Starting phenix.real_space_refine
on Thu Mar  6 02:45:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8afx_15411/03_2025/8afx_15411.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8afx_15411/03_2025/8afx_15411.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8afx_15411/03_2025/8afx_15411.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8afx_15411/03_2025/8afx_15411.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8afx_15411/03_2025/8afx_15411.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8afx_15411/03_2025/8afx_15411.cif"
  }
  resolution = 4.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2498 atoms to isotropic.
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      17      5.16       5
     C    1603      2.51       5
     N     406      2.21       5
     O     472      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 2498
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 321, 2498
          Classifications: {'peptide': 321}
          Link IDs: {'PTRANS': 16, 'TRANS': 304}
          Chain breaks: 4
  Time building chain proxies: 2.54, per 1000 atoms: 1.02
  Number of scatterers: 2498
  At special positions: 0
  Unit cell: (68.7898, 65.4342, 69.6287, 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      17     16.00
     O     472      8.00
     N     406      7.00
     C    1603      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 314.4 milliseconds
  

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  600

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 45.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13
      removed outlier: 4.119A  pdb=" N   PHE A  10 " --> pdb=" O   GLY A  23 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   GLY A  23 " --> pdb=" O   PHE A  10 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ASN A  12 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TYR A  40 " --> pdb=" O   ILE A  30 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   ASN A  32 " --> pdb=" O   LYS A  38 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   LYS A  38 " --> pdb=" O   ASN A  32 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 52
      removed outlier: 6.755A  pdb=" N   VAL A  62 " --> pdb=" O   ALA A  48 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   VAL A  50 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   ALA A  60 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   LEU A  75 " --> pdb=" O   GLU A  88 " (cutoff:3.500A)
      removed outlier: 4.999A  pdb=" N   GLU A  88 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   ILE A  77 " --> pdb=" O   ILE A  86 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER A  84 " --> pdb=" O   ASN A  79 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 108
      removed outlier: 7.134A  pdb=" N   ILE A 113 " --> pdb=" O   THR A 126 " (cutoff:3.500A)
      removed outlier: 5.005A  pdb=" N   THR A 126 " --> pdb=" O   ILE A 113 " (cutoff:3.500A)
      removed outlier: 7.246A  pdb=" N   ILE A 115 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139
      removed outlier: 3.556A  pdb=" N   TYR A 150 " --> pdb=" O   ILE A 228 " (cutoff:3.500A)
      removed outlier: 7.414A  pdb=" N   GLY A 225 " --> pdb=" O   GLU A 242 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   GLU A 242 " --> pdb=" O   GLY A 225 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL A 227 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   VAL A 240 " --> pdb=" O   VAL A 227 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   VAL A 229 " --> pdb=" O   THR A 238 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLN A 236 " --> pdb=" O   ASN A 231 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 253
      removed outlier: 6.211A  pdb=" N   ALA A 263 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   MET A 251 " --> pdb=" O   ALA A 261 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ALA A 261 " --> pdb=" O   MET A 251 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   ILE A 253 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   LEU A 259 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ARG A 271 " --> pdb=" O   THR A 262 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   SER A 264 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ILE A 269 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   TYR A 282 " --> pdb=" O   VAL A 272 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP A 274 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   LYS A 280 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 293 through 298
      removed outlier: 6.991A  pdb=" N   THR A 308 " --> pdb=" O   TYR A 294 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   ILE A 296 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   ALA A 306 " --> pdb=" O   ILE A 296 " (cutoff:3.500A)
      removed outlier: 5.046A  pdb=" N   PHE A 298 " --> pdb=" O   TYR A 304 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   TYR A 304 " --> pdb=" O   PHE A 298 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   GLY A 309 " --> pdb=" O   THR A 313 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   THR A 313 " --> pdb=" O   GLY A 309 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE A 316 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ALA A 413 " --> pdb=" O   ILE A 316 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 427 through 431
      removed outlier: 3.571A  pdb=" N   ARG A 468 " --> pdb=" O   SER A 430 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   MET A 462 " --> pdb=" O   ILE A 437 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ILE A 437 " --> pdb=" O   MET A 462 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 427 through 431
      removed outlier: 3.571A  pdb=" N   ARG A 468 " --> pdb=" O   SER A 430 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TYR A 475 " --> pdb=" O   SER A 471 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   ASN A 478 " --> pdb=" O   LEU A 492 " (cutoff:3.500A)

    60 hydrogen bonds defined for protein.
    165 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: 0.69

  Time building geometry restraints manager: 0.73 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 784
        1.34 -     1.46: 559
        1.46 -     1.58: 1170
        1.58 -     1.70: 2
        1.70 -     1.81: 30
  Bond restraints: 2545
  Sorted by residual:
  bond pdb=" CB  PRO A 483 "
       pdb=" CG  PRO A 483 "
    ideal  model  delta    sigma   weight residual
    1.492  1.652 -0.160 5.00e-02 4.00e+02 1.03e+01
  bond pdb=" N   PRO A 483 "
       pdb=" CA  PRO A 483 "
    ideal  model  delta    sigma   weight residual
    1.470  1.446  0.025 1.01e-02 9.80e+03 5.90e+00
  bond pdb=" CB  PRO A 141 "
       pdb=" CG  PRO A 141 "
    ideal  model  delta    sigma   weight residual
    1.492  1.602 -0.110 5.00e-02 4.00e+02 4.86e+00
  bond pdb=" N   PRO A 483 "
       pdb=" CD  PRO A 483 "
    ideal  model  delta    sigma   weight residual
    1.473  1.499 -0.026 1.40e-02 5.10e+03 3.58e+00
  bond pdb=" CG  PRO A 483 "
       pdb=" CD  PRO A 483 "
    ideal  model  delta    sigma   weight residual
    1.503  1.446  0.057 3.40e-02 8.65e+02 2.81e+00
  ... (remaining 2540 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.35: 3411
        3.35 -     6.71: 22
        6.71 -    10.06: 7
       10.06 -    13.41: 1
       13.41 -    16.76: 1
  Bond angle restraints: 3442
  Sorted by residual:
  angle pdb=" CA  PRO A 483 "
        pdb=" N   PRO A 483 "
        pdb=" CD  PRO A 483 "
      ideal   model   delta    sigma   weight residual
     112.00   95.24   16.76 1.40e+00 5.10e-01 1.43e+02
  angle pdb=" N   PRO A 483 "
        pdb=" CD  PRO A 483 "
        pdb=" CG  PRO A 483 "
      ideal   model   delta    sigma   weight residual
     103.20   95.59    7.61 1.50e+00 4.44e-01 2.57e+01
  angle pdb=" C   PRO A 483 "
        pdb=" CA  PRO A 483 "
        pdb=" CB  PRO A 483 "
      ideal   model   delta    sigma   weight residual
     110.00  114.53   -4.53 1.12e+00 7.97e-01 1.64e+01
  angle pdb=" CA  PRO A 141 "
        pdb=" N   PRO A 141 "
        pdb=" CD  PRO A 141 "
      ideal   model   delta    sigma   weight residual
     112.00  106.66    5.34 1.40e+00 5.10e-01 1.46e+01
  angle pdb=" CA  LEU A 417 "
        pdb=" CB  LEU A 417 "
        pdb=" CG  LEU A 417 "
      ideal   model   delta    sigma   weight residual
     116.30  128.37  -12.07 3.50e+00 8.16e-02 1.19e+01
  ... (remaining 3437 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.68: 1315
       16.68 -    33.36: 178
       33.36 -    50.04: 38
       50.04 -    66.72: 6
       66.72 -    83.40: 3
  Dihedral angle restraints: 1540
    sinusoidal: 610
      harmonic: 930
  Sorted by residual:
  dihedral pdb=" CA  MET A 462 "
           pdb=" C   MET A 462 "
           pdb=" N   LYS A 463 "
           pdb=" CA  LYS A 463 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.79  -20.21     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  LEU A 108 "
           pdb=" C   LEU A 108 "
           pdb=" N   LEU A 109 "
           pdb=" CA  LEU A 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.43   17.57     0      5.00e+00 4.00e-02 1.24e+01
  dihedral pdb=" CA  VAL A  98 "
           pdb=" C   VAL A  98 "
           pdb=" N   LYS A  99 "
           pdb=" CA  LYS A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.50   16.50     0      5.00e+00 4.00e-02 1.09e+01
  ... (remaining 1537 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 284
       0.047 -    0.094: 85
       0.094 -    0.141: 36
       0.141 -    0.188: 0
       0.188 -    0.235: 1
  Chirality restraints: 406
  Sorted by residual:
  chirality pdb=" CA  PRO A 483 "
            pdb=" N   PRO A 483 "
            pdb=" C   PRO A 483 "
            pdb=" CB  PRO A 483 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.48    0.23 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  THR A  56 "
            pdb=" N   THR A  56 "
            pdb=" C   THR A  56 "
            pdb=" CB  THR A  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.40    0.13 2.00e-01 2.50e+01 4.19e-01
  chirality pdb=" CA  ILE A  85 "
            pdb=" N   ILE A  85 "
            pdb=" C   ILE A  85 "
            pdb=" CB  ILE A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.17e-01
  ... (remaining 403 not shown)

  Planarity restraints: 430
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 482 "   -0.084 5.00e-02 4.00e+02   1.14e-01 2.08e+01
        pdb=" N   PRO A 483 "    0.197 5.00e-02 4.00e+02
        pdb=" CA  PRO A 483 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO A 483 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 417 "   -0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO A 418 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 418 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 418 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 140 "   -0.026 5.00e-02 4.00e+02   3.85e-02 2.37e+00
        pdb=" N   PRO A 141 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 141 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 141 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 427 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 123
        2.71 -     3.26: 2430
        3.26 -     3.80: 3814
        3.80 -     4.35: 4506
        4.35 -     4.90: 7520
  Nonbonded interactions: 18393
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 471 "
            pdb=" OD1 ASP A 473 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OD1 ASN A  79 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OD1 ASN A 101 "
            pdb=" N   SER A 103 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" OG  SER A  44 "
            pdb=" OH  TYR A  47 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OD1 ASN A  14 "
            pdb=" N   GLY A  17 "
     model   vdw
     2.238 3.120
  ... (remaining 18388 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:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.070
  Find NCS groups from input model:        0.030
  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:3.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   17.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
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      :  0.005   0.160   2545  Z= 0.292
  Angle     :  0.901  16.763   3442  Z= 0.482
  Chirality :  0.051   0.235    406
  Planarity :  0.007   0.114    430
  Dihedral  : 16.079  83.399    940
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 17.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 28.22 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.46), residues: 311
  helix:  None (None), residues: 0
  sheet:  1.07 (0.45), residues: 121
  loop : -1.34 (0.43), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 411 
 PHE   0.019   0.002   PHE A 317 
 TYR   0.018   0.002   TYR A 116 
 ARG   0.003   0.001   ARG A 286 

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

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

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 72
  average time/residue: 0.1282
  time to fit residues: 11.2999
Evaluate side-chains
  64 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 13 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    0.9186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.121485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.110605 restraints weight = 5989.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.112271 restraints weight = 4253.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.113535 restraints weight = 3257.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   2545  Z= 0.227
  Angle     :  0.646   6.898   3442  Z= 0.330
  Chirality :  0.050   0.161    406
  Planarity :  0.005   0.054    430
  Dihedral  :  5.291  19.502    342
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.45), residues: 311
  helix:  None (None), residues: 0
  sheet:  1.07 (0.44), residues: 122
  loop : -1.34 (0.42), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 315 
 PHE   0.014   0.002   PHE A  39 
 TYR   0.010   0.001   TYR A 116 
 ARG   0.004   0.001   ARG A 292 

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

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

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.427 
Fit side-chains
REVERT: A  296 ILE cc_start: 0.9111 (pt) cc_final: 0.8896 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1539
  time to fit residues: 15.5773
Evaluate side-chains
  61 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 31 optimal weight:    6.9990
   chunk 22 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.106669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.096402 restraints weight = 6531.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.098118 restraints weight = 4472.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.099403 restraints weight = 3315.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   2545  Z= 0.271
  Angle     :  0.705   7.688   3442  Z= 0.353
  Chirality :  0.051   0.149    406
  Planarity :  0.004   0.039    430
  Dihedral  :  5.493  17.828    342
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.43), residues: 311
  helix:  None (None), residues: 0
  sheet:  0.55 (0.43), residues: 122
  loop : -1.57 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 315 
 PHE   0.022   0.003   PHE A  13 
 TYR   0.016   0.002   TYR A  47 
 ARG   0.003   0.001   ARG A 292 

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

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

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.312 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1284
  time to fit residues: 11.6558
Evaluate side-chains
  61 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.109029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.2967 r_free = 0.2967 target = 0.099238 restraints weight = 6345.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.101064 restraints weight = 4189.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.102434 restraints weight = 3030.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2545  Z= 0.205
  Angle     :  0.655   7.622   3442  Z= 0.327
  Chirality :  0.051   0.145    406
  Planarity :  0.004   0.033    430
  Dihedral  :  5.415  20.373    342
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.43), residues: 311
  helix:  None (None), residues: 0
  sheet:  0.51 (0.43), residues: 122
  loop : -1.55 (0.40), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  83 
 PHE   0.016   0.002   PHE A  39 
 TYR   0.019   0.002   TYR A  47 
 ARG   0.002   0.000   ARG A 134 

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

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

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LEU cc_start: 0.8939 (tp) cc_final: 0.8707 (tt)
REVERT: A  298 PHE cc_start: 0.8812 (m-80) cc_final: 0.8400 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1362
  time to fit residues: 13.5718
Evaluate side-chains
  64 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 28 optimal weight:    0.4980
   chunk 13 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.116550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.106307 restraints weight = 6227.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.108096 restraints weight = 4205.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.109502 restraints weight = 3094.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2545  Z= 0.234
  Angle     :  0.691   7.412   3442  Z= 0.347
  Chirality :  0.053   0.184    406
  Planarity :  0.004   0.045    430
  Dihedral  :  5.534  20.379    342
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.44), residues: 311
  helix:  None (None), residues: 0
  sheet:  0.67 (0.45), residues: 116
  loop : -1.61 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A 244 
 PHE   0.021   0.002   PHE A  13 
 TYR   0.027   0.002   TYR A 442 
 ARG   0.002   0.001   ARG A 485 

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

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

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 CYS cc_start: 0.8185 (m) cc_final: 0.7828 (m)
REVERT: A   34 GLU cc_start: 0.8847 (tp30) cc_final: 0.8188 (tm-30)
REVERT: A   47 TYR cc_start: 0.8680 (m-10) cc_final: 0.8161 (m-10)
REVERT: A   75 LEU cc_start: 0.9007 (tp) cc_final: 0.8518 (tt)
REVERT: A  298 PHE cc_start: 0.8858 (m-80) cc_final: 0.8518 (m-10)
REVERT: A  319 LEU cc_start: 0.8950 (mt) cc_final: 0.8736 (mt)
REVERT: A  492 LEU cc_start: 0.9261 (tp) cc_final: 0.8874 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1284
  time to fit residues: 12.6372
Evaluate side-chains
  63 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 0 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.117014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.106750 restraints weight = 6118.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.108371 restraints weight = 4271.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.109665 restraints weight = 3225.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2545  Z= 0.205
  Angle     :  0.659   7.750   3442  Z= 0.329
  Chirality :  0.052   0.196    406
  Planarity :  0.004   0.044    430
  Dihedral  :  5.297  21.921    342
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 11.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.44), residues: 311
  helix:  None (None), residues: 0
  sheet:  0.72 (0.45), residues: 116
  loop : -1.67 (0.40), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 315 
 PHE   0.024   0.002   PHE A 412 
 TYR   0.016   0.002   TYR A  47 
 ARG   0.003   0.000   ARG A 286 

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

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

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A   33 CYS cc_start: 0.8131 (m) cc_final: 0.7748 (m)
REVERT: A  134 ARG cc_start: 0.8934 (ttm110) cc_final: 0.8331 (mtp-110)
REVERT: A  136 LEU cc_start: 0.8937 (mm) cc_final: 0.8700 (mm)
REVERT: A  148 LEU cc_start: 0.8695 (tp) cc_final: 0.8454 (tp)
REVERT: A  298 PHE cc_start: 0.8803 (m-80) cc_final: 0.8508 (m-10)
REVERT: A  319 LEU cc_start: 0.9002 (mt) cc_final: 0.8771 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1335
  time to fit residues: 12.8189
Evaluate side-chains
  62 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0000
   chunk 4 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0980
   chunk 22 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 0 optimal weight:    0.5980
   overall best weight:    0.5386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.111722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.100937 restraints weight = 6365.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.102881 restraints weight = 4307.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.104373 restraints weight = 3145.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.3560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2545  Z= 0.181
  Angle     :  0.668   8.483   3442  Z= 0.325
  Chirality :  0.051   0.188    406
  Planarity :  0.003   0.041    430
  Dihedral  :  5.179  21.763    342
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.44), residues: 311
  helix:  None (None), residues: 0
  sheet:  1.01 (0.45), residues: 111
  loop : -1.81 (0.40), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  83 
 PHE   0.020   0.002   PHE A 317 
 TYR   0.020   0.002   TYR A  47 
 ARG   0.003   0.000   ARG A 286 

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

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

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A   33 CYS cc_start: 0.7719 (m) cc_final: 0.7198 (m)
REVERT: A   36 PHE cc_start: 0.7426 (t80) cc_final: 0.7205 (t80)
REVERT: A   75 LEU cc_start: 0.8825 (tp) cc_final: 0.8518 (tt)
REVERT: A   87 CYS cc_start: 0.8451 (p) cc_final: 0.8206 (p)
REVERT: A  134 ARG cc_start: 0.8860 (ttm110) cc_final: 0.8454 (mtp-110)
REVERT: A  136 LEU cc_start: 0.8909 (mm) cc_final: 0.8619 (mm)
REVERT: A  148 LEU cc_start: 0.8860 (tp) cc_final: 0.8551 (tp)
REVERT: A  273 PHE cc_start: 0.7256 (m-80) cc_final: 0.6788 (m-10)
REVERT: A  298 PHE cc_start: 0.8867 (m-80) cc_final: 0.8618 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1315
  time to fit residues: 12.9700
Evaluate side-chains
  65 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 29 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.123765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.112384 restraints weight = 6021.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.114266 restraints weight = 4242.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.115634 restraints weight = 3179.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2545  Z= 0.194
  Angle     :  0.668   8.488   3442  Z= 0.327
  Chirality :  0.051   0.189    406
  Planarity :  0.003   0.040    430
  Dihedral  :  5.194  23.389    342
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.44), residues: 311
  helix:  None (None), residues: 0
  sheet:  0.73 (0.44), residues: 123
  loop : -1.91 (0.41), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  83 
 PHE   0.018   0.002   PHE A 317 
 TYR   0.019   0.002   TYR A  47 
 ARG   0.003   0.000   ARG A 286 

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

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

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A   33 CYS cc_start: 0.7667 (m) cc_final: 0.7234 (m)
REVERT: A   75 LEU cc_start: 0.8868 (tp) cc_final: 0.8659 (tt)
REVERT: A   96 LEU cc_start: 0.8149 (tt) cc_final: 0.7884 (tt)
REVERT: A  134 ARG cc_start: 0.8972 (ttm110) cc_final: 0.8339 (mtp-110)
REVERT: A  136 LEU cc_start: 0.8858 (mm) cc_final: 0.8485 (mm)
REVERT: A  137 MET cc_start: 0.7513 (pmm) cc_final: 0.7270 (pmm)
REVERT: A  273 PHE cc_start: 0.7338 (m-80) cc_final: 0.6860 (m-10)
REVERT: A  280 LYS cc_start: 0.7929 (ptmt) cc_final: 0.7703 (ptmt)
REVERT: A  298 PHE cc_start: 0.8875 (m-80) cc_final: 0.8577 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1366
  time to fit residues: 13.0507
Evaluate side-chains
  63 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    0.1980
   chunk 11 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.5982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.124372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.113303 restraints weight = 5915.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.115182 restraints weight = 4098.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.116622 restraints weight = 3071.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2545  Z= 0.180
  Angle     :  0.675   9.123   3442  Z= 0.325
  Chirality :  0.051   0.189    406
  Planarity :  0.003   0.040    430
  Dihedral  :  5.138  23.956    342
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.45), residues: 311
  helix:  None (None), residues: 0
  sheet:  0.67 (0.47), residues: 120
  loop : -1.84 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  83 
 PHE   0.018   0.002   PHE A 317 
 TYR   0.017   0.001   TYR A  47 
 ARG   0.004   0.000   ARG A 286 

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

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

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A   33 CYS cc_start: 0.7812 (m) cc_final: 0.7412 (m)
REVERT: A   47 TYR cc_start: 0.8456 (m-10) cc_final: 0.8201 (m-10)
REVERT: A   75 LEU cc_start: 0.8809 (tp) cc_final: 0.8569 (tt)
REVERT: A  134 ARG cc_start: 0.8904 (ttm110) cc_final: 0.8377 (mtp-110)
REVERT: A  136 LEU cc_start: 0.8860 (mm) cc_final: 0.8565 (mm)
REVERT: A  251 MET cc_start: 0.8934 (mtp) cc_final: 0.8670 (mtp)
REVERT: A  273 PHE cc_start: 0.7118 (m-80) cc_final: 0.6786 (m-10)
REVERT: A  298 PHE cc_start: 0.8884 (m-80) cc_final: 0.8558 (m-10)
REVERT: A  319 LEU cc_start: 0.8930 (mt) cc_final: 0.8713 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1273
  time to fit residues: 11.5559
Evaluate side-chains
  60 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0070
   overall best weight:    0.5598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.123005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.111975 restraints weight = 6037.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.113846 restraints weight = 4182.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.115318 restraints weight = 3126.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.3950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   2545  Z= 0.172
  Angle     :  0.665   9.103   3442  Z= 0.321
  Chirality :  0.051   0.191    406
  Planarity :  0.003   0.040    430
  Dihedral  :  5.090  24.470    342
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.75 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.45), residues: 311
  helix:  None (None), residues: 0
  sheet:  0.36 (0.45), residues: 125
  loop : -1.77 (0.41), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  83 
 PHE   0.013   0.002   PHE A 317 
 TYR   0.014   0.001   TYR A  47 
 ARG   0.006   0.001   ARG A 286 

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

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

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  622 Ramachandran restraints generated.
    311 Oldfield, 0 Emsley, 311 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A   33 CYS cc_start: 0.7676 (m) cc_final: 0.7431 (m)
REVERT: A   47 TYR cc_start: 0.8436 (m-10) cc_final: 0.8221 (m-10)
REVERT: A   75 LEU cc_start: 0.8731 (tp) cc_final: 0.8394 (tt)
REVERT: A  134 ARG cc_start: 0.8889 (ttm110) cc_final: 0.8407 (mtp-110)
REVERT: A  136 LEU cc_start: 0.8788 (mm) cc_final: 0.8459 (mm)
REVERT: A  137 MET cc_start: 0.7337 (pmm) cc_final: 0.6879 (pmm)
REVERT: A  273 PHE cc_start: 0.7188 (m-80) cc_final: 0.6716 (m-10)
REVERT: A  298 PHE cc_start: 0.8823 (m-80) cc_final: 0.8485 (m-10)
REVERT: A  319 LEU cc_start: 0.8977 (mt) cc_final: 0.8738 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1253
  time to fit residues: 11.7275
Evaluate side-chains
  61 residues out of total 287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 32
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:    0.2980
   chunk 1 optimal weight:    0.7980
   chunk 21 optimal weight:    0.0070
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0010
   chunk 10 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.2204

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.115702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.103934 restraints weight = 6069.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.105937 restraints weight = 4188.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.107471 restraints weight = 3114.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.4145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   2545  Z= 0.149
  Angle     :  0.651   8.865   3442  Z= 0.312
  Chirality :  0.051   0.189    406
  Planarity :  0.003   0.030    430
  Dihedral  :  4.778  24.201    342
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.46), residues: 311
  helix:  None (None), residues: 0
  sheet:  0.77 (0.47), residues: 118
  loop : -1.81 (0.41), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  83 
 PHE   0.012   0.001   PHE A  39 
 TYR   0.013   0.001   TYR A  47 
 ARG   0.004   0.000   ARG A 286 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1311.91 seconds
wall clock time: 23 minutes 41.81 seconds (1421.81 seconds total)