Starting phenix.real_space_refine
on Tue Feb  3 14:51:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lk7_63170/02_2026/9lk7_63170.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lk7_63170/02_2026/9lk7_63170.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lk7_63170/02_2026/9lk7_63170.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lk7_63170/02_2026/9lk7_63170.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lk7_63170/02_2026/9lk7_63170.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lk7_63170/02_2026/9lk7_63170.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.035
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      41      5.16       5
     C    2625      2.51       5
     N     591      2.21       5
     O     674      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3931
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3931
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 497, 3931
          Classifications: {'peptide': 497}
          Link IDs: {'PTRANS': 24, 'TRANS': 472}
          Chain breaks: 4
  Time building chain proxies: 1.01, per 1000 atoms: 0.26
  Number of scatterers: 3931
  At special positions: 0
  Unit cell: (77.35, 65.45, 90.95, 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      41     16.00
     O     674      8.00
     N     591      7.00
     C    2625      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  98 " - pdb=" SG  CYS A 515 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 126 " - pdb=" SG  CYS A 486 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 171 " - pdb=" SG  CYS A 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 334 " - pdb=" SG  CYS A 338 " distance=2.07
    Simple disulfide: pdb=" SG  CYS A 334 " - pdb=" SG  CYS A 339 " 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: 0.30
  Conformation dependent library (CDL) restraints added in 145.8 milliseconds
  

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  914

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 1 sheets defined
      71.8% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 83
    Processing helix  chain 'A' and resid 85 through 87
      No H-bonds generated for 'chain 'A' and resid 85 through 87'
    Processing helix  chain 'A' and resid 88 through 95
    Processing helix  chain 'A' and resid 100 through 115
    Processing helix  chain 'A' and resid 120 through 125
      removed outlier: 4.053A  pdb=" N   VAL A 125 " --> pdb=" O   CYS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 129 through 147
      removed outlier: 3.927A  pdb=" N   GLY A 133 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   VAL A 145 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   TYR A 146 " --> pdb=" O   HIS A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 161
    Processing helix  chain 'A' and resid 201 through 210
    Processing helix  chain 'A' and resid 225 through 238
      removed outlier: 3.559A  pdb=" N   CYS A 231 " --> pdb=" O   GLU A 227 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ILE A 238 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 258
      removed outlier: 3.827A  pdb=" N   ALA A 258 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 255 through 258'
    Processing helix  chain 'A' and resid 259 through 275
    Processing helix  chain 'A' and resid 278 through 287
      removed outlier: 3.619A  pdb=" N   ILE A 282 " --> pdb=" O   ALA A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 294
      removed outlier: 3.610A  pdb=" N   LEU A 293 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   SER A 294 " --> pdb=" O   SER A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 306
      removed outlier: 4.140A  pdb=" N   TRP A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A 302 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 364
      removed outlier: 3.673A  pdb=" N   SER A 354 " --> pdb=" O   PHE A 350 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   VAL A 355 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU A 356 " --> pdb=" O   ILE A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 370
      removed outlier: 3.556A  pdb=" N   VAL A 370 " --> pdb=" O   ILE A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 379
    Processing helix  chain 'A' and resid 380 through 388
    Processing helix  chain 'A' and resid 391 through 423
      removed outlier: 3.693A  pdb=" N   LEU A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   PHE A 399 " --> pdb=" O   TRP A 395 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   PHE A 400 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ASP A 409 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   SER A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ALA A 421 " --> pdb=" O   SER A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 452
      removed outlier: 3.511A  pdb=" N   VAL A 445 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A 452 " --> pdb=" O   TYR A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 456
      removed outlier: 4.060A  pdb=" N   THR A 456 " --> pdb=" O   VAL A 453 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 453 through 456'
    Processing helix  chain 'A' and resid 458 through 470
      removed outlier: 4.256A  pdb=" N   ILE A 462 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE A 463 " --> pdb=" O   GLY A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 489
      removed outlier: 3.977A  pdb=" N   ILE A 487 " --> pdb=" O   GLU A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 504
    Processing helix  chain 'A' and resid 509 through 518
      removed outlier: 4.313A  pdb=" N   LYS A 513 " --> pdb=" O   PRO A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 534
      removed outlier: 3.820A  pdb=" N   CYS A 524 " --> pdb=" O   THR A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 543
      No H-bonds generated for 'chain 'A' and resid 541 through 543'
    Processing helix  chain 'A' and resid 547 through 563
      removed outlier: 3.566A  pdb=" N   TYR A 551 " --> pdb=" O   PRO A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 575
      removed outlier: 3.580A  pdb=" N   LEU A 567 " --> pdb=" O   LEU A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 589
      removed outlier: 3.714A  pdb=" N   LEU A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 539 through 540

    209 hydrogen bonds defined for protein.
    615 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.59

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 611
        1.32 -     1.45: 1190
        1.45 -     1.57: 2191
        1.57 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 4050
  Sorted by residual:
  bond pdb=" N   CYS A 334 "
       pdb=" CA  CYS A 334 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.034 1.08e-02 8.57e+03 1.01e+01
  bond pdb=" C   PRO A  91 "
       pdb=" O   PRO A  91 "
    ideal  model  delta    sigma   weight residual
    1.237  1.200  0.037 1.26e-02 6.30e+03 8.72e+00
  bond pdb=" C   PRO A 167 "
       pdb=" O   PRO A 167 "
    ideal  model  delta    sigma   weight residual
    1.238  1.205  0.033 1.22e-02 6.72e+03 7.38e+00
  bond pdb=" N   PRO A  91 "
       pdb=" CA  PRO A  91 "
    ideal  model  delta    sigma   weight residual
    1.472  1.444  0.028 1.32e-02 5.74e+03 4.46e+00
  bond pdb=" C   LEU A 166 "
       pdb=" N   PRO A 167 "
    ideal  model  delta    sigma   weight residual
    1.337  1.359 -0.022 1.24e-02 6.50e+03 3.18e+00
  ... (remaining 4045 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 5346
        1.40 -     2.80: 128
        2.80 -     4.20: 32
        4.20 -     5.59: 14
        5.59 -     6.99: 3
  Bond angle restraints: 5523
  Sorted by residual:
  angle pdb=" C   PRO A  91 "
        pdb=" CA  PRO A  91 "
        pdb=" CB  PRO A  91 "
      ideal   model   delta    sigma   weight residual
     112.62  106.74    5.88 1.65e+00 3.67e-01 1.27e+01
  angle pdb=" N   PRO A  91 "
        pdb=" CA  PRO A  91 "
        pdb=" C   PRO A  91 "
      ideal   model   delta    sigma   weight residual
     113.53  108.68    4.85 1.39e+00 5.18e-01 1.22e+01
  angle pdb=" O   ILE A  90 "
        pdb=" C   ILE A  90 "
        pdb=" N   PRO A  91 "
      ideal   model   delta    sigma   weight residual
     120.07  117.94    2.13 7.10e-01 1.98e+00 9.01e+00
  angle pdb=" C   PRO A 167 "
        pdb=" CA  PRO A 167 "
        pdb=" CB  PRO A 167 "
      ideal   model   delta    sigma   weight residual
     111.31  106.59    4.72 1.61e+00 3.86e-01 8.58e+00
  angle pdb=" CA  ILE A  90 "
        pdb=" C   ILE A  90 "
        pdb=" N   PRO A  91 "
      ideal   model   delta    sigma   weight residual
     121.00  123.30   -2.30 8.30e-01 1.45e+00 7.70e+00
  ... (remaining 5518 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.95: 1932
       13.95 -    27.90: 246
       27.90 -    41.85: 106
       41.85 -    55.80: 18
       55.80 -    69.75: 14
  Dihedral angle restraints: 2316
    sinusoidal: 882
      harmonic: 1434
  Sorted by residual:
  dihedral pdb=" CB  CYS A  98 "
           pdb=" SG  CYS A  98 "
           pdb=" SG  CYS A 515 "
           pdb=" CB  CYS A 515 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.32  -61.32     1      1.00e+01 1.00e-02 4.99e+01
  dihedral pdb=" CB  CYS A 334 "
           pdb=" SG  CYS A 334 "
           pdb=" SG  CYS A 338 "
           pdb=" CB  CYS A 338 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -53.96  -32.04     1      1.00e+01 1.00e-02 1.46e+01
  dihedral pdb=" CA  ILE A 518 "
           pdb=" C   ILE A 518 "
           pdb=" N   MET A 519 "
           pdb=" CA  MET A 519 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.32  -16.68     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 2313 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 386
       0.031 -    0.061: 168
       0.061 -    0.092: 48
       0.092 -    0.123: 17
       0.123 -    0.153: 3
  Chirality restraints: 622
  Sorted by residual:
  chirality pdb=" CB  ILE A  68 "
            pdb=" CA  ILE A  68 "
            pdb=" CG1 ILE A  68 "
            pdb=" CG2 ILE A  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.88e-01
  chirality pdb=" CA  CYS A 515 "
            pdb=" N   CYS A 515 "
            pdb=" C   CYS A 515 "
            pdb=" CB  CYS A 515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  VAL A 365 "
            pdb=" N   VAL A 365 "
            pdb=" C   VAL A 365 "
            pdb=" CB  VAL A 365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.08e-01
  ... (remaining 619 not shown)

  Planarity restraints: 670
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  96 "   -0.010 2.00e-02 2.50e+03   1.52e-02 4.03e+00
        pdb=" CG  PHE A  96 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  96 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  96 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  96 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  96 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  96 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 175 "   -0.012 2.00e-02 2.50e+03   1.15e-02 3.28e+00
        pdb=" CG  TRP A 175 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 175 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 175 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 175 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 175 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 175 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 175 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 175 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 175 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 365 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO A 366 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 366 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 366 "    0.022 5.00e-02 4.00e+02
  ... (remaining 667 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 38
        2.66 -     3.22: 3808
        3.22 -     3.78: 5879
        3.78 -     4.34: 7601
        4.34 -     4.90: 12618
  Nonbonded interactions: 29944
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 310 "
            pdb=" OE1 GLU A 483 "
     model   vdw
     2.101 3.040
  nonbonded pdb=" O   ASP A 467 "
            pdb=" OG  SER A 472 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" O   SER A 373 "
            pdb=" OG  SER A 373 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG  SER A 201 "
            pdb=" OE1 GLN A 363 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" O   PRO A 383 "
            pdb=" OG1 THR A 387 "
     model   vdw
     2.293 3.040
  ... (remaining 29939 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:             0.900
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.630
  Find NCS groups from input model:        0.010
  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:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
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      :  0.003   0.043   4055  Z= 0.159
  Angle     :  0.610   7.902   5533  Z= 0.334
  Chirality :  0.039   0.153    622
  Planarity :  0.004   0.040    670
  Dihedral  : 15.880  69.749   1387
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  : 25.59 %
    Favored  : 74.17 %
  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 are not related in a simple way.
  whole: -0.42 (0.39), residues: 487
  helix:  0.58 (0.30), residues: 311
  sheet:  None (None), residues: 0
  loop : -1.81 (0.48), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 123 
 TYR   0.026   0.001   TYR A 310 
 PHE   0.034   0.001   PHE A  96 
 TRP   0.031   0.001   TRP A 175 
 HIS   0.002   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4050)
  covalent geometry    : angle       0.59860 ( 5523)
  SS BOND              : bond        0.02033 (    5)
  SS BOND              : angle       2.76892 (   10)
  hydrogen bonds       : bond        0.22531 (  209)
  hydrogen bonds       : angle       6.57910 (  615)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.139 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 80
  average time/residue: 0.0599
  time to fit residues: 6.2087
Evaluate side-chains
  78 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 363 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.180578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.165117 restraints weight = 5405.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.168572 restraints weight = 3127.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.170919 restraints weight = 2054.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.172559 restraints weight = 1490.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.173584 restraints weight = 1158.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4055  Z= 0.198
  Angle     :  0.673   9.957   5533  Z= 0.350
  Chirality :  0.044   0.132    622
  Planarity :  0.005   0.039    670
  Dihedral  :  4.648  36.480    532
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 22.51 %
    Favored  : 71.80 %
  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 are not related in a simple way.
  whole: -0.51 (0.38), residues: 487
  helix:  0.65 (0.29), residues: 315
  sheet:  None (None), residues: 0
  loop : -2.24 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 292 
 TYR   0.017   0.002   TYR A  78 
 PHE   0.016   0.002   PHE A 530 
 TRP   0.015   0.002   TRP A 175 
 HIS   0.004   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 4050)
  covalent geometry    : angle       0.66453 ( 5523)
  SS BOND              : bond        0.00627 (    5)
  SS BOND              : angle       2.62830 (   10)
  hydrogen bonds       : bond        0.05781 (  209)
  hydrogen bonds       : angle       4.56940 (  615)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7484 (t80)
REVERT: A  230 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7965 (tp)
REVERT: A  336 MET cc_start: 0.6113 (tpt) cc_final: 0.5706 (tpt)
REVERT: A  502 ASP cc_start: 0.6340 (t0) cc_final: 0.6115 (t0)
  outliers start: 24
  outliers final: 12
  residues processed: 90
  average time/residue: 0.0374
  time to fit residues: 4.5268
Evaluate side-chains
  85 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  306 ILE
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain A residue  553 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0020
   chunk 3 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.6388

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.185380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.168879 restraints weight = 5266.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.172476 restraints weight = 3018.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.174984 restraints weight = 1983.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.176618 restraints weight = 1435.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.177778 restraints weight = 1117.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7176
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   4055  Z= 0.139
  Angle     :  0.639  10.652   5533  Z= 0.325
  Chirality :  0.041   0.175    622
  Planarity :  0.004   0.040    670
  Dihedral  :  4.667  39.176    532
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 22.75 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.39), residues: 487
  helix:  1.04 (0.30), residues: 315
  sheet:  None (None), residues: 0
  loop : -2.29 (0.46), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 332 
 TYR   0.012   0.001   TYR A 310 
 PHE   0.010   0.001   PHE A 530 
 TRP   0.028   0.001   TRP A 175 
 HIS   0.002   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4050)
  covalent geometry    : angle       0.60223 ( 5523)
  SS BOND              : bond        0.01876 (    5)
  SS BOND              : angle       5.04244 (   10)
  hydrogen bonds       : bond        0.04768 (  209)
  hydrogen bonds       : angle       4.23008 (  615)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7159 (t80)
REVERT: A  336 MET cc_start: 0.6223 (tpt) cc_final: 0.5889 (tpt)
REVERT: A  452 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8355 (mp)
  outliers start: 22
  outliers final: 12
  residues processed: 90
  average time/residue: 0.0570
  time to fit residues: 6.8053
Evaluate side-chains
  82 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  240 TYR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  541 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0370
   chunk 11 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.5264

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.187348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.172185 restraints weight = 5317.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.175226 restraints weight = 3210.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.177173 restraints weight = 2198.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.178691 restraints weight = 1663.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.179951 restraints weight = 1328.867|
|-----------------------------------------------------------------------------|
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   4055  Z= 0.181
  Angle     :  0.667  10.732   5533  Z= 0.338
  Chirality :  0.043   0.152    622
  Planarity :  0.005   0.042    670
  Dihedral  :  4.706  40.659    532
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  6.87 %
    Allowed  : 21.33 %
    Favored  : 71.80 %
  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 are not related in a simple way.
  whole: -0.29 (0.39), residues: 487
  helix:  0.97 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -2.48 (0.45), residues: 173

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 292 
 TYR   0.014   0.001   TYR A  78 
 PHE   0.014   0.001   PHE A 530 
 TRP   0.027   0.002   TRP A 175 
 HIS   0.002   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 4050)
  covalent geometry    : angle       0.64293 ( 5523)
  SS BOND              : bond        0.00960 (    5)
  SS BOND              : angle       4.18785 (   10)
  hydrogen bonds       : bond        0.05108 (  209)
  hydrogen bonds       : angle       4.26517 (  615)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 73
  time to evaluate  : 0.135 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7465 (t80)
REVERT: A  230 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7897 (tp)
REVERT: A  336 MET cc_start: 0.6394 (tpt) cc_final: 0.6059 (tpt)
REVERT: A  452 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8341 (mp)
  outliers start: 29
  outliers final: 22
  residues processed: 93
  average time/residue: 0.0514
  time to fit residues: 6.4158
Evaluate side-chains
  96 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  230 LEU
Chi-restraints excluded: chain A residue  240 TYR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  298 VAL
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  327 ASN
Chi-restraints excluded: chain A residue  331 TYR
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  553 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0770
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 33 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0670
   overall best weight:    1.0280

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.183213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.166831 restraints weight = 5380.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.170426 restraints weight = 3139.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.172867 restraints weight = 2082.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.174431 restraints weight = 1523.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.175572 restraints weight = 1197.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   4055  Z= 0.145
  Angle     :  0.625  10.600   5533  Z= 0.315
  Chirality :  0.042   0.191    622
  Planarity :  0.004   0.044    670
  Dihedral  :  4.713  42.613    532
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  6.64 %
    Allowed  : 22.75 %
    Favored  : 70.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.39), residues: 487
  helix:  1.17 (0.30), residues: 316
  sheet:  None (None), residues: 0
  loop : -2.45 (0.46), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 292 
 TYR   0.009   0.001   TYR A 240 
 PHE   0.013   0.001   PHE A 530 
 TRP   0.018   0.001   TRP A 175 
 HIS   0.004   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4050)
  covalent geometry    : angle       0.60169 ( 5523)
  SS BOND              : bond        0.01250 (    5)
  SS BOND              : angle       4.03129 (   10)
  hydrogen bonds       : bond        0.04539 (  209)
  hydrogen bonds       : angle       4.12185 (  615)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7226 (t80)
REVERT: A  151 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6510 (mt)
REVERT: A  182 GLU cc_start: 0.6169 (mm-30) cc_final: 0.5941 (mm-30)
REVERT: A  264 MET cc_start: 0.7622 (tpt) cc_final: 0.7335 (mmm)
REVERT: A  336 MET cc_start: 0.6305 (tpt) cc_final: 0.5946 (tpt)
REVERT: A  452 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8341 (mp)
  outliers start: 28
  outliers final: 17
  residues processed: 94
  average time/residue: 0.0525
  time to fit residues: 6.5491
Evaluate side-chains
  90 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  240 TYR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  370 VAL
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  541 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 45 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0060
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0970
   chunk 0 optimal weight:    7.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.184277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.167642 restraints weight = 5412.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.171315 restraints weight = 3123.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.173767 restraints weight = 2068.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.175512 restraints weight = 1505.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.176783 restraints weight = 1167.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4055  Z= 0.123
  Angle     :  0.598  10.743   5533  Z= 0.300
  Chirality :  0.040   0.200    622
  Planarity :  0.004   0.042    670
  Dihedral  :  4.628  43.589    532
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 25.36 %
    Favored  : 69.43 %
  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 are not related in a simple way.
  whole:  0.21 (0.40), residues: 487
  helix:  1.32 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -2.31 (0.48), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 292 
 TYR   0.009   0.001   TYR A 240 
 PHE   0.009   0.001   PHE A 530 
 TRP   0.013   0.001   TRP A 568 
 HIS   0.001   0.001   HIS A 173 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4050)
  covalent geometry    : angle       0.57523 ( 5523)
  SS BOND              : bond        0.01166 (    5)
  SS BOND              : angle       3.91870 (   10)
  hydrogen bonds       : bond        0.04096 (  209)
  hydrogen bonds       : angle       3.98913 (  615)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 74
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7062 (t80)
REVERT: A  151 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6510 (mt)
REVERT: A  182 GLU cc_start: 0.6144 (mm-30) cc_final: 0.5917 (mm-30)
REVERT: A  336 MET cc_start: 0.6274 (tpt) cc_final: 0.5907 (tpt)
REVERT: A  452 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8298 (mp)
  outliers start: 22
  outliers final: 16
  residues processed: 88
  average time/residue: 0.0566
  time to fit residues: 6.5270
Evaluate side-chains
  93 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  240 TYR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  331 TYR
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  455 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 4 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 42 optimal weight:    0.7980
   chunk 15 optimal weight:    0.3980
   chunk 19 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.192853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.178508 restraints weight = 5334.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.181412 restraints weight = 3299.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.183478 restraints weight = 2292.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.184767 restraints weight = 1724.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.185930 restraints weight = 1393.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.2190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4055  Z= 0.125
  Angle     :  0.601  10.609   5533  Z= 0.302
  Chirality :  0.041   0.217    622
  Planarity :  0.004   0.041    670
  Dihedral  :  4.620  44.549    532
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 25.36 %
    Favored  : 69.19 %
  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 are not related in a simple way.
  whole:  0.27 (0.40), residues: 487
  helix:  1.40 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.29 (0.48), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 292 
 TYR   0.009   0.001   TYR A 240 
 PHE   0.009   0.001   PHE A 530 
 TRP   0.013   0.001   TRP A 549 
 HIS   0.001   0.000   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 4050)
  covalent geometry    : angle       0.57508 ( 5523)
  SS BOND              : bond        0.01194 (    5)
  SS BOND              : angle       4.11599 (   10)
  hydrogen bonds       : bond        0.04094 (  209)
  hydrogen bonds       : angle       3.95700 (  615)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8039 (OUTLIER) cc_final: 0.7151 (t80)
REVERT: A  151 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6822 (mt)
REVERT: A  264 MET cc_start: 0.7463 (tpt) cc_final: 0.7180 (mmm)
REVERT: A  336 MET cc_start: 0.6272 (tpt) cc_final: 0.5988 (tpt)
REVERT: A  452 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8332 (mp)
  outliers start: 23
  outliers final: 17
  residues processed: 92
  average time/residue: 0.0572
  time to fit residues: 6.9391
Evaluate side-chains
  92 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  240 TYR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  339 CYS
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  541 ASN
Chi-restraints excluded: chain A residue  553 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 19 optimal weight:    0.4980
   chunk 1 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0970
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.190303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.175893 restraints weight = 5336.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.178689 restraints weight = 3317.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.180804 restraints weight = 2332.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.182281 restraints weight = 1755.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.183182 restraints weight = 1404.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   4055  Z= 0.131
  Angle     :  0.614  11.087   5533  Z= 0.314
  Chirality :  0.041   0.222    622
  Planarity :  0.004   0.041    670
  Dihedral  :  4.795  45.078    532
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 24.64 %
    Favored  : 69.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.29 (0.40), residues: 487
  helix:  1.43 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -2.40 (0.48), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 292 
 TYR   0.009   0.001   TYR A 240 
 PHE   0.008   0.001   PHE A 530 
 TRP   0.013   0.001   TRP A 549 
 HIS   0.001   0.000   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 4050)
  covalent geometry    : angle       0.60613 ( 5523)
  SS BOND              : bond        0.01827 (    5)
  SS BOND              : angle       2.41528 (   10)
  hydrogen bonds       : bond        0.03972 (  209)
  hydrogen bonds       : angle       3.91590 (  615)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A   95 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7070 (t80)
REVERT: A  151 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6822 (mt)
REVERT: A  182 GLU cc_start: 0.6860 (mm-30) cc_final: 0.6247 (mm-30)
REVERT: A  264 MET cc_start: 0.7464 (tpt) cc_final: 0.7183 (mmm)
REVERT: A  336 MET cc_start: 0.6128 (tpt) cc_final: 0.5920 (tpt)
REVERT: A  452 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8340 (mp)
  outliers start: 24
  outliers final: 16
  residues processed: 88
  average time/residue: 0.0573
  time to fit residues: 6.6755
Evaluate side-chains
  88 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  240 TYR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  331 TYR
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  443 LEU
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  541 ASN
Chi-restraints excluded: chain A residue  553 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 23 optimal weight:    0.1980
   chunk 28 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0060
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 22 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.186640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.170375 restraints weight = 5366.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.173965 restraints weight = 3080.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.176212 restraints weight = 2031.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.178039 restraints weight = 1498.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.179183 restraints weight = 1160.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075   4055  Z= 0.133
  Angle     :  0.634  12.003   5533  Z= 0.321
  Chirality :  0.041   0.224    622
  Planarity :  0.004   0.041    670
  Dihedral  :  5.043  51.275    532
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 25.83 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.40), residues: 487
  helix:  1.40 (0.30), residues: 327
  sheet:  None (None), residues: 0
  loop : -2.60 (0.47), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 292 
 TYR   0.009   0.001   TYR A 240 
 PHE   0.008   0.001   PHE A  76 
 TRP   0.014   0.001   TRP A 549 
 HIS   0.001   0.000   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 4050)
  covalent geometry    : angle       0.60849 ( 5523)
  SS BOND              : bond        0.02284 (    5)
  SS BOND              : angle       4.26221 (   10)
  hydrogen bonds       : bond        0.03820 (  209)
  hydrogen bonds       : angle       3.85969 (  615)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.097 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.6829 (t80)
REVERT: A  151 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6673 (mt)
REVERT: A  182 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6274 (mm-30)
REVERT: A  264 MET cc_start: 0.7465 (tpt) cc_final: 0.7165 (mmm)
REVERT: A  336 MET cc_start: 0.6156 (tpt) cc_final: 0.5922 (tpt)
REVERT: A  452 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8313 (mp)
  outliers start: 20
  outliers final: 16
  residues processed: 86
  average time/residue: 0.0438
  time to fit residues: 5.1382
Evaluate side-chains
  88 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 69
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  240 TYR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  331 TYR
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  541 ASN
Chi-restraints excluded: chain A residue  553 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.183844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.169573 restraints weight = 5373.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.172663 restraints weight = 3292.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.174500 restraints weight = 2256.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.176104 restraints weight = 1704.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.177002 restraints weight = 1347.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.113   4055  Z= 0.153
  Angle     :  0.692  17.049   5533  Z= 0.347
  Chirality :  0.042   0.233    622
  Planarity :  0.004   0.041    670
  Dihedral  :  5.194  53.775    532
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 25.59 %
    Favored  : 69.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.40), residues: 487
  helix:  1.34 (0.30), residues: 328
  sheet:  None (None), residues: 0
  loop : -2.56 (0.48), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 292 
 TYR   0.009   0.001   TYR A 240 
 PHE   0.009   0.001   PHE A 530 
 TRP   0.015   0.001   TRP A 549 
 HIS   0.001   0.000   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 4050)
  covalent geometry    : angle       0.64524 ( 5523)
  SS BOND              : bond        0.02708 (    5)
  SS BOND              : angle       5.94540 (   10)
  hydrogen bonds       : bond        0.03946 (  209)
  hydrogen bonds       : angle       3.88429 (  615)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A   95 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7032 (t80)
REVERT: A  151 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6773 (mt)
REVERT: A  182 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6287 (mm-30)
REVERT: A  264 MET cc_start: 0.7463 (tpt) cc_final: 0.7178 (mmm)
REVERT: A  336 MET cc_start: 0.6308 (tpt) cc_final: 0.6001 (tpt)
REVERT: A  452 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8298 (mp)
  outliers start: 20
  outliers final: 14
  residues processed: 86
  average time/residue: 0.0527
  time to fit residues: 6.0631
Evaluate side-chains
  86 residues out of total 422 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue   95 PHE
Chi-restraints excluded: chain A residue   98 CYS
Chi-restraints excluded: chain A residue  144 ASN
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  215 SER
Chi-restraints excluded: chain A residue  240 TYR
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  331 TYR
Chi-restraints excluded: chain A residue  350 PHE
Chi-restraints excluded: chain A residue  392 SER
Chi-restraints excluded: chain A residue  452 LEU
Chi-restraints excluded: chain A residue  553 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 26 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 541 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.178470 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.162940 restraints weight = 5416.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.166281 restraints weight = 3095.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.168662 restraints weight = 2042.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.170260 restraints weight = 1476.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.171292 restraints weight = 1144.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.118   4055  Z= 0.214
  Angle     :  0.767  16.867   5533  Z= 0.392
  Chirality :  0.045   0.266    622
  Planarity :  0.005   0.043    670
  Dihedral  :  5.551  53.117    532
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 25.59 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.21 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.40), residues: 487
  helix:  0.99 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -2.39 (0.50), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 332 
 TYR   0.017   0.002   TYR A 331 
 PHE   0.018   0.002   PHE A 530 
 TRP   0.033   0.002   TRP A 122 
 HIS   0.003   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00520 ( 4050)
  covalent geometry    : angle       0.72158 ( 5523)
  SS BOND              : bond        0.02752 (    5)
  SS BOND              : angle       6.12855 (   10)
  hydrogen bonds       : bond        0.05296 (  209)
  hydrogen bonds       : angle       4.31538 (  615)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 814.66 seconds
wall clock time: 14 minutes 44.39 seconds (884.39 seconds total)