Starting phenix.real_space_refine
on Wed Sep 17 10:13:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qbf_52997/09_2025/9qbf_52997.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qbf_52997/09_2025/9qbf_52997.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/9qbf_52997/09_2025/9qbf_52997.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qbf_52997/09_2025/9qbf_52997.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qbf_52997/09_2025/9qbf_52997.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qbf_52997/09_2025/9qbf_52997.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.045
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: 5
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    2421      2.51       5
     N     698      2.21       5
     O     732      1.98       5
     H    3736      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7628
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7628
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 504, 7628
          Classifications: {'peptide': 504}
          Link IDs: {'PTRANS': 27, 'TRANS': 476}
          Chain breaks: 2
  Time building chain proxies: 1.56, per 1000 atoms: 0.20
  Number of scatterers: 7628
  At special positions: 0
  Unit cell: (65.1, 87.234, 85.932, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     O     732      8.00
     N     698      7.00
     C    2421      6.00
     H    3736      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  26 " - pdb=" SG  CYS A  53 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 192 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 195 " - pdb=" SG  CYS A 204 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 199 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 220 " - pdb=" SG  CYS A 227 " distance=2.17
    Simple disulfide: pdb=" SG  CYS A 224 " - pdb=" SG  CYS A 235 " distance=2.09
    Simple disulfide: pdb=" SG  CYS A 236 " - pdb=" SG  CYS A 244 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 240 " - pdb=" SG  CYS A 252 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 255 " - pdb=" SG  CYS A 264 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 268 " - pdb=" SG  CYS A 295 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 299 " - pdb=" SG  CYS A 311 " distance=1.86
    Simple disulfide: pdb=" SG  CYS A 315 " - pdb=" SG  CYS A 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 334 " - pdb=" SG  CYS A 338 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 342 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 475 " - pdb=" SG  CYS A 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 511 " - pdb=" SG  CYS A 520 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 515 " - pdb=" SG  CYS A 528 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 531 " - pdb=" SG  CYS A 540 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 339.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  926

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 8 sheets defined
      22.2% alpha, 13.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 51
      removed outlier: 4.187A  pdb=" N   ASP A  44 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 77
      removed outlier: 3.537A  pdb=" N   ILE A  77 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 110
    Processing helix  chain 'A' and resid 168 through 173
    Processing helix  chain 'A' and resid 199 through 203
    Processing helix  chain 'A' and resid 208 through 212
    Processing helix  chain 'A' and resid 231 through 235
    Processing helix  chain 'A' and resid 248 through 252
      removed outlier: 4.111A  pdb=" N   CYS A 252 " --> pdb=" O   HIS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 351
    Processing helix  chain 'A' and resid 357 through 361
    Processing helix  chain 'A' and resid 377 through 383
    Processing helix  chain 'A' and resid 384 through 388
    Processing helix  chain 'A' and resid 393 through 401
      removed outlier: 3.787A  pdb=" N   GLN A 398 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   PHE A 400 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 426
    Processing helix  chain 'A' and resid 436 through 439
    Processing helix  chain 'A' and resid 481 through 485
    Processing helix  chain 'A' and resid 500 through 507
    Processing helix  chain 'A' and resid 515 through 519
    Processing helix  chain 'A' and resid 524 through 528
      removed outlier: 3.844A  pdb=" N   CYS A 528 " --> pdb=" O   PRO A 525 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 27
      removed outlier: 6.749A  pdb=" N   CYS A  26 " --> pdb=" O   GLN A  57 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63
      removed outlier: 7.296A  pdb=" N   LEU A 154 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   ALA A 115 " --> pdb=" O   LEU A 154 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   VAL A 153 " --> pdb=" O   LEU A 183 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 102
    Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 265
      removed outlier: 5.676A  pdb=" N   ASN A 259 " --> pdb=" O   CYS A 295 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   THR A 290 " --> pdb=" O   CYS A 311 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 272 through 274
    Processing sheet with id=AA6, first strand: chain 'A' and resid 369 through 370
    Processing sheet with id=AA7, first strand: chain 'A' and resid 374 through 376
      removed outlier: 5.789A  pdb=" N   LEU A 465 " --> pdb=" O   TYR A 441 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   ALA A 497 " --> pdb=" O   HIS A 469 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 534 through 536

    90 hydrogen bonds defined for protein.
    162 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: 1.61

  Time building geometry restraints manager: 0.94 seconds

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

  Histogram of bond lengths:
        0.95 -     1.15: 3736
        1.15 -     1.34: 1300
        1.34 -     1.54: 2392
        1.54 -     1.73: 241
        1.73 -     1.93: 44
  Bond restraints: 7713
  Sorted by residual:
  bond pdb=" NH1 ARG A 226 "
       pdb="HH12 ARG A 226 "
    ideal  model  delta    sigma   weight residual
    0.860  1.054 -0.194 2.00e-02 2.50e+03 9.36e+01
  bond pdb=" NE1 TRP A 169 "
       pdb=" HE1 TRP A 169 "
    ideal  model  delta    sigma   weight residual
    0.860  1.050 -0.190 2.00e-02 2.50e+03 9.04e+01
  bond pdb=" NE2 GLN A 320 "
       pdb="HE21 GLN A 320 "
    ideal  model  delta    sigma   weight residual
    0.860  1.049 -0.189 2.00e-02 2.50e+03 8.92e+01
  bond pdb=" NE1 TRP A 452 "
       pdb=" HE1 TRP A 452 "
    ideal  model  delta    sigma   weight residual
    0.860  1.048 -0.188 2.00e-02 2.50e+03 8.83e+01
  bond pdb=" NE2 HIS A 495 "
       pdb=" HE2 HIS A 495 "
    ideal  model  delta    sigma   weight residual
    0.860  1.044 -0.184 2.00e-02 2.50e+03 8.49e+01
  ... (remaining 7708 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 11146
        2.50 -     4.99: 1947
        4.99 -     7.49: 631
        7.49 -     9.98: 169
        9.98 -    12.48: 15
  Bond angle restraints: 13908
  Sorted by residual:
  angle pdb=" C   GLY A 246 "
        pdb=" N   PRO A 247 "
        pdb=" CA  PRO A 247 "
      ideal   model   delta    sigma   weight residual
     119.56  129.28   -9.72 1.02e+00 9.61e-01 9.08e+01
  angle pdb=" C   GLY A 229 "
        pdb=" N   PRO A 230 "
        pdb=" CA  PRO A 230 "
      ideal   model   delta    sigma   weight residual
     119.76  128.57   -8.81 1.03e+00 9.43e-01 7.31e+01
  angle pdb=" C   GLY A 524 "
        pdb=" N   PRO A 525 "
        pdb=" CA  PRO A 525 "
      ideal   model   delta    sigma   weight residual
     119.56  128.22   -8.66 1.02e+00 9.61e-01 7.20e+01
  angle pdb=" N   ARG A 434 "
        pdb=" CA  ARG A 434 "
        pdb=" C   ARG A 434 "
      ideal   model   delta    sigma   weight residual
     111.36  103.07    8.29 1.09e+00 8.42e-01 5.78e+01
  angle pdb=" CA  ASN A 259 "
        pdb=" CB  ASN A 259 "
        pdb=" CG  ASN A 259 "
      ideal   model   delta    sigma   weight residual
     112.60  120.09   -7.49 1.00e+00 1.00e+00 5.61e+01
  ... (remaining 13903 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 3458
       17.51 -    35.02: 159
       35.02 -    52.53: 62
       52.53 -    70.03: 20
       70.03 -    87.54: 6
  Dihedral angle restraints: 3705
    sinusoidal: 2039
      harmonic: 1666
  Sorted by residual:
  dihedral pdb=" CB  CYS A 195 "
           pdb=" SG  CYS A 195 "
           pdb=" SG  CYS A 204 "
           pdb=" CB  CYS A 204 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -168.54   82.54     1      1.00e+01 1.00e-02 8.35e+01
  dihedral pdb=" CB  CYS A 268 "
           pdb=" SG  CYS A 268 "
           pdb=" SG  CYS A 295 "
           pdb=" CB  CYS A 295 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.67  -57.67     1      1.00e+01 1.00e-02 4.47e+01
  dihedral pdb=" N   CYS A 311 "
           pdb=" C   CYS A 311 "
           pdb=" CA  CYS A 311 "
           pdb=" CB  CYS A 311 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.06  -12.26     0      2.50e+00 1.60e-01 2.40e+01
  ... (remaining 3702 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 337
       0.076 -    0.152: 156
       0.152 -    0.228: 76
       0.228 -    0.304: 26
       0.304 -    0.380: 8
  Chirality restraints: 603
  Sorted by residual:
  chirality pdb=" CA  CYS A 311 "
            pdb=" N   CYS A 311 "
            pdb=" C   CYS A 311 "
            pdb=" CB  CYS A 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.61e+00
  chirality pdb=" CA  CYS A 264 "
            pdb=" N   CYS A 264 "
            pdb=" C   CYS A 264 "
            pdb=" CB  CYS A 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.60e+00
  chirality pdb=" CG  LEU A 465 "
            pdb=" CB  LEU A 465 "
            pdb=" CD1 LEU A 465 "
            pdb=" CD2 LEU A 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.23   -0.35 2.00e-01 2.50e+01 3.15e+00
  ... (remaining 600 not shown)

  Planarity restraints: 1189
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 158 "    0.080 2.00e-02 2.50e+03   8.18e-02 1.00e+02
        pdb=" CG  ASN A 158 "    0.009 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 158 "   -0.088 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 158 "    0.010 2.00e-02 2.50e+03
        pdb="HD21 ASN A 158 "    0.108 2.00e-02 2.50e+03
        pdb="HD22 ASN A 158 "   -0.119 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 409 "   -0.109 2.00e-02 2.50e+03   4.64e-02 6.45e+01
        pdb=" CG  TYR A 409 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 409 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 409 "    0.036 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 409 "    0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 409 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 409 "   -0.014 2.00e-02 2.50e+03
        pdb=" OH  TYR A 409 "   -0.081 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 409 "    0.010 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 409 "    0.056 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 409 "    0.033 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 409 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 490 "    0.044 2.00e-02 2.50e+03   3.61e-02 2.94e+01
        pdb=" CG  HIS A 490 "    0.023 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 490 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 490 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 490 "    0.012 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 490 "   -0.007 2.00e-02 2.50e+03
        pdb=" HD1 HIS A 490 "   -0.079 2.00e-02 2.50e+03
        pdb=" HD2 HIS A 490 "   -0.035 2.00e-02 2.50e+03
        pdb=" HE1 HIS A 490 "    0.038 2.00e-02 2.50e+03
  ... (remaining 1186 not shown)

  Histogram of nonbonded interaction distances:
        1.29 -     1.95: 223
        1.95 -     2.61: 9143
        2.61 -     3.27: 24872
        3.27 -     3.94: 32548
        3.94 -     4.60: 49542
  Nonbonded interactions: 116328
  Sorted by model distance:
  nonbonded pdb=" HG  SER A  38 "
            pdb=" HG1 THR A  41 "
     model   vdw
     1.286 2.100
  nonbonded pdb=" H   SER A 413 "
            pdb=" H   ALA A 414 "
     model   vdw
     1.328 2.100
  nonbonded pdb=" H   THR A 278 "
            pdb=" H   PHE A 279 "
     model   vdw
     1.356 2.100
  nonbonded pdb=" H   LEU A 313 "
            pdb=" H   VAL A 314 "
     model   vdw
     1.365 2.100
  nonbonded pdb=" O   THR A 290 "
            pdb=" HG1 THR A 290 "
     model   vdw
     1.626 2.450
  ... (remaining 116323 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:             0.580
  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:             0.040
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     9.150
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6462
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      :  0.024   0.214   3995  Z= 1.286
  Angle     :  2.168  12.478   5440  Z= 1.451
  Chirality :  0.113   0.380    603
  Planarity :  0.010   0.050    714
  Dihedral  : 11.585  87.543   1452
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.22 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.37), residues: 498
  helix: -2.81 (0.58), residues: 42
  sheet: -0.61 (0.85), residues: 45
  loop :  0.41 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 190 
 TYR   0.092   0.012   TYR A 409 
 PHE   0.030   0.008   PHE A 400 
 TRP   0.034   0.010   TRP A 521 
 HIS   0.019   0.004   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.02392 ( 3977)
  covalent geometry    : angle       2.16041 ( 5404)
  SS BOND              : bond        0.05453 (   18)
  SS BOND              : angle       3.10313 (   36)
  hydrogen bonds       : bond        0.20810 (   90)
  hydrogen bonds       : angle      11.95965 (  162)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.190 
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: symmetry clash
   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: symmetry clash
   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: A  458 LEU cc_start: 0.8747 (tp) cc_final: 0.8410 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.2441
  time to fit residues: 19.5476
Evaluate side-chains
  44 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 319 ASN
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 495 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.084822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.072434 restraints weight = 73395.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.075249 restraints weight = 40354.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.077205 restraints weight = 25582.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.078539 restraints weight = 17909.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.079446 restraints weight = 13477.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6656
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3995  Z= 0.205
  Angle     :  0.777   6.150   5440  Z= 0.434
  Chirality :  0.046   0.162    603
  Planarity :  0.006   0.043    714
  Dihedral  :  6.432  24.299    541
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 16.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.42 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  :  5.08 %
    Favored  : 93.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.89 (0.38), residues: 498
  helix: -2.34 (0.64), residues: 43
  sheet: -1.49 (0.72), residues: 64
  loop : -0.18 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 226 
 TYR   0.015   0.002   TYR A 409 
 PHE   0.015   0.002   PHE A 258 
 TRP   0.010   0.002   TRP A 521 
 HIS   0.012   0.003   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 3977)
  covalent geometry    : angle       0.77197 ( 5404)
  SS BOND              : bond        0.00589 (   18)
  SS BOND              : angle       1.31190 (   36)
  hydrogen bonds       : bond        0.06333 (   90)
  hydrogen bonds       : angle       9.96550 (  162)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.137 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 ILE cc_start: 0.8154 (mm) cc_final: 0.7790 (pt)
  outliers start: 7
  outliers final: 6
  residues processed: 54
  average time/residue: 0.2377
  time to fit residues: 15.0190
Evaluate side-chains
  46 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  495 HIS
Chi-restraints excluded: chain A residue  499 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 19 optimal weight:    0.8980
   chunk 1 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 495 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.083694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.071875 restraints weight = 72474.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.074736 restraints weight = 40082.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.076642 restraints weight = 25064.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.077859 restraints weight = 17279.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.078676 restraints weight = 12933.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.3875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3995  Z= 0.183
  Angle     :  0.686   5.120   5440  Z= 0.380
  Chirality :  0.043   0.139    603
  Planarity :  0.005   0.039    714
  Dihedral  :  6.203  22.128    541
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  7.62 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.11 (0.37), residues: 498
  helix: -1.97 (0.68), residues: 44
  sheet: -1.74 (0.83), residues: 50
  loop : -0.45 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 517 
 TYR   0.014   0.002   TYR A 409 
 PHE   0.018   0.002   PHE A 258 
 TRP   0.006   0.001   TRP A 415 
 HIS   0.009   0.002   HIS A 495 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 3977)
  covalent geometry    : angle       0.68356 ( 5404)
  SS BOND              : bond        0.00523 (   18)
  SS BOND              : angle       1.02050 (   36)
  hydrogen bonds       : bond        0.04813 (   90)
  hydrogen bonds       : angle       9.45087 (  162)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.219 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 ILE cc_start: 0.8196 (mm) cc_final: 0.7668 (pt)
  outliers start: 9
  outliers final: 6
  residues processed: 43
  average time/residue: 0.2745
  time to fit residues: 13.6722
Evaluate side-chains
  44 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  499 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 11 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 28 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 141 GLN
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 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 = 0.4195 r_free = 0.4195 target = 0.084353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.072886 restraints weight = 73363.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.075677 restraints weight = 40728.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.077526 restraints weight = 25531.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.078745 restraints weight = 17586.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.079539 restraints weight = 13066.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6711
moved from start:          0.4337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3995  Z= 0.145
  Angle     :  0.615   4.715   5440  Z= 0.339
  Chirality :  0.042   0.134    603
  Planarity :  0.005   0.040    714
  Dihedral  :  5.907  23.558    541
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  :  9.24 %
    Favored  : 88.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.38), residues: 498
  helix: -1.83 (0.68), residues: 51
  sheet: -2.00 (0.73), residues: 60
  loop : -0.59 (0.32), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 517 
 TYR   0.011   0.002   TYR A 409 
 PHE   0.014   0.002   PHE A 258 
 TRP   0.005   0.001   TRP A 482 
 HIS   0.006   0.002   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3977)
  covalent geometry    : angle       0.61243 ( 5404)
  SS BOND              : bond        0.00386 (   18)
  SS BOND              : angle       0.94433 (   36)
  hydrogen bonds       : bond        0.04316 (   90)
  hydrogen bonds       : angle       9.03036 (  162)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.192 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  468 ILE cc_start: 0.8114 (mm) cc_final: 0.7602 (pt)
  outliers start: 8
  outliers final: 7
  residues processed: 45
  average time/residue: 0.2526
  time to fit residues: 13.2303
Evaluate side-chains
  46 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  156 GLN
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  499 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 40 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 30 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.081781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.070707 restraints weight = 76094.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.073330 restraints weight = 42425.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.075065 restraints weight = 26822.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.076222 restraints weight = 18525.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.076995 restraints weight = 13880.167|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6812
moved from start:          0.5034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3995  Z= 0.201
  Angle     :  0.670   4.764   5440  Z= 0.366
  Chirality :  0.042   0.132    603
  Planarity :  0.005   0.041    714
  Dihedral  :  5.964  24.008    541
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 19.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  :  9.70 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (0.39), residues: 498
  helix: -1.88 (0.68), residues: 51
  sheet: -2.31 (0.77), residues: 50
  loop : -0.82 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 517 
 TYR   0.013   0.002   TYR A 409 
 PHE   0.016   0.002   PHE A 258 
 TRP   0.006   0.002   TRP A 482 
 HIS   0.006   0.002   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 3977)
  covalent geometry    : angle       0.66594 ( 5404)
  SS BOND              : bond        0.00597 (   18)
  SS BOND              : angle       1.09901 (   36)
  hydrogen bonds       : bond        0.04119 (   90)
  hydrogen bonds       : angle       9.06177 (  162)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.135 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 9
  residues processed: 47
  average time/residue: 0.2479
  time to fit residues: 13.6222
Evaluate side-chains
  48 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  156 GLN
Chi-restraints excluded: chain A residue  176 ASN
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  249 HIS
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  499 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 8 optimal weight:    4.9990
   chunk 21 optimal weight:    0.3980
   chunk 37 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.084268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.072814 restraints weight = 72903.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.075550 restraints weight = 40332.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.077408 restraints weight = 25322.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.078662 restraints weight = 17389.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.079428 restraints weight = 12885.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
moved from start:          0.5145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3995  Z= 0.119
  Angle     :  0.583   4.704   5440  Z= 0.316
  Chirality :  0.042   0.164    603
  Planarity :  0.005   0.040    714
  Dihedral  :  5.670  24.605    541
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.32 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.38), residues: 498
  helix: -1.72 (0.69), residues: 51
  sheet: -2.38 (0.70), residues: 60
  loop : -0.90 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 517 
 TYR   0.011   0.002   TYR A 409 
 PHE   0.014   0.001   PHE A 258 
 TRP   0.008   0.001   TRP A 482 
 HIS   0.005   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 3977)
  covalent geometry    : angle       0.58118 ( 5404)
  SS BOND              : bond        0.00272 (   18)
  SS BOND              : angle       0.82650 (   36)
  hydrogen bonds       : bond        0.03872 (   90)
  hydrogen bonds       : angle       8.82464 (  162)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.184 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.9166 (m-40) cc_final: 0.8911 (m-40)
  outliers start: 7
  outliers final: 6
  residues processed: 43
  average time/residue: 0.2605
  time to fit residues: 13.0272
Evaluate side-chains
  44 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  347 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 26 optimal weight:    5.9990
   chunk 48 optimal weight:    0.1980
   chunk 45 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 42 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.083871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.071818 restraints weight = 73413.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.074695 restraints weight = 40639.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.076630 restraints weight = 25591.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.077899 restraints weight = 17699.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.078770 restraints weight = 13321.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.5359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3995  Z= 0.114
  Angle     :  0.564   4.084   5440  Z= 0.304
  Chirality :  0.041   0.164    603
  Planarity :  0.005   0.043    714
  Dihedral  :  5.430  23.500    541
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.83 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.32 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.68 (0.38), residues: 498
  helix: -1.58 (0.68), residues: 51
  sheet: -2.47 (0.68), residues: 60
  loop : -0.84 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 499 
 TYR   0.012   0.002   TYR A 441 
 PHE   0.012   0.001   PHE A 258 
 TRP   0.006   0.001   TRP A 482 
 HIS   0.005   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3977)
  covalent geometry    : angle       0.56203 ( 5404)
  SS BOND              : bond        0.00269 (   18)
  SS BOND              : angle       0.84006 (   36)
  hydrogen bonds       : bond        0.03621 (   90)
  hydrogen bonds       : angle       8.52382 (  162)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.207 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.9183 (m-40) cc_final: 0.8908 (m-40)
  outliers start: 6
  outliers final: 6
  residues processed: 41
  average time/residue: 0.2582
  time to fit residues: 12.2297
Evaluate side-chains
  43 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  347 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 17 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 41 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.083167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.071733 restraints weight = 74624.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.074517 restraints weight = 40921.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.076352 restraints weight = 25601.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.077586 restraints weight = 17671.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.078415 restraints weight = 13092.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.4107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6761
moved from start:          0.5576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3995  Z= 0.127
  Angle     :  0.566   4.199   5440  Z= 0.306
  Chirality :  0.041   0.153    603
  Planarity :  0.005   0.039    714
  Dihedral  :  5.426  24.087    541
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.78 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.38), residues: 498
  helix: -1.49 (0.69), residues: 51
  sheet: -2.53 (0.67), residues: 60
  loop : -0.90 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 143 
 TYR   0.009   0.002   TYR A 409 
 PHE   0.013   0.001   PHE A 258 
 TRP   0.006   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3977)
  covalent geometry    : angle       0.56423 ( 5404)
  SS BOND              : bond        0.00352 (   18)
  SS BOND              : angle       0.80995 (   36)
  hydrogen bonds       : bond        0.03583 (   90)
  hydrogen bonds       : angle       8.42458 (  162)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.206 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.9146 (m-40) cc_final: 0.8869 (m-40)
REVERT: A  427 ASN cc_start: 0.9056 (t0) cc_final: 0.8813 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 42
  average time/residue: 0.2592
  time to fit residues: 12.5982
Evaluate side-chains
  45 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  347 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 48 optimal weight:    0.8980
   chunk 30 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0470
   chunk 14 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 6 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.9280

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

Flipped N/Q/H residues before XYZ refinement:
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.083677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.072087 restraints weight = 74524.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.074922 restraints weight = 40760.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.076811 restraints weight = 25495.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.078060 restraints weight = 17469.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.078923 restraints weight = 12948.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6750
moved from start:          0.5693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3995  Z= 0.115
  Angle     :  0.561   4.170   5440  Z= 0.301
  Chirality :  0.041   0.151    603
  Planarity :  0.004   0.041    714
  Dihedral  :  5.355  23.642    541
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 14.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.01 %
    Favored  : 86.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.38), residues: 498
  helix: -1.37 (0.71), residues: 51
  sheet: -2.57 (0.66), residues: 60
  loop : -0.85 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 143 
 TYR   0.013   0.002   TYR A 441 
 PHE   0.013   0.001   PHE A 258 
 TRP   0.006   0.001   TRP A 482 
 HIS   0.004   0.001   HIS A 257 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3977)
  covalent geometry    : angle       0.55930 ( 5404)
  SS BOND              : bond        0.00271 (   18)
  SS BOND              : angle       0.79206 (   36)
  hydrogen bonds       : bond        0.03568 (   90)
  hydrogen bonds       : angle       8.34200 (  162)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.219 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.9122 (m-40) cc_final: 0.8843 (m-40)
REVERT: A  427 ASN cc_start: 0.9054 (t0) cc_final: 0.8808 (t0)
  outliers start: 5
  outliers final: 5
  residues processed: 42
  average time/residue: 0.2717
  time to fit residues: 13.2449
Evaluate side-chains
  43 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  347 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 49 optimal weight:    0.6980
   chunk 3 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.083846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.073042 restraints weight = 75679.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.075735 restraints weight = 41092.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.077495 restraints weight = 25612.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.078659 restraints weight = 17575.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.079451 restraints weight = 13031.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.4125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6768
moved from start:          0.5901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3995  Z= 0.123
  Angle     :  0.560   4.042   5440  Z= 0.301
  Chirality :  0.041   0.149    603
  Planarity :  0.005   0.039    714
  Dihedral  :  5.327  23.602    541
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 12.47 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.67 (0.38), residues: 498
  helix: -1.34 (0.71), residues: 51
  sheet: -2.57 (0.66), residues: 60
  loop : -0.86 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 143 
 TYR   0.009   0.002   TYR A 409 
 PHE   0.012   0.001   PHE A 258 
 TRP   0.005   0.001   TRP A 482 
 HIS   0.004   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3977)
  covalent geometry    : angle       0.55833 ( 5404)
  SS BOND              : bond        0.00331 (   18)
  SS BOND              : angle       0.80523 (   36)
  hydrogen bonds       : bond        0.03497 (   90)
  hydrogen bonds       : angle       8.23679 (  162)

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

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

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  996 Ramachandran restraints generated.
    498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.237 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASN cc_start: 0.9074 (m-40) cc_final: 0.8786 (m-40)
REVERT: A  427 ASN cc_start: 0.9087 (t0) cc_final: 0.8834 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 42
  average time/residue: 0.2638
  time to fit residues: 12.8033
Evaluate side-chains
  43 residues out of total 433 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 TYR
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  347 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 47 optimal weight:    8.9990
   chunk 4 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0570
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.6902

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

Flipped N/Q/H residues before XYZ refinement:
** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 491 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.084762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.073906 restraints weight = 74747.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.076623 restraints weight = 40255.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.078414 restraints weight = 24988.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.079576 restraints weight = 17082.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.080374 restraints weight = 12688.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6733
moved from start:          0.5951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3995  Z= 0.107
  Angle     :  0.547   3.980   5440  Z= 0.293
  Chirality :  0.041   0.150    603
  Planarity :  0.004   0.041    714
  Dihedral  :  5.235  22.974    541
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.24 %
    Favored  : 86.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.56 (0.38), residues: 498
  helix: -1.22 (0.74), residues: 51
  sheet: -2.37 (0.74), residues: 50
  loop : -0.86 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 143 
 TYR   0.016   0.002   TYR A 441 
 PHE   0.013   0.001   PHE A 258 
 TRP   0.006   0.001   TRP A 482 
 HIS   0.004   0.001   HIS A 470 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 3977)
  covalent geometry    : angle       0.54560 ( 5404)
  SS BOND              : bond        0.00229 (   18)
  SS BOND              : angle       0.77603 (   36)
  hydrogen bonds       : bond        0.03424 (   90)
  hydrogen bonds       : angle       8.19739 (  162)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2239.47 seconds
wall clock time: 38 minutes 43.67 seconds (2323.67 seconds total)