT: B  108 ARG cc_start: 0.6613 (OUTLIER) cc_final: 0.5359 (pmt-80)
REVERT: C   15 GLU cc_start: 0.9076 (tp30) cc_final: 0.8107 (mp0)
REVERT: C   51 HIS cc_start: 0.6639 (m-70) cc_final: 0.5943 (t-90)
REVERT: C   62 LEU cc_start: 0.9433 (tt) cc_final: 0.9193 (mm)
REVERT: C  117 LYS cc_start: 0.6143 (mttt) cc_final: 0.5636 (mmtp)
REVERT: C  275 LEU cc_start: 0.8412 (pp) cc_final: 0.8119 (pp)
  outliers start: 15
  outliers final: 11
  residues processed: 62
  average time/residue: 0.1771
  time to fit residues: 14.1723
Evaluate side-chains
  61 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  156 TYR
Chi-restraints excluded: chain C residue  285 ARG
Chi-restraints excluded: chain C residue  332 PHE
Chi-restraints excluded: chain C residue  379 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 34 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 43 optimal weight:    8.9990
   chunk 56 optimal weight:    0.5980
   chunk 30 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 31 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** B  26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 HIS
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 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 = 0.4226 r_free = 0.4226 target = 0.079658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.062227 restraints weight = 26893.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.063597 restraints weight = 18539.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.064539 restraints weight = 14132.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.4427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4790  Z= 0.206
  Angle     :  0.763  10.828   6495  Z= 0.375
  Chirality :  0.042   0.126    747
  Planarity :  0.005   0.056    848
  Dihedral  :  6.017  29.745    643
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 18.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.22 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 29.31 %
    Favored  : 68.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.34), residues: 586
  helix: -0.74 (0.33), residues: 219
  sheet: -2.83 (0.58), residues: 66
  loop : -2.43 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  34 
 HIS   0.005   0.001   HIS C 186 
 PHE   0.013   0.001   PHE C  84 
 TYR   0.012   0.001   TYR C 393 
 ARG   0.003   0.000   ARG B 125 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ILE cc_start: 0.9385 (tp) cc_final: 0.9112 (pt)
REVERT: B   75 LEU cc_start: 0.8848 (pp) cc_final: 0.8442 (mt)
REVERT: B  108 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.5196 (pmt-80)
REVERT: B  163 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.6884 (t70)
REVERT: C   15 GLU cc_start: 0.9040 (tp30) cc_final: 0.8077 (mp0)
REVERT: C   51 HIS cc_start: 0.6351 (m-70) cc_final: 0.5751 (t-90)
REVERT: C   62 LEU cc_start: 0.9369 (tt) cc_final: 0.9148 (mm)
REVERT: C  147 ARG cc_start: 0.9175 (ptp-170) cc_final: 0.8970 (ptp-170)
REVERT: C  275 LEU cc_start: 0.8293 (pp) cc_final: 0.8014 (pp)
  outliers start: 13
  outliers final: 8
  residues processed: 63
  average time/residue: 0.1742
  time to fit residues: 14.1793
Evaluate side-chains
  58 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  163 HIS
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  285 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 21 optimal weight:    0.0030
   chunk 15 optimal weight:    8.9990
   chunk 28 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 44 optimal weight:   20.0000
   chunk 49 optimal weight:    5.9990
   chunk 52 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0770
   chunk 51 optimal weight:    0.9980
   overall best weight:    1.0152

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

Flipped N/Q/H residues before XYZ refinement:
** B  26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 HIS
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 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 = 0.4244 r_free = 0.4244 target = 0.079820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.061620 restraints weight = 27165.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.063008 restraints weight = 18930.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.064014 restraints weight = 14553.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.4682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4790  Z= 0.211
  Angle     :  0.767  11.292   6495  Z= 0.377
  Chirality :  0.041   0.125    747
  Planarity :  0.004   0.052    848
  Dihedral  :  5.924  29.311    643
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 17.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.90 %
    Favored  : 90.10 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 29.12 %
    Favored  : 68.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.34), residues: 586
  helix: -0.55 (0.34), residues: 219
  sheet: -2.80 (0.60), residues: 66
  loop : -2.35 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 179 
 HIS   0.005   0.001   HIS B 163 
 PHE   0.012   0.001   PHE C 315 
 TYR   0.007   0.001   TYR B 227 
 ARG   0.003   0.000   ARG C 285 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ILE cc_start: 0.9369 (tp) cc_final: 0.9135 (pt)
REVERT: B   75 LEU cc_start: 0.8845 (pp) cc_final: 0.8419 (mt)
REVERT: B  101 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7612 (mt-10)
REVERT: B  108 ARG cc_start: 0.6632 (OUTLIER) cc_final: 0.5198 (pmt-80)
REVERT: B  163 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.7099 (t-90)
REVERT: C   15 GLU cc_start: 0.9035 (tp30) cc_final: 0.8131 (mp0)
REVERT: C   62 LEU cc_start: 0.9366 (tt) cc_final: 0.9147 (mm)
REVERT: C   84 PHE cc_start: 0.7735 (m-80) cc_final: 0.7170 (m-80)
REVERT: C  147 ARG cc_start: 0.9180 (ptp-170) cc_final: 0.8972 (ptp-170)
REVERT: C  275 LEU cc_start: 0.8366 (pp) cc_final: 0.8086 (pp)
  outliers start: 15
  outliers final: 11
  residues processed: 64
  average time/residue: 0.1970
  time to fit residues: 15.9368
Evaluate side-chains
  65 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 51
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  163 HIS
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  285 ARG
Chi-restraints excluded: chain C residue  332 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 41 optimal weight:    6.9990
   chunk 14 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0570
   chunk 18 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7302

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

Flipped N/Q/H residues before XYZ refinement:
** B  26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 HIS
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 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 = 0.4241 r_free = 0.4241 target = 0.079768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.062523 restraints weight = 27112.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.063913 restraints weight = 18343.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.064946 restraints weight = 13827.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4790  Z= 0.211
  Angle     :  0.793  14.612   6495  Z= 0.389
  Chirality :  0.041   0.127    747
  Planarity :  0.004   0.050    848
  Dihedral  :  5.869  29.201    643
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 17.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.73 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 29.50 %
    Favored  : 67.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.34), residues: 586
  helix: -0.47 (0.34), residues: 217
  sheet: -2.67 (0.61), residues: 66
  loop : -2.31 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 179 
 HIS   0.008   0.002   HIS B  26 
 PHE   0.012   0.001   PHE C 315 
 TYR   0.007   0.001   TYR B 165 
 ARG   0.008   0.001   ARG B  29 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ILE cc_start: 0.9349 (tp) cc_final: 0.9134 (pt)
REVERT: B   75 LEU cc_start: 0.8843 (pp) cc_final: 0.8428 (mt)
REVERT: B  101 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7542 (mm-30)
REVERT: B  108 ARG cc_start: 0.6592 (OUTLIER) cc_final: 0.5130 (pmt-80)
REVERT: B  163 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7232 (t70)
REVERT: B  174 ASP cc_start: 0.7725 (p0) cc_final: 0.7290 (t70)
REVERT: B  205 GLU cc_start: 0.8287 (mp0) cc_final: 0.7842 (mm-30)
REVERT: C   15 GLU cc_start: 0.8993 (tp30) cc_final: 0.8116 (mp0)
REVERT: C   51 HIS cc_start: 0.6300 (m-70) cc_final: 0.5782 (t-90)
REVERT: C  275 LEU cc_start: 0.8349 (pp) cc_final: 0.8071 (pp)
  outliers start: 15
  outliers final: 10
  residues processed: 64
  average time/residue: 0.1989
  time to fit residues: 16.1400
Evaluate side-chains
  62 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 CYS
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  163 HIS
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  285 ARG
Chi-restraints excluded: chain C residue  332 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 16 optimal weight:    8.9990
   chunk 50 optimal weight:    0.4980
   chunk 8 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 17 optimal weight:    0.3980
   chunk 18 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
** B  26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  53 GLN
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 HIS
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.080040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.062235 restraints weight = 27471.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.063643 restraints weight = 18716.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.064653 restraints weight = 14168.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.5077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4790  Z= 0.212
  Angle     :  0.803  12.516   6495  Z= 0.391
  Chirality :  0.042   0.167    747
  Planarity :  0.004   0.049    848
  Dihedral  :  5.848  29.204    643
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 18.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.73 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 28.93 %
    Favored  : 68.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.34), residues: 586
  helix: -0.41 (0.33), residues: 217
  sheet: -2.73 (0.61), residues: 67
  loop : -2.25 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 179 
 HIS   0.005   0.001   HIS B  26 
 PHE   0.011   0.001   PHE C 315 
 TYR   0.006   0.001   TYR B 253 
 ARG   0.006   0.001   ARG B  29 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ILE cc_start: 0.9350 (tp) cc_final: 0.9137 (pt)
REVERT: B   75 LEU cc_start: 0.8858 (pp) cc_final: 0.8442 (mt)
REVERT: B  101 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7552 (mt-10)
REVERT: B  108 ARG cc_start: 0.6602 (OUTLIER) cc_final: 0.5140 (pmt-80)
REVERT: B  163 HIS cc_start: 0.7533 (OUTLIER) cc_final: 0.7148 (t-90)
REVERT: C   15 GLU cc_start: 0.9003 (tp30) cc_final: 0.8399 (mm-30)
REVERT: C   51 HIS cc_start: 0.6425 (m-70) cc_final: 0.5936 (t-90)
REVERT: C   84 PHE cc_start: 0.7754 (m-80) cc_final: 0.7165 (m-80)
REVERT: C  275 LEU cc_start: 0.8335 (pp) cc_final: 0.8054 (pp)
  outliers start: 15
  outliers final: 11
  residues processed: 60
  average time/residue: 0.1977
  time to fit residues: 15.0541
Evaluate side-chains
  61 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 ARG
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  163 HIS
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  285 ARG
Chi-restraints excluded: chain C residue  332 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 35 optimal weight:   20.0000
   chunk 19 optimal weight:    1.9990
   chunk 28 optimal weight:   20.0000
   chunk 15 optimal weight:    0.1980
   chunk 8 optimal weight:    6.9990
   chunk 48 optimal weight:   20.0000
   chunk 40 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** B  26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 163 HIS
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 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 = 0.4221 r_free = 0.4221 target = 0.078722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.060979 restraints weight = 27547.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.062375 restraints weight = 18928.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.063371 restraints weight = 14419.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.5263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4790  Z= 0.239
  Angle     :  0.821  12.683   6495  Z= 0.396
  Chirality :  0.043   0.250    747
  Planarity :  0.005   0.051    848
  Dihedral  :  5.912  30.843    643
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 20.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.41 %
    Favored  : 89.59 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 29.31 %
    Favored  : 67.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.39 (0.35), residues: 586
  helix: -0.43 (0.33), residues: 219
  sheet: -2.85 (0.61), residues: 65
  loop : -2.20 (0.37), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 179 
 HIS   0.010   0.002   HIS B 163 
 PHE   0.010   0.002   PHE C  84 
 TYR   0.007   0.001   TYR C 393 
 ARG   0.006   0.001   ARG B  29 

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 47
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   30 ILE cc_start: 0.9337 (tp) cc_final: 0.9128 (pt)
REVERT: B   75 LEU cc_start: 0.8854 (pp) cc_final: 0.8405 (mt)
REVERT: B  101 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7609 (mt-10)
REVERT: B  108 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.5119 (pmt-80)
REVERT: B  163 HIS cc_start: 0.7643 (OUTLIER) cc_final: 0.7111 (t-90)
REVERT: C   15 GLU cc_start: 0.8988 (tp30) cc_final: 0.8441 (mm-30)
REVERT: C   51 HIS cc_start: 0.6579 (m-70) cc_final: 0.6073 (t-90)
REVERT: C   84 PHE cc_start: 0.7754 (m-80) cc_final: 0.7128 (m-80)
REVERT: C  275 LEU cc_start: 0.8279 (pp) cc_final: 0.7985 (pp)
  outliers start: 15
  outliers final: 12
  residues processed: 59
  average time/residue: 0.2110
  time to fit residues: 15.8564
Evaluate side-chains
  61 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   29 ARG
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  108 ARG
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  163 HIS
Chi-restraints excluded: chain B residue  164 VAL
Chi-restraints excluded: chain B residue  198 ARG
Chi-restraints excluded: chain B residue  258 ILE
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   64 THR
Chi-restraints excluded: chain C residue   86 ILE
Chi-restraints excluded: chain C residue  203 ARG
Chi-restraints excluded: chain C residue  285 ARG
Chi-restraints excluded: chain C residue  332 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0070
   chunk 55 optimal weight:   20.0000
   chunk 57 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0030
   chunk 40 optimal weight:    0.0470
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   overall best weight:    0.3706

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

Flipped N/Q/H residues before XYZ refinement:
B 127 ASN
B 163 HIS
** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.080285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.062815 restraints weight = 27294.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.064276 restraints weight = 18455.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.065307 restraints weight = 13891.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.5420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4790  Z= 0.204
  Angle     :  0.824  12.937   6495  Z= 0.394
  Chirality :  0.042   0.152    747
  Planarity :  0.004   0.046    848
  Dihedral  :  5.773  29.598    643
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.22 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 30.46 %
    Favored  : 67.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.27 (0.35), residues: 586
  helix: -0.34 (0.34), residues: 219
  sheet: -2.78 (0.62), residues: 65
  loop : -2.12 (0.38), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 179 
 HIS   0.006   0.001   HIS B 163 
 PHE   0.010   0.001   PHE C 315 
 TYR   0.007   0.001   TYR B 166 
 ARG   0.005   0.000   ARG B  29 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2192.98 seconds
wall clock time: 39 minutes 48.76 seconds (2388.76 seconds total)