Starting phenix.real_space_refine
on Thu Mar  6 03:11:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f6o_50236/03_2025/9f6o_50236.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f6o_50236/03_2025/9f6o_50236.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f6o_50236/03_2025/9f6o_50236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f6o_50236/03_2025/9f6o_50236.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f6o_50236/03_2025/9f6o_50236.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f6o_50236/03_2025/9f6o_50236.cif"
  }
  resolution = 3.9
  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=   0.001 sd=   0.025
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      25      5.16       5
     C    2995      2.51       5
     N     747      2.21       5
     O     804      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4571
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 471, 3651
          Classifications: {'peptide': 471}
          Link IDs: {'PTRANS': 16, 'TRANS': 454}
    Chain: "B"
      Number of atoms: 920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 920
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
  Time building chain proxies: 3.20, per 1000 atoms: 0.70
  Number of scatterers: 4571
  At special positions: 0
  Unit cell: (100.254, 72.912, 88.536, 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      25     16.00
     O     804      8.00
     N     747      7.00
     C    2995      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 363 " - pdb=" SG  CYS A 394 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 550.6 milliseconds
  

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1074

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 3 sheets defined
      70.1% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 102
    Processing helix  chain 'A' and resid 104 through 112
      removed outlier: 3.823A  pdb=" N   LEU A 108 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ILE A 111 " --> pdb=" O   PHE A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 128
      removed outlier: 3.623A  pdb=" N   SER A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 158
      removed outlier: 3.577A  pdb=" N   LEU A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 168
    Processing helix  chain 'A' and resid 171 through 205
      removed outlier: 3.578A  pdb=" N   ALA A 185 " --> pdb=" O   MET A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
      removed outlier: 3.866A  pdb=" N   THR A 218 " --> pdb=" O   GLY A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 232
      removed outlier: 3.728A  pdb=" N   THR A 222 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 259
    Processing helix  chain 'A' and resid 261 through 271
    Processing helix  chain 'A' and resid 278 through 293
    Processing helix  chain 'A' and resid 296 through 308
      removed outlier: 3.660A  pdb=" N   ARG A 308 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 350
      removed outlier: 4.011A  pdb=" N   VAL A 318 " --> pdb=" O   ASN A 314 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ARG A 319 " --> pdb=" O   LYS A 315 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLU A 320 " --> pdb=" O   GLN A 316 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ALA A 350 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 367
      removed outlier: 3.603A  pdb=" N   VAL A 359 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 430
      Proline residue:  A 398  - end of helix
      removed outlier: 3.739A  pdb=" N   LEU A 401 " --> pdb=" O   GLY A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 459
      removed outlier: 3.692A  pdb=" N   ILE A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
      removed outlier: 3.688A  pdb=" N   LEU A 454 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 478
      removed outlier: 3.867A  pdb=" N   ASN A 468 " --> pdb=" O   LEU A 464 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ASP A 469 " --> pdb=" O   THR A 465 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   PHE A 470 " --> pdb=" O   GLY A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 482
    Processing helix  chain 'A' and resid 483 through 490
      removed outlier: 3.640A  pdb=" N   LEU A 487 " --> pdb=" O   LEU A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 497
    Processing helix  chain 'A' and resid 502 through 532
      removed outlier: 3.645A  pdb=" N   VAL A 525 " --> pdb=" O   MET A 521 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A 526 " --> pdb=" O   TYR A 522 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU A 531 " --> pdb=" O   TYR A 527 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLY A 532 " --> pdb=" O   VAL A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 562
    Processing helix  chain 'B' and resid 28 through 32
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.628A  pdb=" N   THR B  91 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.857A  pdb=" N   GLN B   3 " --> pdb=" O   SER B  25 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER B  25 " --> pdb=" O   GLN B   3 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   VAL B  79 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.462A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   SER B 120 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   VAL B  12 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS B  99 " --> pdb=" O   GLY B  33 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   GLY B  33 " --> pdb=" O   LYS B  99 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ARG B  38 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 5.207A  pdb=" N   GLY B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.462A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 7.774A  pdb=" N   SER B 120 " --> pdb=" O   GLY B  10 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   VAL B  12 " --> pdb=" O   SER B 120 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   VAL B  98 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   TYR B 110 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ASP B 100 " --> pdb=" O   TYR B 108 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   TYR B 108 " --> pdb=" O   ASP B 100 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    933 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.30

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1421
        1.34 -     1.46: 1181
        1.46 -     1.58: 2040
        1.58 -     1.70: 0
        1.70 -     1.82: 39
  Bond restraints: 4681
  Sorted by residual:
  bond pdb=" N   GLY B  16 "
       pdb=" CA  GLY B  16 "
    ideal  model  delta    sigma   weight residual
    1.444  1.474 -0.030 9.60e-03 1.09e+04 9.47e+00
  bond pdb=" N   ARG B  19 "
       pdb=" CA  ARG B  19 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.25e-02 6.40e+03 7.17e+00
  bond pdb=" CA  SER A 414 "
       pdb=" CB  SER A 414 "
    ideal  model  delta    sigma   weight residual
    1.530  1.489  0.041 1.57e-02 4.06e+03 6.70e+00
  bond pdb=" N   LEU B  20 "
       pdb=" CA  LEU B  20 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.31e-02 5.83e+03 6.67e+00
  bond pdb=" CA  SER A 476 "
       pdb=" CB  SER A 476 "
    ideal  model  delta    sigma   weight residual
    1.528  1.488  0.040 1.66e-02 3.63e+03 5.93e+00
  ... (remaining 4676 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 6172
        1.90 -     3.79: 138
        3.79 -     5.69: 44
        5.69 -     7.59: 7
        7.59 -     9.48: 7
  Bond angle restraints: 6368
  Sorted by residual:
  angle pdb=" N   ILE B  51 "
        pdb=" CA  ILE B  51 "
        pdb=" C   ILE B  51 "
      ideal   model   delta    sigma   weight residual
     111.88  104.09    7.79 1.06e+00 8.90e-01 5.41e+01
  angle pdb=" N   GLY B  10 "
        pdb=" CA  GLY B  10 "
        pdb=" C   GLY B  10 "
      ideal   model   delta    sigma   weight residual
     110.46  117.17   -6.71 1.43e+00 4.89e-01 2.20e+01
  angle pdb=" CA  THR A 103 "
        pdb=" CB  THR A 103 "
        pdb=" OG1 THR A 103 "
      ideal   model   delta    sigma   weight residual
     109.60  103.33    6.27 1.50e+00 4.44e-01 1.74e+01
  angle pdb=" N   SER A 476 "
        pdb=" CA  SER A 476 "
        pdb=" C   SER A 476 "
      ideal   model   delta    sigma   weight residual
     111.82  107.22    4.60 1.16e+00 7.43e-01 1.57e+01
  angle pdb=" N   GLN A 478 "
        pdb=" CA  GLN A 478 "
        pdb=" C   GLN A 478 "
      ideal   model   delta    sigma   weight residual
     113.15  108.97    4.18 1.19e+00 7.06e-01 1.23e+01
  ... (remaining 6363 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.07: 2202
       15.07 -    30.14: 327
       30.14 -    45.21: 131
       45.21 -    60.27: 42
       60.27 -    75.34: 2
  Dihedral angle restraints: 2704
    sinusoidal: 1015
      harmonic: 1689
  Sorted by residual:
  dihedral pdb=" CA  ASN B  52 "
           pdb=" C   ASN B  52 "
           pdb=" N   SER B  53 "
           pdb=" CA  SER B  53 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.30  -17.70     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  TYR B  80 "
           pdb=" C   TYR B  80 "
           pdb=" N   LEU B  81 "
           pdb=" CA  LEU B  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.68   16.32     0      5.00e+00 4.00e-02 1.07e+01
  dihedral pdb=" N   TYR A 231 "
           pdb=" CA  TYR A 231 "
           pdb=" CB  TYR A 231 "
           pdb=" CG  TYR A 231 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.14  -59.86     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 2701 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 525
       0.040 -    0.079: 152
       0.079 -    0.119: 45
       0.119 -    0.159: 8
       0.159 -    0.199: 5
  Chirality restraints: 735
  Sorted by residual:
  chirality pdb=" CA  ILE B  51 "
            pdb=" N   ILE B  51 "
            pdb=" C   ILE B  51 "
            pdb=" CB  ILE B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.86e-01
  chirality pdb=" CB  ILE B  51 "
            pdb=" CA  ILE B  51 "
            pdb=" CG1 ILE B  51 "
            pdb=" CG2 ILE B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.20 2.00e-01 2.50e+01 9.51e-01
  chirality pdb=" CA  CYS B  22 "
            pdb=" N   CYS B  22 "
            pdb=" C   CYS B  22 "
            pdb=" CB  CYS B  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.01e-01
  ... (remaining 732 not shown)

  Planarity restraints: 792
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 475 "    0.018 2.00e-02 2.50e+03   3.60e-02 1.30e+01
        pdb=" C   GLN A 475 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   GLN A 475 "    0.023 2.00e-02 2.50e+03
        pdb=" N   SER A 476 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 301 "   -0.009 2.00e-02 2.50e+03   1.76e-02 3.10e+00
        pdb=" C   HIS A 301 "    0.030 2.00e-02 2.50e+03
        pdb=" O   HIS A 301 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   SER A 302 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 104 "   -0.027 5.00e-02 4.00e+02   4.04e-02 2.62e+00
        pdb=" N   PRO A 105 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 105 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 105 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 789 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1226
        2.79 -     3.32: 4704
        3.32 -     3.85: 7890
        3.85 -     4.37: 8410
        4.37 -     4.90: 14273
  Nonbonded interactions: 36503
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 377 "
            pdb=" OG  SER A 379 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   SER B  85 "
            pdb=" OG  SER B  85 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   GLY A 353 "
            pdb=" ND2 ASN B  74 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   LEU A 487 "
            pdb=" OG  SER A 491 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" N   GLN B  13 "
            pdb=" OE1 GLN B  13 "
     model   vdw
     2.324 3.120
  ... (remaining 36498 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     14.910
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
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      :  0.004   0.063   4681  Z= 0.255
  Angle     :  0.798   9.483   6368  Z= 0.440
  Chirality :  0.043   0.199    735
  Planarity :  0.004   0.040    792
  Dihedral  : 17.495  75.343   1624
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 40.78 %
    Favored  : 56.15 %
  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:  0.92 (0.35), residues: 587
  helix:  1.62 (0.27), residues: 379
  sheet: -0.29 (0.59), residues: 65
  loop : -1.68 (0.49), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  36 
 HIS   0.004   0.001   HIS A 301 
 PHE   0.015   0.001   PHE A 347 
 TYR   0.016   0.001   TYR B  95 
 ARG   0.007   0.001   ARG B  67 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8587 (tm-30)
REVERT: A  347 PHE cc_start: 0.8947 (m-80) cc_final: 0.8452 (t80)
REVERT: A  478 GLN cc_start: 0.9334 (pp30) cc_final: 0.8968 (pp30)
REVERT: A  521 MET cc_start: 0.8459 (ppp) cc_final: 0.8166 (ppp)
REVERT: A  537 TYR cc_start: 0.3868 (OUTLIER) cc_final: 0.1977 (t80)
REVERT: B   21 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.8155 (p)
REVERT: B   80 TYR cc_start: 0.8030 (m-10) cc_final: 0.7644 (m-10)
REVERT: B   99 LYS cc_start: 0.8723 (mmmm) cc_final: 0.7959 (mmtm)
  outliers start: 15
  outliers final: 6
  residues processed: 129
  average time/residue: 0.1215
  time to fit residues: 21.1046
Evaluate side-chains
  123 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  231 TYR
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 44 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.131101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.108994 restraints weight = 9681.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.112251 restraints weight = 5027.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.114365 restraints weight = 3079.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4681  Z= 0.255
  Angle     :  0.650   8.882   6368  Z= 0.336
  Chirality :  0.041   0.201    735
  Planarity :  0.004   0.044    792
  Dihedral  :  6.763  57.039    653
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  8.81 %
    Allowed  : 31.35 %
    Favored  : 59.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.91 (0.34), residues: 587
  helix:  1.61 (0.26), residues: 388
  sheet: -0.40 (0.69), residues: 57
  loop : -1.78 (0.46), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 179 
 HIS   0.002   0.001   HIS A 301 
 PHE   0.017   0.001   PHE A 347 
 TYR   0.010   0.001   TYR B 103 
 ARG   0.005   0.001   ARG A 440 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 121
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 ASP cc_start: 0.8527 (p0) cc_final: 0.7993 (p0)
REVERT: A  153 ARG cc_start: 0.7565 (mtp180) cc_final: 0.7083 (mtp180)
REVERT: A  269 MET cc_start: 0.7719 (ttm) cc_final: 0.7494 (ttp)
REVERT: A  283 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8583 (tm-30)
REVERT: A  347 PHE cc_start: 0.9136 (OUTLIER) cc_final: 0.8808 (t80)
REVERT: A  395 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.8506 (m-10)
REVERT: A  435 TRP cc_start: 0.7689 (OUTLIER) cc_final: 0.7318 (m-10)
REVERT: A  537 TYR cc_start: 0.4039 (OUTLIER) cc_final: 0.1991 (t80)
REVERT: B   20 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8625 (tm)
REVERT: B   99 LYS cc_start: 0.8798 (mmmm) cc_final: 0.8512 (mmmm)
  outliers start: 43
  outliers final: 28
  residues processed: 152
  average time/residue: 0.1247
  time to fit residues: 25.5418
Evaluate side-chains
  144 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 111
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  181 MET
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  395 TYR
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  416 THR
Chi-restraints excluded: chain A residue  418 THR
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  435 TRP
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Chi-restraints excluded: chain B residue  118 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   chunk 37 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 20 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  82 GLN
B 116 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.131651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.109536 restraints weight = 9817.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.112734 restraints weight = 5081.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.114914 restraints weight = 3133.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4681  Z= 0.190
  Angle     :  0.621   9.782   6368  Z= 0.313
  Chirality :  0.040   0.222    735
  Planarity :  0.003   0.042    792
  Dihedral  :  6.267  56.617    650
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 31.97 %
    Favored  : 61.89 %
  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:  1.04 (0.35), residues: 587
  helix:  1.74 (0.26), residues: 387
  sheet: -0.54 (0.67), residues: 57
  loop : -1.71 (0.47), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 179 
 HIS   0.005   0.001   HIS A 301 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.004   0.000   ARG A 440 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7154 (mtp180)
REVERT: A  225 PHE cc_start: 0.7926 (OUTLIER) cc_final: 0.7669 (t80)
REVERT: A  283 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8602 (tm-30)
REVERT: A  347 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8755 (t80)
REVERT: A  472 ASN cc_start: 0.9220 (t0) cc_final: 0.8941 (t0)
REVERT: A  496 MET cc_start: 0.8775 (tpp) cc_final: 0.8534 (tpp)
REVERT: A  521 MET cc_start: 0.8338 (ppp) cc_final: 0.7909 (ppp)
REVERT: A  537 TYR cc_start: 0.3864 (OUTLIER) cc_final: 0.2021 (t80)
REVERT: B   20 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8439 (tm)
REVERT: B   99 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8522 (mmmm)
  outliers start: 30
  outliers final: 18
  residues processed: 148
  average time/residue: 0.1165
  time to fit residues: 23.3598
Evaluate side-chains
  145 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 123
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  258 VAL
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9980
   chunk 36 optimal weight:    0.1980
   chunk 40 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 57 optimal weight:    5.9990
   chunk 19 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   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 192 GLN
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.133102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.110620 restraints weight = 9852.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.113956 restraints weight = 5069.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.116255 restraints weight = 3100.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7586
moved from start:          0.1680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4681  Z= 0.180
  Angle     :  0.612  13.350   6368  Z= 0.306
  Chirality :  0.040   0.218    735
  Planarity :  0.004   0.042    792
  Dihedral  :  5.795  58.522    647
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 30.53 %
    Favored  : 61.89 %
  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:  1.19 (0.35), residues: 587
  helix:  1.84 (0.26), residues: 387
  sheet: -0.43 (0.68), residues: 57
  loop : -1.63 (0.48), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 179 
 HIS   0.003   0.001   HIS A 301 
 PHE   0.016   0.001   PHE B  68 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.003   0.000   ARG A 440 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 125
  time to evaluate  : 0.477 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.7674 (mtp180) cc_final: 0.7208 (mtp180)
REVERT: A  183 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8528 (mp0)
REVERT: A  225 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7667 (t80)
REVERT: A  283 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8592 (tm-30)
REVERT: A  347 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8811 (t80)
REVERT: A  427 MET cc_start: 0.8955 (mtp) cc_final: 0.8686 (ttm)
REVERT: A  472 ASN cc_start: 0.9218 (t0) cc_final: 0.9009 (t0)
REVERT: A  496 MET cc_start: 0.8836 (tpp) cc_final: 0.8518 (tpp)
REVERT: A  521 MET cc_start: 0.8406 (ppp) cc_final: 0.7926 (ppp)
REVERT: A  537 TYR cc_start: 0.3827 (OUTLIER) cc_final: 0.2024 (t80)
REVERT: B   20 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8668 (tm)
REVERT: B   46 GLU cc_start: 0.8410 (tm-30) cc_final: 0.7996 (pp20)
REVERT: B   80 TYR cc_start: 0.7967 (m-10) cc_final: 0.7596 (m-10)
REVERT: B   99 LYS cc_start: 0.8843 (mmmm) cc_final: 0.8472 (mmmm)
REVERT: B  115 THR cc_start: 0.7367 (OUTLIER) cc_final: 0.7113 (t)
  outliers start: 37
  outliers final: 18
  residues processed: 151
  average time/residue: 0.1256
  time to fit residues: 25.4974
Evaluate side-chains
  142 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  183 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Chi-restraints excluded: chain B residue  115 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0570
   chunk 55 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9990
   chunk 18 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.132671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.110035 restraints weight = 10003.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.113342 restraints weight = 5205.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.115616 restraints weight = 3196.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4681  Z= 0.195
  Angle     :  0.636  12.651   6368  Z= 0.316
  Chirality :  0.040   0.210    735
  Planarity :  0.004   0.044    792
  Dihedral  :  5.865  59.666    647
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  : 31.76 %
    Favored  : 61.68 %
  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:  1.18 (0.35), residues: 587
  helix:  1.83 (0.26), residues: 387
  sheet: -0.52 (0.67), residues: 57
  loop : -1.60 (0.48), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 179 
 HIS   0.003   0.001   HIS A 301 
 PHE   0.016   0.001   PHE B  68 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.003   0.000   ARG A 440 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8747 (m-80) cc_final: 0.8449 (m-80)
REVERT: A  115 ASP cc_start: 0.8436 (p0) cc_final: 0.8221 (p0)
REVERT: A  192 GLN cc_start: 0.8583 (pt0) cc_final: 0.7895 (mt0)
REVERT: A  225 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7617 (t80)
REVERT: A  283 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8551 (tm-30)
REVERT: A  347 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8722 (t80)
REVERT: A  472 ASN cc_start: 0.9162 (t0) cc_final: 0.8915 (t0)
REVERT: A  496 MET cc_start: 0.8819 (tpp) cc_final: 0.8504 (tpp)
REVERT: A  537 TYR cc_start: 0.3866 (OUTLIER) cc_final: 0.1998 (t80)
REVERT: B   11 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8191 (mp)
REVERT: B   20 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8700 (tm)
REVERT: B   46 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8153 (pp20)
REVERT: B   59 TYR cc_start: 0.5092 (OUTLIER) cc_final: 0.3860 (p90)
REVERT: B   99 LYS cc_start: 0.8851 (mmmm) cc_final: 0.8553 (mmmm)
REVERT: B  115 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.7102 (t)
  outliers start: 32
  outliers final: 18
  residues processed: 142
  average time/residue: 0.1176
  time to fit residues: 22.6748
Evaluate side-chains
  141 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  115 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   chunk 47 optimal weight:    6.9990
   chunk 22 optimal weight:    0.0970
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:    0.3980
   chunk 35 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.133246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.110746 restraints weight = 9801.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.114103 restraints weight = 5073.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.116402 restraints weight = 3111.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3524
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4681  Z= 0.184
  Angle     :  0.636  14.695   6368  Z= 0.315
  Chirality :  0.040   0.197    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.768  59.115    647
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  5.94 %
    Allowed  : 32.79 %
    Favored  : 61.27 %
  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:  1.23 (0.35), residues: 587
  helix:  1.84 (0.26), residues: 390
  sheet: -0.66 (0.65), residues: 57
  loop : -1.47 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 179 
 HIS   0.003   0.000   HIS A 301 
 PHE   0.018   0.001   PHE B  68 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.004   0.000   ARG A 440 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8770 (m-80) cc_final: 0.8492 (m-80)
REVERT: A  115 ASP cc_start: 0.8467 (p0) cc_final: 0.8192 (p0)
REVERT: A  153 ARG cc_start: 0.7614 (mtp180) cc_final: 0.7289 (mtp180)
REVERT: A  225 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7561 (t80)
REVERT: A  283 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8625 (tm-30)
REVERT: A  347 PHE cc_start: 0.8972 (OUTLIER) cc_final: 0.8734 (t80)
REVERT: A  488 THR cc_start: 0.8772 (m) cc_final: 0.8507 (p)
REVERT: A  496 MET cc_start: 0.8900 (tpp) cc_final: 0.8491 (tpp)
REVERT: A  537 TYR cc_start: 0.3790 (OUTLIER) cc_final: 0.2004 (t80)
REVERT: B   11 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8174 (mp)
REVERT: B   20 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8753 (tm)
REVERT: B   59 TYR cc_start: 0.5106 (OUTLIER) cc_final: 0.3907 (p90)
REVERT: B   99 LYS cc_start: 0.8886 (mmmm) cc_final: 0.8597 (mmmm)
  outliers start: 29
  outliers final: 18
  residues processed: 142
  average time/residue: 0.1316
  time to fit residues: 24.7404
Evaluate side-chains
  141 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Chi-restraints excluded: chain B residue   59 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.132494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.109761 restraints weight = 9853.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.113115 restraints weight = 5102.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.115421 restraints weight = 3143.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4681  Z= 0.206
  Angle     :  0.677  14.482   6368  Z= 0.336
  Chirality :  0.041   0.189    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.751  58.221    647
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 33.81 %
    Favored  : 60.86 %
  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:  1.23 (0.35), residues: 587
  helix:  1.82 (0.26), residues: 390
  sheet: -0.54 (0.64), residues: 52
  loop : -1.46 (0.50), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 179 
 HIS   0.003   0.001   HIS A 301 
 PHE   0.014   0.001   PHE A 347 
 TYR   0.011   0.001   TYR B 103 
 ARG   0.009   0.000   ARG B  38 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  115 ASP cc_start: 0.8424 (p0) cc_final: 0.8177 (p0)
REVERT: A  153 ARG cc_start: 0.7685 (mtp180) cc_final: 0.7306 (mtp180)
REVERT: A  192 GLN cc_start: 0.8607 (pt0) cc_final: 0.7869 (mt0)
REVERT: A  225 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7576 (t80)
REVERT: A  283 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8605 (tm-30)
REVERT: A  347 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8767 (t80)
REVERT: A  488 THR cc_start: 0.8775 (m) cc_final: 0.8514 (p)
REVERT: A  496 MET cc_start: 0.8909 (tpp) cc_final: 0.8513 (tpp)
REVERT: A  537 TYR cc_start: 0.3832 (OUTLIER) cc_final: 0.2017 (t80)
REVERT: B   11 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8182 (mp)
REVERT: B   82 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7754 (tm-30)
  outliers start: 26
  outliers final: 20
  residues processed: 131
  average time/residue: 0.1261
  time to fit residues: 22.3217
Evaluate side-chains
  136 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  347 PHE
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   36 TRP
Chi-restraints excluded: chain B residue   54 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.132675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.109740 restraints weight = 9795.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.113091 restraints weight = 5151.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.115429 restraints weight = 3199.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   4681  Z= 0.208
  Angle     :  0.670  15.471   6368  Z= 0.329
  Chirality :  0.042   0.249    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.701  58.968    647
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 32.79 %
    Favored  : 61.68 %
  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:  1.28 (0.35), residues: 587
  helix:  1.86 (0.26), residues: 390
  sheet: -0.51 (0.65), residues: 52
  loop : -1.42 (0.50), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 179 
 HIS   0.003   0.000   HIS A 301 
 PHE   0.024   0.001   PHE B  68 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.007   0.000   ARG B  38 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8794 (m-80) cc_final: 0.8537 (m-80)
REVERT: A  115 ASP cc_start: 0.8458 (p0) cc_final: 0.8170 (p0)
REVERT: A  153 ARG cc_start: 0.7744 (mtp180) cc_final: 0.7520 (mtp180)
REVERT: A  225 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7568 (t80)
REVERT: A  283 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8590 (tm-30)
REVERT: A  496 MET cc_start: 0.8913 (tpp) cc_final: 0.8525 (tpp)
REVERT: A  537 TYR cc_start: 0.3825 (OUTLIER) cc_final: 0.1996 (t80)
REVERT: B   35 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7688 (mp0)
REVERT: B   95 TYR cc_start: 0.8720 (m-80) cc_final: 0.8477 (m-10)
  outliers start: 27
  outliers final: 21
  residues processed: 134
  average time/residue: 0.1303
  time to fit residues: 23.2495
Evaluate side-chains
  136 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  486 ILE
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   36 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 36 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0270
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7038

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

Flipped N/Q/H residues before XYZ refinement:
A 192 GLN
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.132742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.109830 restraints weight = 9934.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.113135 restraints weight = 5227.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.115387 restraints weight = 3267.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4681  Z= 0.215
  Angle     :  0.689  15.754   6368  Z= 0.343
  Chirality :  0.042   0.187    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.442  58.459    645
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 13.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 34.02 %
    Favored  : 61.27 %
  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:  1.25 (0.35), residues: 587
  helix:  1.84 (0.27), residues: 391
  sheet: -0.72 (0.63), residues: 52
  loop : -1.41 (0.51), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 179 
 HIS   0.003   0.001   HIS A 301 
 PHE   0.033   0.001   PHE B  68 
 TYR   0.012   0.001   TYR B 103 
 ARG   0.007   0.000   ARG B  38 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8792 (m-80) cc_final: 0.8459 (m-80)
REVERT: A  115 ASP cc_start: 0.8488 (p0) cc_final: 0.8231 (p0)
REVERT: A  153 ARG cc_start: 0.7771 (mtp180) cc_final: 0.7291 (mtp180)
REVERT: A  192 GLN cc_start: 0.8576 (pt0) cc_final: 0.7880 (mt0)
REVERT: A  225 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7542 (t80)
REVERT: A  283 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8617 (tm-30)
REVERT: A  496 MET cc_start: 0.8909 (tpp) cc_final: 0.8489 (tpp)
REVERT: A  537 TYR cc_start: 0.3780 (OUTLIER) cc_final: 0.2004 (t80)
REVERT: B   11 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8100 (mp)
REVERT: B   35 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7669 (mp0)
  outliers start: 23
  outliers final: 19
  residues processed: 132
  average time/residue: 0.1314
  time to fit residues: 22.9090
Evaluate side-chains
  135 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  286 VAL
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue   36 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 40 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 31 optimal weight:    0.5980
   chunk 8 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.133335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.110627 restraints weight = 9755.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.114003 restraints weight = 5064.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.116336 restraints weight = 3119.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   4681  Z= 0.213
  Angle     :  0.693  15.844   6368  Z= 0.340
  Chirality :  0.042   0.187    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.412  58.463    645
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 33.81 %
    Favored  : 61.48 %
  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:  1.26 (0.35), residues: 587
  helix:  1.85 (0.27), residues: 391
  sheet: -0.63 (0.62), residues: 52
  loop : -1.44 (0.50), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 505 
 HIS   0.003   0.000   HIS A 301 
 PHE   0.020   0.001   PHE B  68 
 TYR   0.011   0.001   TYR B 103 
 ARG   0.006   0.001   ARG B  38 

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

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

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1174 Ramachandran restraints generated.
    587 Oldfield, 0 Emsley, 587 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 TYR cc_start: 0.8729 (m-80) cc_final: 0.8378 (m-80)
REVERT: A  115 ASP cc_start: 0.8546 (p0) cc_final: 0.8264 (p0)
REVERT: A  153 ARG cc_start: 0.7746 (mtp180) cc_final: 0.7472 (mtp180)
REVERT: A  192 GLN cc_start: 0.8570 (pt0) cc_final: 0.7934 (mt0)
REVERT: A  496 MET cc_start: 0.8892 (tpp) cc_final: 0.8552 (tpp)
REVERT: A  537 TYR cc_start: 0.3811 (OUTLIER) cc_final: 0.1978 (t80)
REVERT: B   46 GLU cc_start: 0.8562 (pp20) cc_final: 0.8312 (pp20)
  outliers start: 23
  outliers final: 19
  residues processed: 132
  average time/residue: 0.1221
  time to fit residues: 21.7496
Evaluate side-chains
  136 residues out of total 488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.534 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 ILE
Chi-restraints excluded: chain A residue  160 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  244 ILE
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  316 GLN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  338 ILE
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  370 HIS
Chi-restraints excluded: chain A residue  394 CYS
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  537 TYR
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain B residue    7 SER
Chi-restraints excluded: chain B residue   36 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0970
   chunk 40 optimal weight:    0.8980
   chunk 23 optimal weight:    5.9990
   chunk 31 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 56 optimal weight:    5.9990
   chunk 55 optimal weight:   20.0000
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.132793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.109929 restraints weight = 9987.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.113247 restraints weight = 5300.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.115434 restraints weight = 3310.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4681  Z= 0.229
  Angle     :  0.725  15.825   6368  Z= 0.356
  Chirality :  0.043   0.206    735
  Planarity :  0.004   0.043    792
  Dihedral  :  5.381  56.958    645
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 34.43 %
    Favored  : 61.48 %
  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:  1.27 (0.35), residues: 587
  helix:  1.81 (0.26), residues: 391
  sheet: -0.29 (0.68), residues: 44
  loop : -1.39 (0.48), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 179 
 HIS   0.003   0.000   HIS A 301 
 PHE   0.019   0.001   PHE B  68 
 TYR   0.011   0.001   TYR B  94 
 ARG   0.006   0.000   ARG B  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1595.97 seconds
wall clock time: 28 minutes 35.95 seconds (1715.95 seconds total)