Starting phenix.real_space_refine
on Thu Mar  6 06:41:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s8u_24922/03_2025/7s8u_24922.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s8u_24922/03_2025/7s8u_24922.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s8u_24922/03_2025/7s8u_24922.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s8u_24922/03_2025/7s8u_24922.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s8u_24922/03_2025/7s8u_24922.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s8u_24922/03_2025/7s8u_24922.cif"
  }
  resolution = 3.7
  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=  -0.004 sd=   0.073
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      35      5.16       5
     C    3390      2.51       5
     N     854      2.21       5
     O     931      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5210
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5210
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 667, 5210
          Classifications: {'peptide': 667}
          Link IDs: {'PTRANS': 30, 'TRANS': 636}
  Time building chain proxies: 10.12, per 1000 atoms: 1.94
  Number of scatterers: 5210
  At special positions: 0
  Unit cell: (99.146, 100.26, 99.146, 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      35     16.00
     O     931      8.00
     N     854      7.00
     C    3390      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 539 " - pdb=" SG  CYS A 565 " distance=2.03

  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: 4.36
  Conformation dependent library (CDL) restraints added in 869.5 milliseconds
  

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1236

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 4 sheets defined
      55.6% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 45
    Processing helix  chain 'A' and resid 49 through 78
      Proline residue:  A  68  - end of helix
    Processing helix  chain 'A' and resid 80 through 104
    Processing helix  chain 'A' and resid 120 through 153
      Proline residue:  A 142  - end of helix
      removed outlier: 5.023A  pdb=" N   SER A 145 " --> pdb=" O   LYS A 141 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA A 146 " --> pdb=" O   PRO A 142 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   PHE A 152 " --> pdb=" O   GLY A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 187
      removed outlier: 3.535A  pdb=" N   SER A 178 " --> pdb=" O   GLY A 174 " (cutoff:3.500A)
      Proline residue:  A 183  - end of helix
      removed outlier: 3.622A  pdb=" N   VAL A 187 " --> pdb=" O   PRO A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 217
      removed outlier: 4.033A  pdb=" N   ALA A 202 " --> pdb=" O   CYS A 198 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
      removed outlier: 3.643A  pdb=" N   LEU A 209 " --> pdb=" O   VAL A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 249
      removed outlier: 4.391A  pdb=" N   CYS A 240 " --> pdb=" O   LYS A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 269
    Processing helix  chain 'A' and resid 272 through 289
    Processing helix  chain 'A' and resid 291 through 311
      removed outlier: 3.948A  pdb=" N   THR A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 344
      Proline residue:  A 339  - end of helix
      removed outlier: 3.857A  pdb=" N   ASP A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ALA A 343 " --> pdb=" O   PRO A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 384
      removed outlier: 3.556A  pdb=" N   ASP A 384 " --> pdb=" O   GLN A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 582
      No H-bonds generated for 'chain 'A' and resid 580 through 582'
    Processing helix  chain 'A' and resid 583 through 609
    Processing helix  chain 'A' and resid 611 through 613
      No H-bonds generated for 'chain 'A' and resid 611 through 613'
    Processing helix  chain 'A' and resid 614 through 638
    Processing helix  chain 'A' and resid 644 through 669
      removed outlier: 4.047A  pdb=" N   GLU A 648 " --> pdb=" O   LYS A 644 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   PHE A 669 " --> pdb=" O   ILE A 665 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 432
      removed outlier: 8.225A  pdb=" N   HIS A 460 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   GLN A 397 " --> pdb=" O   HIS A 460 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   ILE A 462 " --> pdb=" O   GLN A 397 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   LYS A 399 " --> pdb=" O   ILE A 462 " (cutoff:3.500A)
      removed outlier: 7.884A  pdb=" N   VAL A 464 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
      removed outlier: 6.569A  pdb=" N   LEU A 401 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   ALA A 466 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   TRP A 465 " --> pdb=" O   HIS A 469 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   HIS A 469 " --> pdb=" O   TRP A 465 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 415 through 419
    Processing sheet with id=AA3, first strand: chain 'A' and resid 519 through 521
      removed outlier: 3.904A  pdb=" N   GLN A 519 " --> pdb=" O   ILE A 488 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ILE A 488 " --> pdb=" O   GLN A 519 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ASN A 486 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   TYR A 554 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE A 574 " --> pdb=" O   ALA A 553 " (cutoff:3.500A)
      removed outlier: 6.063A  pdb=" N   THR A 555 " --> pdb=" O   GLY A 572 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   GLY A 572 " --> pdb=" O   THR A 555 " (cutoff:3.500A)
      removed outlier: 7.531A  pdb=" N   VAL A 557 " --> pdb=" O   VAL A 570 " (cutoff:3.500A)
      removed outlier: 5.984A  pdb=" N   VAL A 570 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 510
      removed outlier: 3.667A  pdb=" N   ASN A 509 " --> pdb=" O   PHE A 498 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   PHE A 498 " --> pdb=" O   ASN A 509 " (cutoff:3.500A)

    312 hydrogen bonds defined for protein.
    915 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: 1.86

  Time building geometry restraints manager: 4.87 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 823
        1.31 -     1.44: 1465
        1.44 -     1.56: 2991
        1.56 -     1.69: 0
        1.69 -     1.82: 59
  Bond restraints: 5338
  Sorted by residual:
  bond pdb=" C   TRP A 295 "
       pdb=" O   TRP A 295 "
    ideal  model  delta    sigma   weight residual
    1.237  1.301 -0.064 1.17e-02 7.31e+03 3.04e+01
  bond pdb=" C   LEU A 176 "
       pdb=" O   LEU A 176 "
    ideal  model  delta    sigma   weight residual
    1.236  1.296 -0.060 1.15e-02 7.56e+03 2.73e+01
  bond pdb=" C   VAL A 596 "
       pdb=" O   VAL A 596 "
    ideal  model  delta    sigma   weight residual
    1.236  1.293 -0.057 1.19e-02 7.06e+03 2.31e+01
  bond pdb=" C   GLY A 302 "
       pdb=" O   GLY A 302 "
    ideal  model  delta    sigma   weight residual
    1.235  1.297 -0.062 1.35e-02 5.49e+03 2.10e+01
  bond pdb=" C   PHE A 298 "
       pdb=" O   PHE A 298 "
    ideal  model  delta    sigma   weight residual
    1.236  1.288 -0.052 1.15e-02 7.56e+03 2.01e+01
  ... (remaining 5333 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 6769
        2.41 -     4.82: 422
        4.82 -     7.23: 52
        7.23 -     9.64: 7
        9.64 -    12.05: 1
  Bond angle restraints: 7251
  Sorted by residual:
  angle pdb=" CA  PRO A 183 "
        pdb=" N   PRO A 183 "
        pdb=" CD  PRO A 183 "
      ideal   model   delta    sigma   weight residual
     112.00   99.95   12.05 1.40e+00 5.10e-01 7.40e+01
  angle pdb=" C   PHE A 294 "
        pdb=" N   TRP A 295 "
        pdb=" CA  TRP A 295 "
      ideal   model   delta    sigma   weight residual
     120.28  111.61    8.67 1.34e+00 5.57e-01 4.19e+01
  angle pdb=" N   GLN A 300 "
        pdb=" CA  GLN A 300 "
        pdb=" C   GLN A 300 "
      ideal   model   delta    sigma   weight residual
     111.28  104.30    6.98 1.09e+00 8.42e-01 4.10e+01
  angle pdb=" C   LEU A  38 "
        pdb=" N   ILE A  39 "
        pdb=" CA  ILE A  39 "
      ideal   model   delta    sigma   weight residual
     120.56  113.27    7.29 1.26e+00 6.30e-01 3.35e+01
  angle pdb=" N   GLN A 327 "
        pdb=" CA  GLN A 327 "
        pdb=" C   GLN A 327 "
      ideal   model   delta    sigma   weight residual
     112.54  105.50    7.04 1.22e+00 6.72e-01 3.33e+01
  ... (remaining 7246 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.07: 2834
       16.07 -    32.14: 223
       32.14 -    48.21: 57
       48.21 -    64.28: 21
       64.28 -    80.35: 8
  Dihedral angle restraints: 3143
    sinusoidal: 1218
      harmonic: 1925
  Sorted by residual:
  dihedral pdb=" C   ILE A 585 "
           pdb=" N   ILE A 585 "
           pdb=" CA  ILE A 585 "
           pdb=" CB  ILE A 585 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.18   13.18     0      2.50e+00 1.60e-01 2.78e+01
  dihedral pdb=" N   ILE A 585 "
           pdb=" C   ILE A 585 "
           pdb=" CA  ILE A 585 "
           pdb=" CB  ILE A 585 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.00  -11.60     0      2.50e+00 1.60e-01 2.15e+01
  dihedral pdb=" C   ILE A 289 "
           pdb=" N   ILE A 289 "
           pdb=" CA  ILE A 289 "
           pdb=" CB  ILE A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -131.07    9.07     0      2.50e+00 1.60e-01 1.32e+01
  ... (remaining 3140 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 573
       0.060 -    0.120: 180
       0.120 -    0.181: 54
       0.181 -    0.241: 18
       0.241 -    0.301: 2
  Chirality restraints: 827
  Sorted by residual:
  chirality pdb=" CA  ILE A 585 "
            pdb=" N   ILE A 585 "
            pdb=" C   ILE A 585 "
            pdb=" CB  ILE A 585 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.13    0.30 2.00e-01 2.50e+01 2.26e+00
  chirality pdb=" CB  ILE A 585 "
            pdb=" CA  ILE A 585 "
            pdb=" CG1 ILE A 585 "
            pdb=" CG2 ILE A 585 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" CA  ILE A 319 "
            pdb=" N   ILE A 319 "
            pdb=" C   ILE A 319 "
            pdb=" CB  ILE A 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 824 not shown)

  Planarity restraints: 917
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 182 "   -0.082 5.00e-02 4.00e+02   1.17e-01 2.18e+01
        pdb=" N   PRO A 183 "    0.201 5.00e-02 4.00e+02
        pdb=" CA  PRO A 183 "   -0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A 183 "   -0.065 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 302 "   -0.016 2.00e-02 2.50e+03   3.29e-02 1.08e+01
        pdb=" C   GLY A 302 "    0.057 2.00e-02 2.50e+03
        pdb=" O   GLY A 302 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   SER A 303 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  39 "    0.011 2.00e-02 2.50e+03   2.32e-02 5.37e+00
        pdb=" C   ILE A  39 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ILE A  39 "    0.015 2.00e-02 2.50e+03
        pdb=" N   LEU A  40 "    0.014 2.00e-02 2.50e+03
  ... (remaining 914 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 983
        2.77 -     3.31: 5547
        3.31 -     3.84: 8613
        3.84 -     4.37: 9757
        4.37 -     4.90: 16386
  Nonbonded interactions: 41286
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 555 "
            pdb=" O   PHE A 571 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   VAL A 123 "
            pdb=" OG  SER A 126 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" O   GLN A 301 "
            pdb=" C   GLY A 302 "
     model   vdw
     2.354 3.270
  nonbonded pdb=" OG  SER A 536 "
            pdb=" OE1 GLN A 538 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" O   ILE A  56 "
            pdb=" OG1 THR A  59 "
     model   vdw
     2.382 3.040
  ... (remaining 41281 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             29.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     29.940
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  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:3.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   63.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5918
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      :  0.008   0.064   5338  Z= 0.505
  Angle     :  1.188  12.046   7251  Z= 0.848
  Chirality :  0.070   0.301    827
  Planarity :  0.007   0.117    917
  Dihedral  : 14.003  80.348   1904
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  1.20 %
    Allowed  :  8.27 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  :  3.68 %
    Favored  : 91.75 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.33), residues: 665
  helix:  0.16 (0.28), residues: 339
  sheet:  1.49 (0.72), residues: 54
  loop : -2.48 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 622 
 HIS   0.004   0.001   HIS A 193 
 PHE   0.015   0.002   PHE A 356 
 TYR   0.025   0.002   TYR A  41 
 ARG   0.004   0.001   ARG A 252 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 197
  time to evaluate  : 1.205 
Fit side-chains
REVERT: A   76 ASP cc_start: 0.6653 (t70) cc_final: 0.6325 (m-30)
REVERT: A  183 PRO cc_start: 0.8466 (OUTLIER) cc_final: 0.7871 (Cg_endo)
REVERT: A  286 PHE cc_start: 0.7024 (m-10) cc_final: 0.6651 (t80)
REVERT: A  458 HIS cc_start: 0.4926 (m90) cc_final: 0.4489 (m90)
REVERT: A  465 TRP cc_start: 0.3603 (p90) cc_final: 0.2983 (p90)
REVERT: A  502 MET cc_start: 0.6655 (tmm) cc_final: 0.6420 (ppp)
REVERT: A  541 ARG cc_start: 0.6430 (ptt180) cc_final: 0.6163 (ptt180)
REVERT: A  632 ILE cc_start: 0.8696 (mt) cc_final: 0.8402 (mt)
  outliers start: 26
  outliers final: 7
  residues processed: 211
  average time/residue: 0.1814
  time to fit residues: 50.3475
Evaluate side-chains
  156 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 148
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue  183 PRO
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  292 PRO
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  586 PRO
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
A 193 HIS
A 315 GLN
A 519 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.223366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.202147 restraints weight = 11046.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.203977 restraints weight = 6842.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.206332 restraints weight = 4903.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.4437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6164
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5338  Z= 0.238
  Angle     :  0.758   8.536   7251  Z= 0.403
  Chirality :  0.049   0.217    827
  Planarity :  0.006   0.068    917
  Dihedral  :  6.731  59.696    729
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  :  8.42 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 14.04 %
    Favored  : 81.58 %
  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: -0.72 (0.32), residues: 665
  helix:  0.72 (0.27), residues: 353
  sheet:  1.61 (0.66), residues: 52
  loop : -2.72 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 622 
 HIS   0.007   0.002   HIS A  58 
 PHE   0.034   0.002   PHE A 243 
 TYR   0.021   0.002   TYR A 588 
 ARG   0.004   0.001   ARG A 489 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 150
  time to evaluate  : 0.595 
Fit side-chains
REVERT: A  285 MET cc_start: 0.7675 (ttp) cc_final: 0.7241 (mtp)
REVERT: A  286 PHE cc_start: 0.6845 (m-10) cc_final: 0.6357 (t80)
REVERT: A  301 GLN cc_start: 0.6378 (OUTLIER) cc_final: 0.4644 (tm130)
REVERT: A  541 ARG cc_start: 0.6422 (ptt180) cc_final: 0.6213 (ptt180)
REVERT: A  595 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7685 (tm-30)
REVERT: A  632 ILE cc_start: 0.8831 (mt) cc_final: 0.8568 (mt)
REVERT: A  644 LYS cc_start: 0.7365 (pttm) cc_final: 0.6906 (pttm)
  outliers start: 25
  outliers final: 14
  residues processed: 161
  average time/residue: 0.1644
  time to fit residues: 35.2177
Evaluate side-chains
  146 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 TYR
Chi-restraints excluded: chain A residue   90 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  585 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    0.0770
   chunk 20 optimal weight:    0.5980
   chunk 47 optimal weight:   20.0000
   chunk 18 optimal weight:    0.4980
   chunk 2 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 193 HIS
A 277 GLN
** A 519 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 = 0.4627 r_free = 0.4627 target = 0.224383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.203187 restraints weight = 11092.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.207291 restraints weight = 6426.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.208308 restraints weight = 4189.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.4459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6131
moved from start:          0.3412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5338  Z= 0.212
  Angle     :  0.710   8.822   7251  Z= 0.371
  Chirality :  0.046   0.211    827
  Planarity :  0.005   0.071    917
  Dihedral  :  6.391  59.766    719
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.02 %
    Favored  : 90.68 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 18.60 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.32), residues: 665
  helix:  0.88 (0.27), residues: 354
  sheet:  1.76 (0.68), residues: 52
  loop : -2.48 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 622 
 HIS   0.009   0.002   HIS A 193 
 PHE   0.026   0.002   PHE A 243 
 TYR   0.015   0.002   TYR A 224 
 ARG   0.004   0.001   ARG A 273 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 141
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
REVERT: A  126 SER cc_start: 0.8646 (p) cc_final: 0.8423 (p)
REVERT: A  195 LYS cc_start: 0.7064 (tppt) cc_final: 0.6852 (tppt)
REVERT: A  285 MET cc_start: 0.7472 (ttp) cc_final: 0.7080 (mtp)
REVERT: A  286 PHE cc_start: 0.6777 (m-10) cc_final: 0.6298 (t80)
REVERT: A  301 GLN cc_start: 0.6323 (OUTLIER) cc_final: 0.4736 (tm130)
REVERT: A  371 MET cc_start: 0.7184 (mmm) cc_final: 0.6873 (mtp)
REVERT: A  595 GLU cc_start: 0.7990 (tm-30) cc_final: 0.7597 (tm-30)
REVERT: A  632 ILE cc_start: 0.8784 (mt) cc_final: 0.8512 (mt)
REVERT: A  644 LYS cc_start: 0.7347 (pttm) cc_final: 0.7026 (pttm)
  outliers start: 23
  outliers final: 17
  residues processed: 150
  average time/residue: 0.1347
  time to fit residues: 27.4530
Evaluate side-chains
  151 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 133
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  341 MET
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  608 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 33 optimal weight:    0.0470
   chunk 36 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 30 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0020
   chunk 20 optimal weight:    0.4980
   chunk 44 optimal weight:    0.2980
   chunk 5 optimal weight:    0.8980
   chunk 19 optimal weight:    0.2980
   overall best weight:    0.2286

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 609 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.226098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.204952 restraints weight = 11446.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4458 r_free = 0.4458 target = 0.209400 restraints weight = 6438.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.210582 restraints weight = 4062.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.4469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6084
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5338  Z= 0.189
  Angle     :  0.675   8.438   7251  Z= 0.349
  Chirality :  0.044   0.213    827
  Planarity :  0.005   0.069    917
  Dihedral  :  5.920  54.081    717
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.57 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 21.05 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.33), residues: 665
  helix:  1.08 (0.27), residues: 351
  sheet:  1.87 (0.69), residues: 52
  loop : -2.52 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 622 
 HIS   0.007   0.001   HIS A 193 
 PHE   0.019   0.002   PHE A 243 
 TYR   0.018   0.002   TYR A 224 
 ARG   0.004   0.000   ARG A  28 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.571 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8637 (p) cc_final: 0.8411 (p)
REVERT: A  285 MET cc_start: 0.7366 (ttp) cc_final: 0.7021 (mtp)
REVERT: A  286 PHE cc_start: 0.6861 (m-10) cc_final: 0.6431 (t80)
REVERT: A  301 GLN cc_start: 0.5830 (OUTLIER) cc_final: 0.4463 (tm130)
REVERT: A  541 ARG cc_start: 0.6209 (ptt180) cc_final: 0.5337 (mtm180)
REVERT: A  595 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7652 (tm-30)
REVERT: A  632 ILE cc_start: 0.8725 (mt) cc_final: 0.8441 (mt)
REVERT: A  644 LYS cc_start: 0.7389 (pttm) cc_final: 0.7017 (pttm)
  outliers start: 23
  outliers final: 18
  residues processed: 150
  average time/residue: 0.1905
  time to fit residues: 38.7114
Evaluate side-chains
  147 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  608 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 44 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 55 optimal weight:   20.0000
   chunk 58 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
A 277 GLN
A 458 HIS
** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.222910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.200854 restraints weight = 11386.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.205858 restraints weight = 7101.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.206578 restraints weight = 4204.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.4431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6183
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5338  Z= 0.222
  Angle     :  0.723   8.554   7251  Z= 0.373
  Chirality :  0.045   0.182    827
  Planarity :  0.005   0.063    917
  Dihedral  :  5.983  56.765    717
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  9.17 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 21.93 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.33), residues: 665
  helix:  1.07 (0.27), residues: 354
  sheet:  1.68 (0.69), residues: 52
  loop : -2.44 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 622 
 HIS   0.007   0.001   HIS A 251 
 PHE   0.023   0.002   PHE A 356 
 TYR   0.017   0.002   TYR A 224 
 ARG   0.004   0.000   ARG A 250 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.993 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8695 (p) cc_final: 0.8445 (p)
REVERT: A  285 MET cc_start: 0.7461 (ttp) cc_final: 0.7119 (mtp)
REVERT: A  286 PHE cc_start: 0.6898 (m-10) cc_final: 0.6436 (t80)
REVERT: A  301 GLN cc_start: 0.5721 (OUTLIER) cc_final: 0.4286 (tm130)
REVERT: A  558 MET cc_start: 0.4924 (mmp) cc_final: 0.4686 (mmp)
REVERT: A  632 ILE cc_start: 0.8820 (mt) cc_final: 0.8588 (mt)
REVERT: A  644 LYS cc_start: 0.7417 (pttm) cc_final: 0.7068 (pttm)
  outliers start: 28
  outliers final: 25
  residues processed: 148
  average time/residue: 0.1976
  time to fit residues: 39.3859
Evaluate side-chains
  152 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 PHE
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  666 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 13 optimal weight:   10.0000
   chunk 8 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
A 458 HIS
** A 587 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 = 0.4590 r_free = 0.4590 target = 0.221437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.199650 restraints weight = 11546.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.204578 restraints weight = 7144.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.205185 restraints weight = 4457.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.4409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6221
moved from start:          0.4499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5338  Z= 0.237
  Angle     :  0.730   8.469   7251  Z= 0.378
  Chirality :  0.045   0.166    827
  Planarity :  0.005   0.057    917
  Dihedral  :  6.066  58.129    717
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.72 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  6.14 %
    Allowed  : 21.93 %
    Favored  : 71.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.40 (0.33), residues: 665
  helix:  1.03 (0.27), residues: 354
  sheet:  1.16 (0.67), residues: 54
  loop : -2.57 (0.36), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A  48 
 HIS   0.008   0.002   HIS A 251 
 PHE   0.029   0.002   PHE A 356 
 TYR   0.019   0.002   TYR A 224 
 ARG   0.005   0.001   ARG A 250 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 132
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A  126 SER cc_start: 0.8714 (p) cc_final: 0.8482 (p)
REVERT: A  225 LYS cc_start: 0.7693 (tppt) cc_final: 0.7370 (ptmt)
REVERT: A  285 MET cc_start: 0.7613 (ttp) cc_final: 0.7260 (mtp)
REVERT: A  286 PHE cc_start: 0.6859 (m-10) cc_final: 0.6427 (t80)
REVERT: A  301 GLN cc_start: 0.5890 (OUTLIER) cc_final: 0.4337 (tm130)
REVERT: A  558 MET cc_start: 0.5203 (mmp) cc_final: 0.4957 (mmp)
REVERT: A  632 ILE cc_start: 0.8821 (mt) cc_final: 0.8582 (mt)
REVERT: A  644 LYS cc_start: 0.7490 (pttm) cc_final: 0.7143 (pttm)
REVERT: A  657 LEU cc_start: 0.7501 (tp) cc_final: 0.7224 (mt)
  outliers start: 35
  outliers final: 26
  residues processed: 151
  average time/residue: 0.1637
  time to fit residues: 34.2035
Evaluate side-chains
  153 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  282 THR
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  666 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0670
   chunk 34 optimal weight:    0.8980
   chunk 62 optimal weight:    0.3980
   chunk 21 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS
A 458 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.223278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.201918 restraints weight = 11223.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.206620 restraints weight = 7011.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.208004 restraints weight = 4132.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.4440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6155
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5338  Z= 0.198
  Angle     :  0.703   8.807   7251  Z= 0.360
  Chirality :  0.045   0.170    827
  Planarity :  0.005   0.056    917
  Dihedral  :  5.928  54.680    717
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  8.42 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  5.26 %
    Allowed  : 23.51 %
    Favored  : 71.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.33), residues: 665
  helix:  1.11 (0.27), residues: 354
  sheet:  1.53 (0.67), residues: 52
  loop : -2.47 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 622 
 HIS   0.006   0.001   HIS A  58 
 PHE   0.023   0.001   PHE A 356 
 TYR   0.014   0.002   TYR A  41 
 ARG   0.003   0.000   ARG A 541 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.4298 (OUTLIER) cc_final: 0.3776 (m-80)
REVERT: A  285 MET cc_start: 0.7486 (ttp) cc_final: 0.7142 (mtp)
REVERT: A  286 PHE cc_start: 0.6841 (m-10) cc_final: 0.6475 (t80)
REVERT: A  301 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.4645 (tm130)
REVERT: A  417 MET cc_start: 0.3988 (mmm) cc_final: 0.3716 (ptm)
REVERT: A  558 MET cc_start: 0.5158 (mmp) cc_final: 0.4907 (mmp)
REVERT: A  632 ILE cc_start: 0.8751 (mt) cc_final: 0.8494 (mt)
REVERT: A  644 LYS cc_start: 0.7475 (pttm) cc_final: 0.7156 (pttm)
REVERT: A  657 LEU cc_start: 0.7480 (tp) cc_final: 0.7185 (mt)
  outliers start: 30
  outliers final: 25
  residues processed: 145
  average time/residue: 0.2214
  time to fit residues: 45.5254
Evaluate side-chains
  147 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   18 PHE
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  547 ARG
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  608 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    0.1980
   chunk 12 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 38 optimal weight:    9.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4603 r_free = 0.4603 target = 0.223079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.201742 restraints weight = 11420.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.206958 restraints weight = 7075.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.207689 restraints weight = 4226.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.4436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6157
moved from start:          0.4883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5338  Z= 0.205
  Angle     :  0.715   8.395   7251  Z= 0.366
  Chirality :  0.045   0.201    827
  Planarity :  0.005   0.054    917
  Dihedral  :  6.015  66.587    717
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.47 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 24.04 %
    Favored  : 70.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.33), residues: 665
  helix:  1.12 (0.27), residues: 354
  sheet:  1.47 (0.67), residues: 52
  loop : -2.39 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 622 
 HIS   0.007   0.002   HIS A 193 
 PHE   0.025   0.002   PHE A 356 
 TYR   0.016   0.001   TYR A  41 
 ARG   0.002   0.000   ARG A 250 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.525 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.4630 (OUTLIER) cc_final: 0.4189 (m-80)
REVERT: A  285 MET cc_start: 0.7432 (ttp) cc_final: 0.7108 (mtp)
REVERT: A  286 PHE cc_start: 0.6834 (m-10) cc_final: 0.6459 (t80)
REVERT: A  301 GLN cc_start: 0.5731 (OUTLIER) cc_final: 0.4299 (tm130)
REVERT: A  311 THR cc_start: 0.7806 (p) cc_final: 0.7484 (t)
REVERT: A  558 MET cc_start: 0.5147 (mmp) cc_final: 0.4913 (mmp)
REVERT: A  632 ILE cc_start: 0.8738 (mt) cc_final: 0.8484 (mt)
REVERT: A  644 LYS cc_start: 0.7510 (pttm) cc_final: 0.7176 (pttm)
REVERT: A  657 LEU cc_start: 0.7541 (tp) cc_final: 0.7233 (mt)
  outliers start: 29
  outliers final: 23
  residues processed: 143
  average time/residue: 0.1339
  time to fit residues: 26.2460
Evaluate side-chains
  148 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   18 PHE
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  301 GLN
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  666 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 57 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.221938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4390 r_free = 0.4390 target = 0.200591 restraints weight = 11295.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.205666 restraints weight = 7143.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.206252 restraints weight = 4346.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.4426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6180
moved from start:          0.5082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5338  Z= 0.218
  Angle     :  0.736   9.613   7251  Z= 0.376
  Chirality :  0.045   0.186    827
  Planarity :  0.005   0.053    917
  Dihedral  :  6.019  63.938    717
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.72 %
    Favored  : 91.13 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 24.39 %
    Favored  : 70.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.33), residues: 665
  helix:  1.13 (0.27), residues: 354
  sheet:  1.25 (0.67), residues: 52
  loop : -2.51 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 295 
 HIS   0.007   0.002   HIS A 193 
 PHE   0.018   0.001   PHE A 356 
 TYR   0.015   0.002   TYR A  41 
 ARG   0.004   0.000   ARG A 541 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 131
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.3721 (OUTLIER) cc_final: 0.3413 (m-80)
REVERT: A  285 MET cc_start: 0.7453 (ttp) cc_final: 0.7121 (mtp)
REVERT: A  286 PHE cc_start: 0.6830 (m-10) cc_final: 0.6234 (t80)
REVERT: A  311 THR cc_start: 0.7757 (p) cc_final: 0.7438 (t)
REVERT: A  417 MET cc_start: 0.3676 (mmm) cc_final: 0.3404 (ptm)
REVERT: A  558 MET cc_start: 0.5280 (mmp) cc_final: 0.5072 (mmp)
REVERT: A  632 ILE cc_start: 0.8765 (mt) cc_final: 0.8522 (mt)
REVERT: A  644 LYS cc_start: 0.7478 (pttm) cc_final: 0.7154 (pttm)
REVERT: A  657 LEU cc_start: 0.7494 (tp) cc_final: 0.7239 (mt)
  outliers start: 28
  outliers final: 24
  residues processed: 146
  average time/residue: 0.1346
  time to fit residues: 26.7935
Evaluate side-chains
  152 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 127
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 PHE
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  666 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 9 optimal weight:    0.0010
   chunk 4 optimal weight:    0.8980
   chunk 54 optimal weight:    8.9990
   chunk 61 optimal weight:    0.5980
   chunk 22 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 193 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4596 r_free = 0.4596 target = 0.222450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4392 r_free = 0.4392 target = 0.200940 restraints weight = 11397.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.205938 restraints weight = 7419.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.208186 restraints weight = 4125.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.4445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6128
moved from start:          0.5280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5338  Z= 0.207
  Angle     :  0.738  11.818   7251  Z= 0.375
  Chirality :  0.046   0.190    827
  Planarity :  0.005   0.051    917
  Dihedral  :  5.354  40.141    714
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  8.87 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 25.61 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.33), residues: 665
  helix:  1.13 (0.27), residues: 353
  sheet:  1.32 (0.67), residues: 52
  loop : -2.40 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 622 
 HIS   0.007   0.002   HIS A 193 
 PHE   0.031   0.001   PHE A 356 
 TYR   0.015   0.002   TYR A  41 
 ARG   0.002   0.000   ARG A 250 

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

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

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1330 Ramachandran restraints generated.
    665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A   18 PHE cc_start: 0.3674 (OUTLIER) cc_final: 0.3358 (m-80)
REVERT: A  285 MET cc_start: 0.7476 (ttp) cc_final: 0.7187 (mtp)
REVERT: A  286 PHE cc_start: 0.6747 (m-10) cc_final: 0.6332 (t80)
REVERT: A  417 MET cc_start: 0.3554 (mmm) cc_final: 0.3317 (ptm)
REVERT: A  632 ILE cc_start: 0.8713 (mt) cc_final: 0.8455 (mt)
REVERT: A  644 LYS cc_start: 0.7471 (pttm) cc_final: 0.6579 (pttm)
REVERT: A  657 LEU cc_start: 0.7454 (tp) cc_final: 0.7188 (mt)
  outliers start: 25
  outliers final: 22
  residues processed: 150
  average time/residue: 0.1372
  time to fit residues: 28.2637
Evaluate side-chains
  152 residues out of total 570 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 PHE
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue   82 PHE
Chi-restraints excluded: chain A residue  103 SER
Chi-restraints excluded: chain A residue  104 ILE
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  167 PHE
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  288 TYR
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  319 ILE
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  431 PHE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  528 PHE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  608 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 41 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0980
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 49 optimal weight:    0.2980
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 172 ASN
A 193 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4601 r_free = 0.4601 target = 0.222886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.201548 restraints weight = 11461.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4428 r_free = 0.4428 target = 0.206552 restraints weight = 7027.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.207342 restraints weight = 4133.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.4433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6150
moved from start:          0.5429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5338  Z= 0.212
  Angle     :  0.757  12.128   7251  Z= 0.386
  Chirality :  0.046   0.188    827
  Planarity :  0.005   0.051    917
  Dihedral  :  5.383  39.999    714
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  9.32 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 26.67 %
    Favored  : 68.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.33), residues: 665
  helix:  1.09 (0.27), residues: 353
  sheet:  1.50 (0.68), residues: 52
  loop : -2.44 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 622 
 HIS   0.006   0.001   HIS A  58 
 PHE   0.016   0.001   PHE A 298 
 TYR   0.016   0.002   TYR A 346 
 ARG   0.002   0.000   ARG A 186 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2305.46 seconds
wall clock time: 41 minutes 43.19 seconds (2503.19 seconds total)