Starting phenix.real_space_refine
on Tue Mar 11 19:03:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i4h_35173/03_2025/8i4h_35173.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i4h_35173/03_2025/8i4h_35173.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i4h_35173/03_2025/8i4h_35173.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i4h_35173/03_2025/8i4h_35173.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i4h_35173/03_2025/8i4h_35173.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i4h_35173/03_2025/8i4h_35173.cif"
  }
  resolution = 3.81
  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=   0.002 sd=   0.029
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      32      5.16       5
     C    4194      2.51       5
     N    1075      2.21       5
     O    1238      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 6539
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 598, 4724
          Classifications: {'peptide': 598}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 32, 'TRANS': 565}
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "B"
      Number of atoms: 1815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1815
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 8, 'TRANS': 226}
          Chain breaks: 1
  Time building chain proxies: 4.23, per 1000 atoms: 0.65
  Number of scatterers: 6539
  At special positions: 0
  Unit cell: (71.288, 90.44, 131.936, 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      32     16.00
     O    1238      8.00
     N    1075      7.00
     C    4194      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=11, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 160 " - pdb=" SG  CYS B 234 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.41
  Conformation dependent library (CDL) restraints added in 970.2 milliseconds
  

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1544

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 19 sheets defined
      3.5% alpha, 20.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 301
    Processing helix  chain 'A' and resid 406 through 411
    Processing helix  chain 'A' and resid 502 through 506
      removed outlier: 3.687A  pdb=" N   GLN A 506 " --> pdb=" O   VAL A 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 4.348A  pdb=" N   TYR B  32 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 229
      removed outlier: 3.700A  pdb=" N   THR B 229 " --> pdb=" O   ALA B 226 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29
      removed outlier: 3.724A  pdb=" N   THR A  63 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 267 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49
      removed outlier: 3.923A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.688A  pdb=" N   GLY A 107 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 95
      removed outlier: 5.911A  pdb=" N   SER A 203 " --> pdb=" O   PRO A 225 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 120
      removed outlier: 3.611A  pdb=" N   ILE A 128 " --> pdb=" O   TYR A 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314
      removed outlier: 3.528A  pdb=" N   ALA A 609 " --> pdb=" O   ILE A 598 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A 610 " --> pdb=" O   ILE A 651 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ILE A 651 " --> pdb=" O   VAL A 610 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR A 612 " --> pdb=" O   CYS A 649 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   CYS A 649 " --> pdb=" O   TYR A 612 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLY A 648 " --> pdb=" O   THR A 645 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   THR A 645 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   LEU A 650 " --> pdb=" O   PHE A 643 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   PHE A 643 " --> pdb=" O   LEU A 650 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 326
    Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 357
      removed outlier: 3.883A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ASP A 398 " --> pdb=" O   VAL A 512 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   VAL A 512 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362
      removed outlier: 7.371A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB2, first strand: chain 'A' and resid 655 through 660
      removed outlier: 6.527A  pdb=" N   ASN A 658 " --> pdb=" O   THR A 696 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 664 through 667
      removed outlier: 6.862A  pdb=" N   ILE A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 674 through 675
    Processing sheet with id=AB5, first strand: chain 'B' and resid 5 through 7
    Processing sheet with id=AB6, first strand: chain 'B' and resid 17 through 18
      removed outlier: 3.662A  pdb=" N   MET B  82 " --> pdb=" O   LEU B  18 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 56 through 59
      removed outlier: 3.800A  pdb=" N   ARG B  56 " --> pdb=" O   TYR B  52 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   TRP B  36 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
      removed outlier: 4.722A  pdb=" N   SER B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   MET B  34 " --> pdb=" O   SER B  50 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL B  37 " --> pdb=" O   TYR B  94 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   TYR B  94 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   TYR B  93 " --> pdb=" O   THR B 112 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR B 112 " --> pdb=" O   TYR B  93 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 149 through 150
    Processing sheet with id=AB9, first strand: chain 'B' and resid 157 through 161
      removed outlier: 3.529A  pdb=" N   THR B 207 " --> pdb=" O   GLN B 220 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 171 through 173
      removed outlier: 3.631A  pdb=" N   ALA B 235 " --> pdb=" O   SER B 173 " (cutoff:3.500A)

    112 hydrogen bonds defined for protein.
    264 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: 2.08

  Time building geometry restraints manager: 1.74 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2080
        1.35 -     1.46: 1704
        1.46 -     1.58: 2878
        1.58 -     1.70: 0
        1.70 -     1.81: 41
  Bond restraints: 6703
  Sorted by residual:
  bond pdb=" C   GLU A 212 "
       pdb=" N   PRO A 213 "
    ideal  model  delta    sigma   weight residual
    1.334  1.355 -0.021 2.34e-02 1.83e+03 7.92e-01
  bond pdb=" C   ILE A 664 "
       pdb=" O   ILE A 664 "
    ideal  model  delta    sigma   weight residual
    1.240  1.231  0.009 1.26e-02 6.30e+03 5.02e-01
  bond pdb=" C   GLN A 173 "
       pdb=" N   PRO A 174 "
    ideal  model  delta    sigma   weight residual
    1.330  1.338 -0.008 1.19e-02 7.06e+03 4.31e-01
  bond pdb=" CB  PRO A 330 "
       pdb=" CG  PRO A 330 "
    ideal  model  delta    sigma   weight residual
    1.492  1.523 -0.031 5.00e-02 4.00e+02 3.96e-01
  bond pdb=" N   ASP B  26 "
       pdb=" CA  ASP B  26 "
    ideal  model  delta    sigma   weight residual
    1.460  1.469 -0.009 1.54e-02 4.22e+03 3.31e-01
  ... (remaining 6698 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 8836
        1.03 -     2.06: 207
        2.06 -     3.09: 64
        3.09 -     4.12: 9
        4.12 -     5.15: 2
  Bond angle restraints: 9118
  Sorted by residual:
  angle pdb=" N   ASP A  80 "
        pdb=" CA  ASP A  80 "
        pdb=" C   ASP A  80 "
      ideal   model   delta    sigma   weight residual
     114.56  111.04    3.52 1.27e+00 6.20e-01 7.68e+00
  angle pdb=" CA  ASP A  80 "
        pdb=" C   ASP A  80 "
        pdb=" N   ASN A  81 "
      ideal   model   delta    sigma   weight residual
     119.26  116.87    2.39 1.14e+00 7.69e-01 4.40e+00
  angle pdb=" CA  ASP A  80 "
        pdb=" C   ASP A  80 "
        pdb=" O   ASP A  80 "
      ideal   model   delta    sigma   weight residual
     118.55  120.50   -1.95 1.14e+00 7.69e-01 2.94e+00
  angle pdb=" C   SER B  25 "
        pdb=" N   ASP B  26 "
        pdb=" CA  ASP B  26 "
      ideal   model   delta    sigma   weight residual
     122.46  124.71   -2.25 1.41e+00 5.03e-01 2.55e+00
  angle pdb=" C   PHE A 559 "
        pdb=" N   LEU A 560 "
        pdb=" CA  LEU A 560 "
      ideal   model   delta    sigma   weight residual
     121.80  125.69   -3.89 2.44e+00 1.68e-01 2.54e+00
  ... (remaining 9113 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 3736
       16.03 -    32.05: 166
       32.05 -    48.08: 35
       48.08 -    64.10: 6
       64.10 -    80.13: 1
  Dihedral angle restraints: 3944
    sinusoidal: 1525
      harmonic: 2419
  Sorted by residual:
  dihedral pdb=" N   LYS A 424 "
           pdb=" CA  LYS A 424 "
           pdb=" CB  LYS A 424 "
           pdb=" CG  LYS A 424 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.01  -59.99     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" N   LEU A 390 "
           pdb=" CA  LEU A 390 "
           pdb=" CB  LEU A 390 "
           pdb=" CG  LEU A 390 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.77   56.77     3      1.50e+01 4.44e-03 9.41e+00
  dihedral pdb=" N   PHE A 329 "
           pdb=" CA  PHE A 329 "
           pdb=" CB  PHE A 329 "
           pdb=" CG  PHE A 329 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.13  -54.87     3      1.50e+01 4.44e-03 9.31e+00
  ... (remaining 3941 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 572
       0.025 -    0.050: 259
       0.050 -    0.076: 83
       0.076 -    0.101: 60
       0.101 -    0.126: 29
  Chirality restraints: 1003
  Sorted by residual:
  chirality pdb=" CA  ILE A 101 "
            pdb=" N   ILE A 101 "
            pdb=" C   ILE A 101 "
            pdb=" CB  ILE A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.96e-01
  chirality pdb=" CA  ILE A 584 "
            pdb=" N   ILE A 584 "
            pdb=" C   ILE A 584 "
            pdb=" CB  ILE A 584 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  ILE A 235 "
            pdb=" N   ILE A 235 "
            pdb=" C   ILE A 235 "
            pdb=" CB  ILE A 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 1000 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 173 "    0.037 5.00e-02 4.00e+02   5.59e-02 5.00e+00
        pdb=" N   PRO A 174 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 174 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 174 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 321 "   -0.031 5.00e-02 4.00e+02   4.78e-02 3.65e+00
        pdb=" N   PRO A 322 "    0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 322 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 322 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 336 "    0.019 5.00e-02 4.00e+02   2.83e-02 1.28e+00
        pdb=" N   PRO A 337 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 337 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 337 "    0.016 5.00e-02 4.00e+02
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1589
        2.79 -     3.32: 5895
        3.32 -     3.84: 10478
        3.84 -     4.37: 11962
        4.37 -     4.90: 20458
  Nonbonded interactions: 50382
  Sorted by model distance:
  nonbonded pdb=" O   ASP B  89 "
            pdb=" OH  TYR B  93 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   VAL A 130 "
            pdb=" OG1 THR A 167 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   THR A 393 "
            pdb=" OG1 THR A 523 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OG1 THR A 470 "
            pdb=" OG  SER B  54 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   GLU A 661 "
            pdb=" OH  TYR A 695 "
     model   vdw
     2.295 3.040
  ... (remaining 50377 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:                  0.010
  Normalize map: mean=0, sd=1:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.090
  Process input model:                     18.970
  Find NCS groups from input model:        0.070
  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:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6485
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      :  0.001   0.031   6703  Z= 0.095
  Angle     :  0.433   5.155   9118  Z= 0.240
  Chirality :  0.040   0.126   1003
  Planarity :  0.004   0.056   1175
  Dihedral  :  9.227  80.126   2367
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  5.85 %
    Allowed  :  7.52 %
    Favored  : 86.63 %
  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: -4.65 (0.24), residues: 815
  helix: -2.48 (1.17), residues: 14
  sheet: -2.96 (0.34), residues: 172
  loop : -3.44 (0.20), residues: 629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP B  99 
 HIS   0.001   0.000   HIS A  49 
 PHE   0.005   0.001   PHE A 192 
 TYR   0.005   0.001   TYR B 169 
 ARG   0.001   0.000   ARG A 273 

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 246
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.5984 (t80) cc_final: 0.5726 (t80)
REVERT: A   95 ILE cc_start: 0.7899 (OUTLIER) cc_final: 0.7597 (tp)
REVERT: A  177 MET cc_start: 0.6113 (mmt) cc_final: 0.5836 (mmt)
REVERT: A  294 ASP cc_start: 0.7943 (p0) cc_final: 0.7654 (p0)
REVERT: A  357 ARG cc_start: 0.6937 (ttp80) cc_final: 0.6561 (ttp80)
REVERT: A  368 LEU cc_start: 0.7611 (mm) cc_final: 0.7289 (tp)
REVERT: A  387 LEU cc_start: 0.8674 (mt) cc_final: 0.8255 (tp)
REVERT: A  388 ASN cc_start: 0.7787 (m110) cc_final: 0.7455 (p0)
REVERT: A  394 ASN cc_start: 0.7343 (m-40) cc_final: 0.7117 (m-40)
REVERT: A  395 VAL cc_start: 0.7655 (m) cc_final: 0.7377 (t)
REVERT: A  408 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7476 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7679 (t0) cc_final: 0.7403 (t0)
REVERT: A  428 ASP cc_start: 0.7345 (p0) cc_final: 0.7010 (p0)
REVERT: A  452 LEU cc_start: 0.7605 (mp) cc_final: 0.7186 (tt)
REVERT: A  470 THR cc_start: 0.7394 (p) cc_final: 0.7114 (p)
REVERT: A  490 PHE cc_start: 0.8416 (t80) cc_final: 0.8200 (t80)
REVERT: A  537 LYS cc_start: 0.7724 (tppp) cc_final: 0.7195 (mmmm)
REVERT: A  562 PHE cc_start: 0.6663 (t80) cc_final: 0.5858 (t80)
REVERT: A  699 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8382 (pt)
REVERT: B   82 MET cc_start: 0.8750 (mtt) cc_final: 0.8326 (mtt)
REVERT: B   93 TYR cc_start: 0.6581 (m-80) cc_final: 0.5874 (m-80)
REVERT: B  167 PHE cc_start: 0.6732 (m-80) cc_final: 0.6530 (m-80)
REVERT: B  215 ASN cc_start: 0.8693 (m-40) cc_final: 0.8446 (t0)
REVERT: B  252 THR cc_start: 0.8471 (t) cc_final: 0.8266 (p)
  outliers start: 42
  outliers final: 14
  residues processed: 270
  average time/residue: 0.2262
  time to fit residues: 77.5077
Evaluate side-chains
  218 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 202
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   95 ILE
Chi-restraints excluded: chain A residue  100 ILE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  338 PHE
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  377 PHE
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  547 LYS
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  699 LEU
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue  208 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 34 optimal weight:    0.0870
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9990
   chunk 64 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.1964

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  66 HIS
A  87 ASN
A 165 ASN
A 173 GLN
A 234 ASN
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 ASN
A 321 GLN
A 360 ASN
A 388 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 536 ASN
A 563 GLN
** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   3 GLN
B  13 GLN
B  81 GLN
B 110 GLN
B 141 GLN
B 212 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.174091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.141197 restraints weight = 12436.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.147187 restraints weight = 7325.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.151444 restraints weight = 4919.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6703  Z= 0.233
  Angle     :  0.636   7.475   9118  Z= 0.324
  Chirality :  0.046   0.258   1003
  Planarity :  0.005   0.054   1175
  Dihedral  :  6.645  81.968    950
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.66 %
    Favored  : 88.34 %
  Rotamer:
    Outliers :  6.55 %
    Allowed  : 14.07 %
    Favored  : 79.39 %
  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: -4.09 (0.26), residues: 815
  helix: -2.55 (1.20), residues: 16
  sheet: -2.85 (0.35), residues: 177
  loop : -2.91 (0.22), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 174 
 HIS   0.019   0.003   HIS A 519 
 PHE   0.034   0.001   PHE A 306 
 TYR   0.011   0.001   TYR A 160 
 ARG   0.003   0.000   ARG A 355 

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 231
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7702 (tm-30) cc_final: 0.7359 (tp40)
REVERT: A   67 VAL cc_start: 0.8163 (p) cc_final: 0.7493 (m)
REVERT: A   92 PHE cc_start: 0.6564 (t80) cc_final: 0.6266 (t80)
REVERT: A  177 MET cc_start: 0.6217 (mmt) cc_final: 0.5915 (mmt)
REVERT: A  204 LYS cc_start: 0.8198 (tttp) cc_final: 0.7922 (tttp)
REVERT: A  218 GLN cc_start: 0.7293 (mm-40) cc_final: 0.7085 (mm110)
REVERT: A  241 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8173 (mm)
REVERT: A  265 TYR cc_start: 0.6686 (m-80) cc_final: 0.6384 (m-80)
REVERT: A  319 ARG cc_start: 0.7943 (ptp90) cc_final: 0.7655 (tpt170)
REVERT: A  340 GLU cc_start: 0.7638 (mp0) cc_final: 0.7422 (mp0)
REVERT: A  357 ARG cc_start: 0.7225 (ttp80) cc_final: 0.6734 (ttp80)
REVERT: A  359 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7905 (t)
REVERT: A  368 LEU cc_start: 0.8183 (mm) cc_final: 0.7619 (tp)
REVERT: A  387 LEU cc_start: 0.8683 (mt) cc_final: 0.8336 (tp)
REVERT: A  395 VAL cc_start: 0.7833 (m) cc_final: 0.7466 (m)
REVERT: A  396 TYR cc_start: 0.7161 (m-80) cc_final: 0.6519 (m-10)
REVERT: A  408 ARG cc_start: 0.8075 (ttp-170) cc_final: 0.7654 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7894 (t0) cc_final: 0.7499 (t0)
REVERT: A  424 LYS cc_start: 0.8193 (tmtm) cc_final: 0.7862 (tmtm)
REVERT: A  442 ASP cc_start: 0.8159 (p0) cc_final: 0.7868 (p0)
REVERT: A  452 LEU cc_start: 0.7803 (mp) cc_final: 0.7275 (tt)
REVERT: A  490 PHE cc_start: 0.8263 (t80) cc_final: 0.8003 (t80)
REVERT: A  501 TYR cc_start: 0.7804 (OUTLIER) cc_final: 0.7366 (t80)
REVERT: A  528 LYS cc_start: 0.7679 (mttm) cc_final: 0.7149 (mttp)
REVERT: A  537 LYS cc_start: 0.7857 (tppp) cc_final: 0.7435 (mmmm)
REVERT: A  557 LYS cc_start: 0.6577 (mtmm) cc_final: 0.6358 (ptpp)
REVERT: A  598 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8155 (tp)
REVERT: B   38 ARG cc_start: 0.7297 (ttp-170) cc_final: 0.6688 (ttp-170)
REVERT: B   64 LYS cc_start: 0.8306 (tptt) cc_final: 0.7960 (tptt)
REVERT: B   93 TYR cc_start: 0.6833 (m-80) cc_final: 0.5899 (m-80)
REVERT: B   97 SER cc_start: 0.7692 (OUTLIER) cc_final: 0.7363 (p)
REVERT: B  189 ILE cc_start: 0.8723 (mm) cc_final: 0.8380 (mm)
REVERT: B  211 ASP cc_start: 0.7889 (t0) cc_final: 0.7664 (t0)
REVERT: B  252 THR cc_start: 0.8436 (t) cc_final: 0.8176 (m)
  outliers start: 47
  outliers final: 24
  residues processed: 256
  average time/residue: 0.2209
  time to fit residues: 71.2895
Evaluate side-chains
  242 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 213
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  297 SER
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  359 SER
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  547 LYS
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  143 VAL
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  216 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 63 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 67 optimal weight:    8.9990
   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  52 GLN
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 331 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 690 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.168256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.135869 restraints weight = 12600.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.141771 restraints weight = 7504.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.145845 restraints weight = 5062.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6770
moved from start:          0.3858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6703  Z= 0.186
  Angle     :  0.638   8.531   9118  Z= 0.318
  Chirality :  0.045   0.156   1003
  Planarity :  0.005   0.057   1175
  Dihedral  :  6.410  80.608    940
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.20 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 19.36 %
    Favored  : 76.18 %
  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: -3.80 (0.26), residues: 815
  helix: -2.53 (1.23), residues: 16
  sheet: -2.46 (0.37), residues: 175
  loop : -2.77 (0.22), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP B 174 
 HIS   0.006   0.001   HIS A 519 
 PHE   0.038   0.002   PHE A 275 
 TYR   0.015   0.001   TYR B 107 
 ARG   0.003   0.000   ARG B 205 

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 208
  time to evaluate  : 0.657 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7724 (tm130) cc_final: 0.7339 (tp40)
REVERT: A   67 VAL cc_start: 0.8188 (p) cc_final: 0.7594 (m)
REVERT: A   86 PHE cc_start: 0.8432 (t80) cc_final: 0.8139 (t80)
REVERT: A   92 PHE cc_start: 0.6501 (t80) cc_final: 0.6214 (t80)
REVERT: A  177 MET cc_start: 0.6210 (mmt) cc_final: 0.5895 (mmt)
REVERT: A  265 TYR cc_start: 0.6645 (m-80) cc_final: 0.6332 (m-80)
REVERT: A  313 TYR cc_start: 0.5932 (m-80) cc_final: 0.5449 (m-80)
REVERT: A  340 GLU cc_start: 0.7734 (mp0) cc_final: 0.7483 (mp0)
REVERT: A  357 ARG cc_start: 0.7279 (ttp80) cc_final: 0.6724 (ttp80)
REVERT: A  368 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8079 (tp)
REVERT: A  387 LEU cc_start: 0.8638 (mt) cc_final: 0.8368 (tp)
REVERT: A  396 TYR cc_start: 0.6940 (m-80) cc_final: 0.6332 (m-80)
REVERT: A  401 VAL cc_start: 0.8045 (t) cc_final: 0.7679 (m)
REVERT: A  408 ARG cc_start: 0.8036 (ttp-170) cc_final: 0.7625 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7830 (t0) cc_final: 0.7458 (t0)
REVERT: A  424 LYS cc_start: 0.8097 (tmtm) cc_final: 0.7812 (tmtm)
REVERT: A  425 LEU cc_start: 0.8563 (tp) cc_final: 0.8296 (tp)
REVERT: A  452 LEU cc_start: 0.7539 (mp) cc_final: 0.7039 (tt)
REVERT: A  490 PHE cc_start: 0.8033 (t80) cc_final: 0.7792 (t80)
REVERT: A  501 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7378 (t80)
REVERT: A  588 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8732 (p)
REVERT: A  598 ILE cc_start: 0.8614 (OUTLIER) cc_final: 0.8140 (tp)
REVERT: B   45 PRO cc_start: 0.8675 (Cg_endo) cc_final: 0.8350 (Cg_exo)
REVERT: B   64 LYS cc_start: 0.8199 (tptt) cc_final: 0.7899 (tptt)
REVERT: B   93 TYR cc_start: 0.6686 (m-80) cc_final: 0.6127 (m-80)
REVERT: B  107 TYR cc_start: 0.6068 (t80) cc_final: 0.5446 (t80)
REVERT: B  158 LEU cc_start: 0.7832 (mm) cc_final: 0.6973 (mt)
REVERT: B  159 SER cc_start: 0.8071 (OUTLIER) cc_final: 0.7705 (t)
REVERT: B  189 ILE cc_start: 0.8702 (mm) cc_final: 0.8413 (mm)
REVERT: B  211 ASP cc_start: 0.7872 (t0) cc_final: 0.7628 (t0)
REVERT: B  252 THR cc_start: 0.8225 (t) cc_final: 0.8018 (m)
  outliers start: 32
  outliers final: 15
  residues processed: 226
  average time/residue: 0.2210
  time to fit residues: 63.0500
Evaluate side-chains
  219 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 199
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  368 LEU
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  598 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  231 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 58 optimal weight:    0.4980
   chunk 76 optimal weight:    3.9990
   chunk 59 optimal weight:    8.9990
   chunk 43 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 81 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0980
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.168314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.135784 restraints weight = 12754.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.141434 restraints weight = 7627.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.145413 restraints weight = 5160.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.4428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6703  Z= 0.181
  Angle     :  0.634   9.223   9118  Z= 0.316
  Chirality :  0.045   0.154   1003
  Planarity :  0.005   0.063   1175
  Dihedral  :  6.390  80.807    934
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.04 %
    Favored  : 88.96 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 19.36 %
    Favored  : 75.49 %
  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: -3.48 (0.27), residues: 815
  helix: -0.65 (1.92), residues: 10
  sheet: -2.26 (0.37), residues: 175
  loop : -2.56 (0.23), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP B 174 
 HIS   0.006   0.001   HIS A 519 
 PHE   0.031   0.002   PHE A 275 
 TYR   0.015   0.001   TYR B 107 
 ARG   0.008   0.000   ARG B  38 

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 204
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 VAL cc_start: 0.8344 (p) cc_final: 0.7783 (m)
REVERT: A   86 PHE cc_start: 0.8355 (t80) cc_final: 0.8123 (t80)
REVERT: A  177 MET cc_start: 0.6275 (mmt) cc_final: 0.5961 (mmt)
REVERT: A  204 LYS cc_start: 0.8405 (tppt) cc_final: 0.7972 (tppt)
REVERT: A  224 GLU cc_start: 0.7113 (pm20) cc_final: 0.6725 (pm20)
REVERT: A  265 TYR cc_start: 0.6731 (m-80) cc_final: 0.6245 (m-80)
REVERT: A  313 TYR cc_start: 0.6015 (m-80) cc_final: 0.5472 (m-80)
REVERT: A  340 GLU cc_start: 0.7896 (mp0) cc_final: 0.7561 (mp0)
REVERT: A  355 ARG cc_start: 0.7496 (ttm-80) cc_final: 0.6503 (ttm-80)
REVERT: A  357 ARG cc_start: 0.7305 (ttp80) cc_final: 0.6671 (ttp80)
REVERT: A  359 SER cc_start: 0.8172 (m) cc_final: 0.7700 (t)
REVERT: A  387 LEU cc_start: 0.8667 (mt) cc_final: 0.8415 (mt)
REVERT: A  396 TYR cc_start: 0.6977 (m-80) cc_final: 0.6602 (m-80)
REVERT: A  401 VAL cc_start: 0.8031 (t) cc_final: 0.7630 (m)
REVERT: A  408 ARG cc_start: 0.8003 (ttp-170) cc_final: 0.7605 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7927 (t0) cc_final: 0.7549 (t0)
REVERT: A  424 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7675 (tptt)
REVERT: A  452 LEU cc_start: 0.7471 (mp) cc_final: 0.7008 (tt)
REVERT: A  490 PHE cc_start: 0.8045 (t80) cc_final: 0.7835 (t80)
REVERT: A  501 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7439 (t80)
REVERT: A  518 LEU cc_start: 0.7842 (mm) cc_final: 0.7581 (mt)
REVERT: A  547 LYS cc_start: 0.7511 (mmmt) cc_final: 0.7073 (mmmt)
REVERT: A  588 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8651 (p)
REVERT: A  591 SER cc_start: 0.7823 (m) cc_final: 0.7423 (p)
REVERT: B   45 PRO cc_start: 0.8730 (Cg_endo) cc_final: 0.8461 (Cg_exo)
REVERT: B   64 LYS cc_start: 0.8285 (tptt) cc_final: 0.7925 (tptt)
REVERT: B  159 SER cc_start: 0.7701 (OUTLIER) cc_final: 0.7455 (p)
REVERT: B  189 ILE cc_start: 0.8713 (mm) cc_final: 0.8419 (mm)
REVERT: B  211 ASP cc_start: 0.7914 (t0) cc_final: 0.7567 (t0)
REVERT: B  221 MET cc_start: 0.7193 (mtt) cc_final: 0.6993 (mtm)
REVERT: B  252 THR cc_start: 0.8206 (t) cc_final: 0.7931 (m)
  outliers start: 37
  outliers final: 23
  residues processed: 226
  average time/residue: 0.2195
  time to fit residues: 62.6832
Evaluate side-chains
  229 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 202
  time to evaluate  : 0.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  170 TYR
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  206 PHE
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  231 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0370
   chunk 77 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 43 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   overall best weight:    1.1060

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.163209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.130778 restraints weight = 12575.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.136305 restraints weight = 7362.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.140106 restraints weight = 4929.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6861
moved from start:          0.5005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6703  Z= 0.223
  Angle     :  0.676   8.904   9118  Z= 0.340
  Chirality :  0.046   0.153   1003
  Planarity :  0.005   0.056   1175
  Dihedral  :  6.739  80.301    934
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.41 %
    Favored  : 88.59 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 20.47 %
    Favored  : 74.51 %
  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: -3.50 (0.27), residues: 815
  helix: -0.20 (1.95), residues: 10
  sheet: -2.35 (0.37), residues: 180
  loop : -2.56 (0.23), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.070   0.003   TRP B 174 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.040   0.002   PHE A  55 
 TYR   0.012   0.001   TYR B 107 
 ARG   0.007   0.001   ARG A 328 

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 215
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7715 (tp40) cc_final: 0.7397 (tp40)
REVERT: A   67 VAL cc_start: 0.8469 (p) cc_final: 0.8028 (m)
REVERT: A  177 MET cc_start: 0.6284 (mmt) cc_final: 0.5989 (mmt)
REVERT: A  265 TYR cc_start: 0.6690 (m-80) cc_final: 0.6262 (m-80)
REVERT: A  313 TYR cc_start: 0.6164 (m-80) cc_final: 0.5588 (m-80)
REVERT: A  340 GLU cc_start: 0.8062 (mp0) cc_final: 0.7758 (mp0)
REVERT: A  355 ARG cc_start: 0.7619 (ttm-80) cc_final: 0.7372 (mtp85)
REVERT: A  357 ARG cc_start: 0.7435 (ttp80) cc_final: 0.6753 (ttp80)
REVERT: A  377 PHE cc_start: 0.7104 (t80) cc_final: 0.6738 (t80)
REVERT: A  387 LEU cc_start: 0.8631 (mt) cc_final: 0.8337 (mt)
REVERT: A  396 TYR cc_start: 0.7197 (m-80) cc_final: 0.6398 (m-80)
REVERT: A  401 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7660 (m)
REVERT: A  408 ARG cc_start: 0.8028 (ttp-170) cc_final: 0.7609 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7958 (t0) cc_final: 0.7622 (t0)
REVERT: A  442 ASP cc_start: 0.8226 (p0) cc_final: 0.7765 (p0)
REVERT: A  452 LEU cc_start: 0.7590 (mp) cc_final: 0.7111 (tt)
REVERT: A  501 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7551 (t80)
REVERT: A  542 ASN cc_start: 0.7980 (m-40) cc_final: 0.7254 (p0)
REVERT: A  588 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8694 (p)
REVERT: A  591 SER cc_start: 0.7670 (m) cc_final: 0.7248 (p)
REVERT: B   29 PHE cc_start: 0.8103 (m-80) cc_final: 0.7543 (m-80)
REVERT: B   64 LYS cc_start: 0.8326 (tptt) cc_final: 0.7973 (tptt)
REVERT: B  142 LEU cc_start: 0.8829 (mm) cc_final: 0.8231 (tp)
REVERT: B  189 ILE cc_start: 0.8753 (mm) cc_final: 0.8426 (mm)
REVERT: B  211 ASP cc_start: 0.8022 (t0) cc_final: 0.7720 (t0)
REVERT: B  221 MET cc_start: 0.7188 (mtt) cc_final: 0.6912 (mtt)
REVERT: B  252 THR cc_start: 0.8131 (t) cc_final: 0.7878 (m)
  outliers start: 36
  outliers final: 24
  residues processed: 235
  average time/residue: 0.2365
  time to fit residues: 70.8547
Evaluate side-chains
  223 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 196
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  478 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   58 TYR
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  208 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0060
   chunk 60 optimal weight:    6.9990
   chunk 1 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   overall best weight:    0.8798

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 540 ASN
A 564 GLN
A 607 GLN
B 250 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.163914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.132005 restraints weight = 12398.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.137449 restraints weight = 7236.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.141176 restraints weight = 4856.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6838
moved from start:          0.5388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6703  Z= 0.215
  Angle     :  0.703   9.274   9118  Z= 0.357
  Chirality :  0.046   0.218   1003
  Planarity :  0.005   0.057   1175
  Dihedral  :  6.950  80.711    934
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.17 %
    Favored  : 88.83 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 23.26 %
    Favored  : 72.28 %
  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: -3.46 (0.27), residues: 815
  helix: -1.18 (1.48), residues: 17
  sheet: -2.09 (0.36), residues: 194
  loop : -2.60 (0.23), residues: 604

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.073   0.003   TRP B 174 
 HIS   0.006   0.001   HIS A 519 
 PHE   0.030   0.002   PHE B 165 
 TYR   0.015   0.001   TYR B  94 
 ARG   0.008   0.001   ARG A 328 

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 206
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7666 (tp40) cc_final: 0.7361 (tp40)
REVERT: A   86 PHE cc_start: 0.8564 (t80) cc_final: 0.8002 (t80)
REVERT: A  177 MET cc_start: 0.6319 (mmt) cc_final: 0.6029 (mmt)
REVERT: A  229 LEU cc_start: 0.8473 (tp) cc_final: 0.8188 (mm)
REVERT: A  313 TYR cc_start: 0.6267 (m-80) cc_final: 0.5622 (m-80)
REVERT: A  340 GLU cc_start: 0.8139 (mp0) cc_final: 0.7821 (mp0)
REVERT: A  357 ARG cc_start: 0.7536 (ttp80) cc_final: 0.6936 (ttp80)
REVERT: A  359 SER cc_start: 0.8278 (m) cc_final: 0.7832 (t)
REVERT: A  377 PHE cc_start: 0.7054 (t80) cc_final: 0.6836 (t80)
REVERT: A  387 LEU cc_start: 0.8661 (mt) cc_final: 0.8330 (mt)
REVERT: A  388 ASN cc_start: 0.8274 (p0) cc_final: 0.7896 (t0)
REVERT: A  396 TYR cc_start: 0.7222 (m-80) cc_final: 0.6486 (m-80)
REVERT: A  408 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7610 (ttp-170)
REVERT: A  417 ASN cc_start: 0.8037 (t0) cc_final: 0.7676 (t0)
REVERT: A  424 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7744 (tptt)
REVERT: A  442 ASP cc_start: 0.8288 (p0) cc_final: 0.7841 (p0)
REVERT: A  452 LEU cc_start: 0.7546 (mp) cc_final: 0.7046 (tt)
REVERT: A  501 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7578 (t80)
REVERT: A  547 LYS cc_start: 0.7347 (mmmt) cc_final: 0.6898 (mmmt)
REVERT: A  562 PHE cc_start: 0.6988 (t80) cc_final: 0.6562 (t80)
REVERT: A  588 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8637 (p)
REVERT: B   29 PHE cc_start: 0.8179 (m-80) cc_final: 0.7527 (m-80)
REVERT: B   64 LYS cc_start: 0.8317 (tptt) cc_final: 0.7942 (tptt)
REVERT: B  142 LEU cc_start: 0.8876 (mm) cc_final: 0.8172 (tt)
REVERT: B  158 LEU cc_start: 0.7757 (mm) cc_final: 0.7450 (mt)
REVERT: B  172 MET cc_start: 0.6739 (mpt) cc_final: 0.6475 (mpt)
REVERT: B  189 ILE cc_start: 0.8737 (mm) cc_final: 0.8383 (mm)
REVERT: B  211 ASP cc_start: 0.8018 (t0) cc_final: 0.7662 (t0)
REVERT: B  243 TYR cc_start: 0.7788 (t80) cc_final: 0.7582 (t80)
REVERT: B  252 THR cc_start: 0.8150 (t) cc_final: 0.7874 (m)
  outliers start: 32
  outliers final: 23
  residues processed: 226
  average time/residue: 0.2526
  time to fit residues: 72.8387
Evaluate side-chains
  220 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 194
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  208 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 62 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 218 GLN
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 ASN
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.163144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.131158 restraints weight = 12398.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.136680 restraints weight = 7164.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.140491 restraints weight = 4774.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
moved from start:          0.5698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6703  Z= 0.227
  Angle     :  0.731   9.857   9118  Z= 0.370
  Chirality :  0.047   0.221   1003
  Planarity :  0.005   0.057   1175
  Dihedral  :  6.847  80.878    930
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 16.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.02 %
    Favored  : 87.98 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 23.68 %
    Favored  : 71.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.40 (0.27), residues: 815
  helix: -1.34 (1.35), residues: 17
  sheet: -2.02 (0.37), residues: 191
  loop : -2.56 (0.23), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.071   0.003   TRP B 174 
 HIS   0.010   0.002   HIS A 519 
 PHE   0.027   0.002   PHE A 490 
 TYR   0.016   0.001   TYR B  52 
 ARG   0.009   0.001   ARG A 328 

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 204
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 SER cc_start: 0.8390 (t) cc_final: 0.8164 (p)
REVERT: A   52 GLN cc_start: 0.7709 (tp40) cc_final: 0.7440 (tp40)
REVERT: A   86 PHE cc_start: 0.8603 (t80) cc_final: 0.8353 (t80)
REVERT: A  177 MET cc_start: 0.6357 (mmt) cc_final: 0.6055 (mmt)
REVERT: A  308 VAL cc_start: 0.8359 (p) cc_final: 0.8138 (p)
REVERT: A  313 TYR cc_start: 0.6355 (m-80) cc_final: 0.5734 (m-80)
REVERT: A  328 ARG cc_start: 0.6823 (ttm110) cc_final: 0.6548 (ttm110)
REVERT: A  340 GLU cc_start: 0.8203 (mp0) cc_final: 0.7902 (mp0)
REVERT: A  355 ARG cc_start: 0.7984 (mtp85) cc_final: 0.7250 (mtp85)
REVERT: A  357 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7011 (ttp80)
REVERT: A  359 SER cc_start: 0.8348 (m) cc_final: 0.7902 (t)
REVERT: A  387 LEU cc_start: 0.8701 (mt) cc_final: 0.8418 (mt)
REVERT: A  396 TYR cc_start: 0.7234 (m-80) cc_final: 0.6577 (m-80)
REVERT: A  401 VAL cc_start: 0.7977 (OUTLIER) cc_final: 0.7632 (m)
REVERT: A  408 ARG cc_start: 0.7968 (ttp-170) cc_final: 0.7605 (ttp-170)
REVERT: A  417 ASN cc_start: 0.8057 (t0) cc_final: 0.7685 (t0)
REVERT: A  424 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7756 (tptt)
REVERT: A  442 ASP cc_start: 0.8254 (p0) cc_final: 0.7832 (p0)
REVERT: A  444 LYS cc_start: 0.8876 (ptpt) cc_final: 0.8652 (ptmm)
REVERT: A  452 LEU cc_start: 0.7565 (mp) cc_final: 0.6969 (tt)
REVERT: A  501 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7582 (t80)
REVERT: A  542 ASN cc_start: 0.7799 (m110) cc_final: 0.7511 (t0)
REVERT: A  547 LYS cc_start: 0.7311 (mmmt) cc_final: 0.6631 (mmmt)
REVERT: A  562 PHE cc_start: 0.6756 (t80) cc_final: 0.6464 (t80)
REVERT: A  588 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8574 (p)
REVERT: B   29 PHE cc_start: 0.8205 (m-80) cc_final: 0.7582 (m-80)
REVERT: B   64 LYS cc_start: 0.8330 (tptt) cc_final: 0.7960 (tptt)
REVERT: B  189 ILE cc_start: 0.8730 (mm) cc_final: 0.8374 (mm)
REVERT: B  211 ASP cc_start: 0.7983 (t0) cc_final: 0.7637 (t0)
REVERT: B  221 MET cc_start: 0.7079 (mtt) cc_final: 0.6772 (mtt)
REVERT: B  234 CYS cc_start: 0.4902 (p) cc_final: 0.4201 (p)
REVERT: B  252 THR cc_start: 0.8037 (t) cc_final: 0.7785 (m)
  outliers start: 37
  outliers final: 28
  residues processed: 226
  average time/residue: 0.2139
  time to fit residues: 61.2940
Evaluate side-chains
  230 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 198
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  564 GLN
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  185 TRP
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  208 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   chunk 19 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.161321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.129645 restraints weight = 12512.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.135085 restraints weight = 7296.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.138808 restraints weight = 4869.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
moved from start:          0.6028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6703  Z= 0.261
  Angle     :  0.756  10.391   9118  Z= 0.386
  Chirality :  0.048   0.261   1003
  Planarity :  0.005   0.059   1175
  Dihedral  :  7.072  81.667    930
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 19.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.01 %
    Favored  : 86.99 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 23.96 %
    Favored  : 70.33 %
  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: -3.39 (0.27), residues: 815
  helix: -1.41 (1.29), residues: 17
  sheet: -2.03 (0.36), residues: 210
  loop : -2.55 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.078   0.003   TRP B 174 
 HIS   0.008   0.002   HIS A 519 
 PHE   0.025   0.002   PHE A 275 
 TYR   0.020   0.002   TYR B 243 
 ARG   0.007   0.001   ARG A 493 

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 202
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 SER cc_start: 0.8478 (t) cc_final: 0.8262 (p)
REVERT: A   52 GLN cc_start: 0.7669 (tp40) cc_final: 0.7389 (tp40)
REVERT: A   84 LEU cc_start: 0.8500 (mt) cc_final: 0.8298 (mt)
REVERT: A   86 PHE cc_start: 0.8649 (t80) cc_final: 0.8385 (t80)
REVERT: A  177 MET cc_start: 0.6650 (mmt) cc_final: 0.6335 (mmt)
REVERT: A  229 LEU cc_start: 0.8466 (tp) cc_final: 0.8171 (mm)
REVERT: A  313 TYR cc_start: 0.6591 (m-80) cc_final: 0.5901 (m-80)
REVERT: A  340 GLU cc_start: 0.8257 (mp0) cc_final: 0.7822 (mp0)
REVERT: A  355 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7477 (mtp85)
REVERT: A  359 SER cc_start: 0.8388 (m) cc_final: 0.8156 (t)
REVERT: A  387 LEU cc_start: 0.8735 (mt) cc_final: 0.8475 (mt)
REVERT: A  388 ASN cc_start: 0.8281 (p0) cc_final: 0.7976 (t0)
REVERT: A  390 LEU cc_start: 0.8370 (tp) cc_final: 0.7930 (pt)
REVERT: A  396 TYR cc_start: 0.7240 (m-80) cc_final: 0.6058 (m-80)
REVERT: A  401 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7705 (m)
REVERT: A  408 ARG cc_start: 0.8020 (ttp-170) cc_final: 0.7684 (ttp-170)
REVERT: A  417 ASN cc_start: 0.8150 (t0) cc_final: 0.7777 (t0)
REVERT: A  424 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.7920 (tptt)
REVERT: A  442 ASP cc_start: 0.8266 (p0) cc_final: 0.7883 (p0)
REVERT: A  452 LEU cc_start: 0.7672 (mp) cc_final: 0.7091 (tt)
REVERT: A  501 TYR cc_start: 0.8039 (OUTLIER) cc_final: 0.7637 (t80)
REVERT: A  547 LYS cc_start: 0.7321 (mmmt) cc_final: 0.6998 (mmmt)
REVERT: A  562 PHE cc_start: 0.6769 (t80) cc_final: 0.6508 (t80)
REVERT: A  588 THR cc_start: 0.8837 (OUTLIER) cc_final: 0.8615 (p)
REVERT: A  591 SER cc_start: 0.7703 (m) cc_final: 0.7413 (p)
REVERT: A  675 GLN cc_start: 0.9141 (mp10) cc_final: 0.8881 (mp10)
REVERT: B   29 PHE cc_start: 0.8125 (m-80) cc_final: 0.7586 (m-80)
REVERT: B   64 LYS cc_start: 0.8357 (tptt) cc_final: 0.7990 (tptt)
REVERT: B  142 LEU cc_start: 0.8519 (mm) cc_final: 0.7465 (tt)
REVERT: B  189 ILE cc_start: 0.8730 (mm) cc_final: 0.8369 (mm)
REVERT: B  211 ASP cc_start: 0.8041 (t0) cc_final: 0.7660 (t0)
REVERT: B  234 CYS cc_start: 0.4452 (p) cc_final: 0.2420 (p)
REVERT: B  252 THR cc_start: 0.8043 (t) cc_final: 0.7785 (m)
  outliers start: 41
  outliers final: 34
  residues processed: 225
  average time/residue: 0.2125
  time to fit residues: 60.7171
Evaluate side-chains
  235 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 197
  time to evaluate  : 0.653 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  530 SER
Chi-restraints excluded: chain A residue  549 THR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  696 THR
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  185 TRP
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  216 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 17 optimal weight:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   chunk 70 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
A 613 GLN
B   3 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.155115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.123153 restraints weight = 12578.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.128492 restraints weight = 7339.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.132211 restraints weight = 4919.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7004
moved from start:          0.6689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   6703  Z= 0.366
  Angle     :  0.833  10.206   9118  Z= 0.434
  Chirality :  0.051   0.288   1003
  Planarity :  0.005   0.061   1175
  Dihedral  :  7.759  82.723    930
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 26.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.97 %
    Favored  : 85.03 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 24.09 %
    Favored  : 69.50 %
  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: -3.45 (0.28), residues: 815
  helix: -1.97 (1.06), residues: 23
  sheet: -2.28 (0.36), residues: 200
  loop : -2.48 (0.24), residues: 592

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.106   0.005   TRP B 174 
 HIS   0.007   0.002   HIS A 519 
 PHE   0.042   0.003   PHE A 275 
 TYR   0.019   0.002   TYR A  37 
 ARG   0.012   0.001   ARG A 355 

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 201
  time to evaluate  : 0.653 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7639 (tp40) cc_final: 0.7305 (tp40)
REVERT: A   84 LEU cc_start: 0.8655 (mt) cc_final: 0.8404 (mp)
REVERT: A   86 PHE cc_start: 0.8798 (t80) cc_final: 0.8562 (t80)
REVERT: A  177 MET cc_start: 0.7039 (mmt) cc_final: 0.6700 (mmt)
REVERT: A  229 LEU cc_start: 0.8441 (tp) cc_final: 0.8182 (mm)
REVERT: A  313 TYR cc_start: 0.6793 (m-80) cc_final: 0.6030 (m-80)
REVERT: A  340 GLU cc_start: 0.8299 (mp0) cc_final: 0.7807 (mp0)
REVERT: A  343 ASN cc_start: 0.8375 (t0) cc_final: 0.7877 (p0)
REVERT: A  355 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7757 (mtp85)
REVERT: A  388 ASN cc_start: 0.8277 (p0) cc_final: 0.8036 (t0)
REVERT: A  396 TYR cc_start: 0.7109 (m-80) cc_final: 0.6559 (m-80)
REVERT: A  408 ARG cc_start: 0.8082 (ttp-170) cc_final: 0.7765 (ttp-170)
REVERT: A  417 ASN cc_start: 0.8308 (t0) cc_final: 0.7956 (t0)
REVERT: A  424 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7885 (tptp)
REVERT: A  442 ASP cc_start: 0.8172 (p0) cc_final: 0.7865 (p0)
REVERT: A  452 LEU cc_start: 0.7834 (mp) cc_final: 0.7350 (tt)
REVERT: A  462 LYS cc_start: 0.8800 (tptp) cc_final: 0.8446 (tptp)
REVERT: A  501 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.7642 (t80)
REVERT: A  547 LYS cc_start: 0.7317 (mmmt) cc_final: 0.6967 (mmmt)
REVERT: A  588 THR cc_start: 0.8905 (OUTLIER) cc_final: 0.8628 (p)
REVERT: A  591 SER cc_start: 0.7970 (m) cc_final: 0.7678 (p)
REVERT: A  659 SER cc_start: 0.7886 (m) cc_final: 0.7410 (t)
REVERT: A  675 GLN cc_start: 0.9267 (mp10) cc_final: 0.8791 (mp10)
REVERT: B   29 PHE cc_start: 0.8131 (m-80) cc_final: 0.7542 (m-80)
REVERT: B   64 LYS cc_start: 0.8459 (tptt) cc_final: 0.8095 (tptt)
REVERT: B  165 PHE cc_start: 0.7868 (t80) cc_final: 0.7610 (t80)
REVERT: B  189 ILE cc_start: 0.8654 (mm) cc_final: 0.8450 (mt)
REVERT: B  192 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7249 (tt)
REVERT: B  211 ASP cc_start: 0.8024 (t0) cc_final: 0.7532 (t0)
REVERT: B  221 MET cc_start: 0.7181 (mpp) cc_final: 0.6633 (mpp)
REVERT: B  252 THR cc_start: 0.8010 (t) cc_final: 0.7724 (m)
  outliers start: 46
  outliers final: 33
  residues processed: 223
  average time/residue: 0.2317
  time to fit residues: 66.0463
Evaluate side-chains
  237 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 200
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  265 TYR
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  564 GLN
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  697 MET
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   32 TYR
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   58 TYR
Chi-restraints excluded: chain B residue  185 TRP
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  208 ILE
Chi-restraints excluded: chain B residue  216 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0770
   chunk 40 optimal weight:    9.9990
   chunk 52 optimal weight:    0.0270
   chunk 36 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.161004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.129027 restraints weight = 12500.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.134533 restraints weight = 7247.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.138395 restraints weight = 4818.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.6712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6703  Z= 0.242
  Angle     :  0.821  10.421   9118  Z= 0.419
  Chirality :  0.050   0.289   1003
  Planarity :  0.006   0.110   1175
  Dihedral  :  7.413  82.280    930
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 19.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.37 %
    Favored  : 86.63 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 27.16 %
    Favored  : 68.11 %
  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: -3.29 (0.28), residues: 815
  helix: -1.85 (1.09), residues: 23
  sheet: -2.08 (0.35), residues: 223
  loop : -2.39 (0.25), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.112   0.004   TRP B 174 
 HIS   0.002   0.001   HIS A  49 
 PHE   0.027   0.002   PHE B 206 
 TYR   0.018   0.002   TYR A 660 
 ARG   0.007   0.001   ARG A 328 

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

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

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1630 Ramachandran restraints generated.
    815 Oldfield, 0 Emsley, 815 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 203
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.7571 (tp40) cc_final: 0.7233 (tp-100)
REVERT: A  177 MET cc_start: 0.6917 (mmt) cc_final: 0.6592 (mmt)
REVERT: A  229 LEU cc_start: 0.8365 (tp) cc_final: 0.8149 (mm)
REVERT: A  313 TYR cc_start: 0.6467 (m-80) cc_final: 0.5829 (m-80)
REVERT: A  340 GLU cc_start: 0.8141 (mp0) cc_final: 0.7600 (mp0)
REVERT: A  343 ASN cc_start: 0.8284 (t0) cc_final: 0.7771 (p0)
REVERT: A  355 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7632 (mtp85)
REVERT: A  390 LEU cc_start: 0.8553 (tp) cc_final: 0.8201 (pp)
REVERT: A  396 TYR cc_start: 0.7123 (m-80) cc_final: 0.6207 (m-80)
REVERT: A  408 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7706 (ttp-170)
REVERT: A  417 ASN cc_start: 0.8091 (t0) cc_final: 0.7724 (t0)
REVERT: A  424 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7612 (tptp)
REVERT: A  442 ASP cc_start: 0.8289 (p0) cc_final: 0.7895 (p0)
REVERT: A  501 TYR cc_start: 0.7974 (OUTLIER) cc_final: 0.7646 (t80)
REVERT: A  547 LYS cc_start: 0.7313 (mmmt) cc_final: 0.7027 (mmmt)
REVERT: A  591 SER cc_start: 0.7666 (m) cc_final: 0.7393 (p)
REVERT: A  659 SER cc_start: 0.7855 (m) cc_final: 0.7465 (t)
REVERT: A  675 GLN cc_start: 0.9115 (mp10) cc_final: 0.8763 (mp10)
REVERT: B   29 PHE cc_start: 0.8077 (m-80) cc_final: 0.7512 (m-80)
REVERT: B   64 LYS cc_start: 0.8235 (tptt) cc_final: 0.7957 (tptt)
REVERT: B  189 ILE cc_start: 0.8638 (mm) cc_final: 0.8401 (mt)
REVERT: B  211 ASP cc_start: 0.7971 (t0) cc_final: 0.7547 (t0)
REVERT: B  252 THR cc_start: 0.8074 (t) cc_final: 0.7841 (m)
  outliers start: 34
  outliers final: 23
  residues processed: 219
  average time/residue: 0.2276
  time to fit residues: 63.0736
Evaluate side-chains
  223 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 198
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   78 ARG
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  192 PHE
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  389 ASP
Chi-restraints excluded: chain A residue  422 ASN
Chi-restraints excluded: chain A residue  424 LYS
Chi-restraints excluded: chain A residue  470 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  564 GLN
Chi-restraints excluded: chain A residue  664 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain B residue    1 GLU
Chi-restraints excluded: chain B residue   34 MET
Chi-restraints excluded: chain B residue  185 TRP
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  208 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 46 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0670
   chunk 18 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 53 optimal weight:    0.5980
   overall best weight:    0.8522

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

Flipped N/Q/H residues before XYZ refinement:
** A 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 218 GLN
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 321 GLN
A 360 ASN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.161276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.129083 restraints weight = 12681.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.134565 restraints weight = 7346.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.138394 restraints weight = 4917.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.6841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6703  Z= 0.239
  Angle     :  0.823  12.464   9118  Z= 0.414
  Chirality :  0.050   0.319   1003
  Planarity :  0.006   0.122   1175
  Dihedral  :  7.386  81.908    930
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.87 %
    Favored  : 86.13 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 28.41 %
    Favored  : 67.13 %
  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: -3.16 (0.28), residues: 815
  helix: -1.89 (1.06), residues: 23
  sheet: -1.91 (0.38), residues: 199
  loop : -2.34 (0.24), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.074   0.003   TRP B 174 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.035   0.002   PHE B 165 
 TYR   0.016   0.002   TYR B 233 
 ARG   0.008   0.001   ARG A 328 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2735.89 seconds
wall clock time: 48 minutes 1.88 seconds (2881.88 seconds total)