Starting phenix.real_space_refine
on Sat May 10 15:53:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8i4h_35173/05_2025/8i4h_35173.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i4h_35173/05_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_35173/05_2025/8i4h_35173.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i4h_35173/05_2025/8i4h_35173.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i4h_35173/05_2025/8i4h_35173.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i4h_35173/05_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-5687/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: 1.50
  Conformation dependent library (CDL) restraints added in 852.5 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: 1.03
  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: 2.10

  Time building geometry restraints manager: 1.78 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:                  0.000
  Normalize map: mean=0, sd=1:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.620
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.860
-------------------------------------------------------------------------------
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   6714  Z= 0.080
  Angle     :  0.433   5.155   9140  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22635 (  112)
  hydrogen bonds       : angle       9.04735 (  264)
  SS BOND              : bond        0.00135 (   11)
  SS BOND              : angle       0.42984 (   22)
  covalent geometry    : bond        0.00149 ( 6703)
  covalent geometry    : angle       0.43270 ( 9118)

*********************** 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  : 0.717 
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: 0.2062
  time to fit residues: 70.5866
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  : 0.648 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7964

-------------------------------------------------------------------------------
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 173 GLN
A 271 GLN
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: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.177619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.145893 restraints weight = 12744.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.152050 restraints weight = 7525.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.156114 restraints weight = 5023.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6688
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6714  Z= 0.136
  Angle     :  0.619   7.679   9140  Z= 0.312
  Chirality :  0.045   0.256   1003
  Planarity :  0.004   0.054   1175
  Dihedral  :  6.475  81.573    950
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.31 %
    Favored  : 89.69 %
  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: -4.20 (0.25), residues: 815
  helix: -2.58 (1.17), residues: 16
  sheet: -2.82 (0.33), residues: 197
  loop : -3.01 (0.22), residues: 602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 174 
 HIS   0.017   0.003   HIS A 519 
 PHE   0.034   0.001   PHE A 306 
 TYR   0.010   0.001   TYR A 160 
 ARG   0.003   0.000   ARG A 273 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03239 (  112)
  hydrogen bonds       : angle       7.32000 (  264)
  SS BOND              : bond        0.00665 (   11)
  SS BOND              : angle       1.55846 (   22)
  covalent geometry    : bond        0.00295 ( 6703)
  covalent geometry    : angle       0.61455 ( 9118)

*********************** 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
  271 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 224
  time to evaluate  : 0.747 
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: 0.7670 (tm-30) cc_final: 0.7339 (tp40)
REVERT: A   67 VAL cc_start: 0.8078 (p) cc_final: 0.7319 (m)
REVERT: A   92 PHE cc_start: 0.6445 (t80) cc_final: 0.6169 (t80)
REVERT: A  177 MET cc_start: 0.6148 (mmt) cc_final: 0.5859 (mmt)
REVERT: A  204 LYS cc_start: 0.8181 (tttp) cc_final: 0.7949 (tttp)
REVERT: A  241 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8174 (mm)
REVERT: A  265 TYR cc_start: 0.6679 (m-80) cc_final: 0.6367 (m-80)
REVERT: A  319 ARG cc_start: 0.7858 (ptp90) cc_final: 0.7485 (tpt170)
REVERT: A  340 GLU cc_start: 0.7523 (mp0) cc_final: 0.7306 (mp0)
REVERT: A  357 ARG cc_start: 0.7076 (ttp80) cc_final: 0.6687 (ttp80)
REVERT: A  359 SER cc_start: 0.8133 (OUTLIER) cc_final: 0.7644 (t)
REVERT: A  368 LEU cc_start: 0.8103 (mm) cc_final: 0.7579 (tp)
REVERT: A  387 LEU cc_start: 0.8690 (mt) cc_final: 0.8298 (tp)
REVERT: A  396 TYR cc_start: 0.7068 (m-80) cc_final: 0.6448 (m-80)
REVERT: A  408 ARG cc_start: 0.8076 (ttp-170) cc_final: 0.7619 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7846 (t0) cc_final: 0.7470 (t0)
REVERT: A  424 LYS cc_start: 0.8108 (tmtm) cc_final: 0.7726 (tmtm)
REVERT: A  452 LEU cc_start: 0.7773 (mp) cc_final: 0.7244 (tt)
REVERT: A  462 LYS cc_start: 0.8281 (tptp) cc_final: 0.7833 (tptp)
REVERT: A  490 PHE cc_start: 0.8251 (t80) cc_final: 0.7970 (t80)
REVERT: A  501 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7309 (t80)
REVERT: A  528 LYS cc_start: 0.7597 (mttm) cc_final: 0.6921 (mttp)
REVERT: A  537 LYS cc_start: 0.7794 (tppp) cc_final: 0.7340 (mmmm)
REVERT: A  588 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8649 (p)
REVERT: A  598 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8146 (tp)
REVERT: A  664 ILE cc_start: 0.8781 (pt) cc_final: 0.8488 (pt)
REVERT: B   38 ARG cc_start: 0.7226 (ttp-170) cc_final: 0.6640 (ttp-170)
REVERT: B   64 LYS cc_start: 0.8304 (tptt) cc_final: 0.7969 (tptt)
REVERT: B   93 TYR cc_start: 0.6817 (m-80) cc_final: 0.5990 (m-80)
REVERT: B  189 ILE cc_start: 0.8668 (mm) cc_final: 0.8322 (mm)
REVERT: B  211 ASP cc_start: 0.7878 (t0) cc_final: 0.7660 (t0)
REVERT: B  252 THR cc_start: 0.8445 (t) cc_final: 0.8163 (m)
  outliers start: 47
  outliers final: 21
  residues processed: 249
  average time/residue: 0.2138
  time to fit residues: 66.9891
Evaluate side-chains
  243 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 217
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
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  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   66 LEU
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  208 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 35 optimal weight:    0.0670
   chunk 76 optimal weight:    3.9990
   chunk 72 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 16 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 30 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A 234 ASN
** 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
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 690 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 = 0.4347 r_free = 0.4347 target = 0.170215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.138331 restraints weight = 12592.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.144138 restraints weight = 7504.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.148165 restraints weight = 5063.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.4098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6728
moved from start:          0.3670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6714  Z= 0.120
  Angle     :  0.620   8.378   9140  Z= 0.310
  Chirality :  0.045   0.158   1003
  Planarity :  0.005   0.062   1175
  Dihedral  :  6.243  80.425    940
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.96 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 19.36 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.79 (0.26), residues: 815
  helix: -2.57 (1.23), residues: 16
  sheet: -2.44 (0.38), residues: 167
  loop : -2.77 (0.22), residues: 632

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B 174 
 HIS   0.011   0.002   HIS A 519 
 PHE   0.026   0.002   PHE A 306 
 TYR   0.015   0.001   TYR B 107 
 ARG   0.006   0.001   ARG A 355 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03041 (  112)
  hydrogen bonds       : angle       7.15900 (  264)
  SS BOND              : bond        0.00578 (   11)
  SS BOND              : angle       1.27611 (   22)
  covalent geometry    : bond        0.00264 ( 6703)
  covalent geometry    : angle       0.61718 ( 9118)

*********************** 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
  247 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 213
  time to evaluate  : 0.718 
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: 0.7689 (tm130) cc_final: 0.7283 (tp40)
REVERT: A   67 VAL cc_start: 0.8038 (p) cc_final: 0.7401 (m)
REVERT: A   92 PHE cc_start: 0.6482 (t80) cc_final: 0.6190 (t80)
REVERT: A  177 MET cc_start: 0.6203 (mmt) cc_final: 0.5901 (mmt)
REVERT: A  265 TYR cc_start: 0.6548 (m-80) cc_final: 0.6268 (m-80)
REVERT: A  313 TYR cc_start: 0.5832 (m-80) cc_final: 0.5364 (m-80)
REVERT: A  319 ARG cc_start: 0.7808 (ptp90) cc_final: 0.7577 (tpt170)
REVERT: A  340 GLU cc_start: 0.7629 (mp0) cc_final: 0.7414 (mp0)
REVERT: A  355 ARG cc_start: 0.7689 (mtp85) cc_final: 0.7230 (mtp85)
REVERT: A  357 ARG cc_start: 0.7130 (ttp80) cc_final: 0.6751 (ttp80)
REVERT: A  359 SER cc_start: 0.7937 (m) cc_final: 0.7447 (t)
REVERT: A  368 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7935 (tp)
REVERT: A  387 LEU cc_start: 0.8667 (mt) cc_final: 0.8345 (tp)
REVERT: A  396 TYR cc_start: 0.6843 (m-80) cc_final: 0.6269 (m-80)
REVERT: A  408 ARG cc_start: 0.8025 (ttp-170) cc_final: 0.7578 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7792 (t0) cc_final: 0.7407 (t0)
REVERT: A  452 LEU cc_start: 0.7520 (mp) cc_final: 0.7038 (tt)
REVERT: A  490 PHE cc_start: 0.8022 (t80) cc_final: 0.7778 (t80)
REVERT: A  501 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7320 (t80)
REVERT: A  537 LYS cc_start: 0.7874 (tppp) cc_final: 0.7394 (mmmm)
REVERT: A  564 GLN cc_start: 0.7826 (pp30) cc_final: 0.7609 (tm-30)
REVERT: A  588 THR cc_start: 0.8933 (OUTLIER) cc_final: 0.8690 (p)
REVERT: B   64 LYS cc_start: 0.8256 (tptt) cc_final: 0.7960 (tptt)
REVERT: B   93 TYR cc_start: 0.6692 (m-80) cc_final: 0.6219 (m-80)
REVERT: B  107 TYR cc_start: 0.5600 (t80) cc_final: 0.5050 (t80)
REVERT: B  158 LEU cc_start: 0.7748 (mm) cc_final: 0.6852 (mt)
REVERT: B  159 SER cc_start: 0.8042 (OUTLIER) cc_final: 0.7713 (t)
REVERT: B  189 ILE cc_start: 0.8676 (mm) cc_final: 0.8378 (mm)
REVERT: B  211 ASP cc_start: 0.7898 (t0) cc_final: 0.7628 (t0)
REVERT: B  217 LEU cc_start: 0.8374 (tt) cc_final: 0.7920 (mm)
REVERT: B  252 THR cc_start: 0.8260 (t) cc_final: 0.8028 (m)
  outliers start: 34
  outliers final: 20
  residues processed: 232
  average time/residue: 0.2251
  time to fit residues: 65.3580
Evaluate side-chains
  220 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 196
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
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  204 LYS
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  307 THR
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  547 LYS
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  143 VAL
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:    4.9990
   chunk 58 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 59 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0770
   chunk 5 optimal weight:    0.9990
   chunk 40 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 77 optimal weight:    5.9990
   overall best weight:    1.1744

-------------------------------------------------------------------------------
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 321 GLN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 607 GLN
B   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.164767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.132267 restraints weight = 12668.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.138182 restraints weight = 7407.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.142205 restraints weight = 4940.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6839
moved from start:          0.4445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6714  Z= 0.161
  Angle     :  0.646   8.867   9140  Z= 0.331
  Chirality :  0.045   0.150   1003
  Planarity :  0.005   0.061   1175
  Dihedral  :  6.684  81.552    938
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 19.64 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.59 (0.27), residues: 815
  helix: -1.26 (1.75), residues: 10
  sheet: -2.48 (0.35), residues: 195
  loop : -2.56 (0.23), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP B 174 
 HIS   0.003   0.001   HIS A  66 
 PHE   0.039   0.002   PHE A 275 
 TYR   0.011   0.001   TYR B  93 
 ARG   0.006   0.001   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03291 (  112)
  hydrogen bonds       : angle       7.33083 (  264)
  SS BOND              : bond        0.00675 (   11)
  SS BOND              : angle       1.12677 (   22)
  covalent geometry    : bond        0.00343 ( 6703)
  covalent geometry    : angle       0.64482 ( 9118)

*********************** 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
  259 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 221
  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: A   86 PHE cc_start: 0.8437 (t80) cc_final: 0.8231 (t80)
REVERT: A  170 TYR cc_start: 0.8676 (t80) cc_final: 0.8341 (t80)
REVERT: A  177 MET cc_start: 0.6367 (mmt) cc_final: 0.6050 (mmt)
REVERT: A  310 LYS cc_start: 0.8690 (tppt) cc_final: 0.8437 (mmmm)
REVERT: A  313 TYR cc_start: 0.6109 (m-80) cc_final: 0.5532 (m-80)
REVERT: A  340 GLU cc_start: 0.7944 (mp0) cc_final: 0.7649 (mp0)
REVERT: A  357 ARG cc_start: 0.7508 (ttp80) cc_final: 0.6794 (ttp80)
REVERT: A  359 SER cc_start: 0.8254 (m) cc_final: 0.7865 (t)
REVERT: A  360 ASN cc_start: 0.8506 (p0) cc_final: 0.8260 (p0)
REVERT: A  387 LEU cc_start: 0.8604 (mt) cc_final: 0.8364 (tp)
REVERT: A  396 TYR cc_start: 0.6893 (m-80) cc_final: 0.6219 (m-10)
REVERT: A  401 VAL cc_start: 0.8022 (t) cc_final: 0.7663 (m)
REVERT: A  408 ARG cc_start: 0.7955 (ttp-170) cc_final: 0.7570 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7966 (t0) cc_final: 0.7594 (t0)
REVERT: A  442 ASP cc_start: 0.8292 (p0) cc_final: 0.7836 (p0)
REVERT: A  452 LEU cc_start: 0.7652 (mp) cc_final: 0.7161 (tt)
REVERT: A  490 PHE cc_start: 0.8093 (t80) cc_final: 0.7882 (t80)
REVERT: A  501 TYR cc_start: 0.7964 (OUTLIER) cc_final: 0.7345 (t80)
REVERT: A  537 LYS cc_start: 0.7920 (tppp) cc_final: 0.7461 (mmmm)
REVERT: A  562 PHE cc_start: 0.7023 (t80) cc_final: 0.6563 (t80)
REVERT: A  588 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8711 (p)
REVERT: A  664 ILE cc_start: 0.8836 (pt) cc_final: 0.8495 (pt)
REVERT: B   64 LYS cc_start: 0.8338 (tptt) cc_final: 0.7981 (tptt)
REVERT: B  189 ILE cc_start: 0.8719 (mm) cc_final: 0.8433 (mm)
REVERT: B  211 ASP cc_start: 0.8008 (t0) cc_final: 0.7645 (t0)
REVERT: B  252 THR cc_start: 0.8146 (t) cc_final: 0.7902 (m)
  outliers start: 38
  outliers final: 26
  residues processed: 241
  average time/residue: 0.2319
  time to fit residues: 69.7066
Evaluate side-chains
  234 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 206
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
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   95 ILE
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  274 THR
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  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  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   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  212 ASN
Chi-restraints excluded: chain B residue  216 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.0060
   chunk 55 optimal weight:    0.0670
   chunk 9 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 79 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.6936

-------------------------------------------------------------------------------
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 321 GLN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
A 607 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.167094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.135401 restraints weight = 12626.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.141028 restraints weight = 7288.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.144850 restraints weight = 4852.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6801
moved from start:          0.4874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6714  Z= 0.128
  Angle     :  0.664   8.044   9140  Z= 0.336
  Chirality :  0.046   0.156   1003
  Planarity :  0.005   0.061   1175
  Dihedral  :  6.836  79.216    938
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.31 %
    Favored  : 89.69 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 22.56 %
    Favored  : 72.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.35 (0.27), residues: 815
  helix: -1.04 (1.61), residues: 10
  sheet: -2.28 (0.38), residues: 179
  loop : -2.42 (0.23), residues: 626

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP B 174 
 HIS   0.015   0.002   HIS A 519 
 PHE   0.026   0.002   PHE B 165 
 TYR   0.011   0.001   TYR A 202 
 ARG   0.006   0.001   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03061 (  112)
  hydrogen bonds       : angle       7.02444 (  264)
  SS BOND              : bond        0.00545 (   11)
  SS BOND              : angle       1.00361 (   22)
  covalent geometry    : bond        0.00285 ( 6703)
  covalent geometry    : angle       0.66301 ( 9118)

*********************** 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
  243 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 210
  time to evaluate  : 0.669 
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   34 ARG cc_start: 0.6871 (mmp80) cc_final: 0.4956 (mmp-170)
REVERT: A   52 GLN cc_start: 0.7519 (tp40) cc_final: 0.7218 (tp40)
REVERT: A   86 PHE cc_start: 0.8472 (t80) cc_final: 0.8221 (t80)
REVERT: A  177 MET cc_start: 0.6354 (mmt) cc_final: 0.6033 (mmt)
REVERT: A  224 GLU cc_start: 0.7220 (pm20) cc_final: 0.6714 (pm20)
REVERT: A  229 LEU cc_start: 0.8781 (mp) cc_final: 0.8576 (tp)
REVERT: A  313 TYR cc_start: 0.6136 (m-80) cc_final: 0.5530 (m-80)
REVERT: A  329 PHE cc_start: 0.5939 (t80) cc_final: 0.5350 (t80)
REVERT: A  335 LEU cc_start: 0.7678 (tp) cc_final: 0.7299 (tt)
REVERT: A  340 GLU cc_start: 0.8068 (mp0) cc_final: 0.7760 (mp0)
REVERT: A  355 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7340 (mtp85)
REVERT: A  357 ARG cc_start: 0.7551 (ttp80) cc_final: 0.6891 (ttp80)
REVERT: A  360 ASN cc_start: 0.8450 (p0) cc_final: 0.8190 (p0)
REVERT: A  386 LYS cc_start: 0.8410 (ttpp) cc_final: 0.8121 (ptmm)
REVERT: A  387 LEU cc_start: 0.8675 (mt) cc_final: 0.8412 (mt)
REVERT: A  395 VAL cc_start: 0.7942 (m) cc_final: 0.7742 (t)
REVERT: A  396 TYR cc_start: 0.6902 (m-80) cc_final: 0.6508 (m-10)
REVERT: A  408 ARG cc_start: 0.7878 (ttp-170) cc_final: 0.7503 (ttp-170)
REVERT: A  417 ASN cc_start: 0.7989 (t0) cc_final: 0.7735 (t0)
REVERT: A  424 LYS cc_start: 0.8170 (tmtm) cc_final: 0.7864 (tptp)
REVERT: A  442 ASP cc_start: 0.8338 (p0) cc_final: 0.7866 (p0)
REVERT: A  452 LEU cc_start: 0.7521 (mp) cc_final: 0.7007 (tt)
REVERT: A  490 PHE cc_start: 0.8141 (t80) cc_final: 0.7887 (t80)
REVERT: A  501 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7383 (t80)
REVERT: B   29 PHE cc_start: 0.8051 (m-80) cc_final: 0.7496 (m-80)
REVERT: B   64 LYS cc_start: 0.8306 (tptt) cc_final: 0.7940 (tptt)
REVERT: B  142 LEU cc_start: 0.8772 (mm) cc_final: 0.8199 (tp)
REVERT: B  158 LEU cc_start: 0.7870 (mm) cc_final: 0.7548 (mt)
REVERT: B  189 ILE cc_start: 0.8741 (mm) cc_final: 0.8408 (mm)
REVERT: B  197 TYR cc_start: 0.6996 (m-80) cc_final: 0.6785 (m-80)
REVERT: B  211 ASP cc_start: 0.7935 (t0) cc_final: 0.7558 (t0)
REVERT: B  252 THR cc_start: 0.8151 (t) cc_final: 0.7854 (m)
  outliers start: 33
  outliers final: 23
  residues processed: 231
  average time/residue: 0.2244
  time to fit residues: 65.1114
Evaluate side-chains
  217 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 193
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
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  274 THR
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  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  569 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   60 ASN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  206 PHE
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:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    0.4980
   chunk 77 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 72 optimal weight:    0.1980
   chunk 21 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 505 HIS
** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 540 ASN
A 690 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.165974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.133986 restraints weight = 12448.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.139506 restraints weight = 7155.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.143345 restraints weight = 4766.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.5282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6714  Z= 0.129
  Angle     :  0.701   7.982   9140  Z= 0.356
  Chirality :  0.046   0.171   1003
  Planarity :  0.005   0.061   1175
  Dihedral  :  6.802  80.137    934
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 14.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  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: -3.34 (0.27), residues: 815
  helix: -1.00 (1.61), residues: 10
  sheet: -2.28 (0.36), residues: 187
  loop : -2.41 (0.23), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP B 174 
 HIS   0.011   0.002   HIS A 519 
 PHE   0.019   0.001   PHE A 275 
 TYR   0.014   0.001   TYR B  32 
 ARG   0.008   0.001   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03018 (  112)
  hydrogen bonds       : angle       6.93935 (  264)
  SS BOND              : bond        0.00422 (   11)
  SS BOND              : angle       1.06086 (   22)
  covalent geometry    : bond        0.00293 ( 6703)
  covalent geometry    : angle       0.69959 ( 9118)

*********************** 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
  232 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 200
  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: A   34 ARG cc_start: 0.6899 (mmp80) cc_final: 0.4560 (mmp-170)
REVERT: A   52 GLN cc_start: 0.7515 (tp40) cc_final: 0.7197 (tp40)
REVERT: A   86 PHE cc_start: 0.8444 (t80) cc_final: 0.8160 (t80)
REVERT: A  177 MET cc_start: 0.6449 (mmt) cc_final: 0.6132 (mmt)
REVERT: A  313 TYR cc_start: 0.6115 (m-80) cc_final: 0.5493 (m-80)
REVERT: A  335 LEU cc_start: 0.7677 (tp) cc_final: 0.7316 (tt)
REVERT: A  340 GLU cc_start: 0.8103 (mp0) cc_final: 0.7791 (mp0)
REVERT: A  355 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7269 (mtp85)
REVERT: A  357 ARG cc_start: 0.7530 (ttp80) cc_final: 0.7028 (ttp80)
REVERT: A  359 SER cc_start: 0.8224 (m) cc_final: 0.7748 (t)
REVERT: A  360 ASN cc_start: 0.8483 (p0) cc_final: 0.8227 (p0)
REVERT: A  386 LYS cc_start: 0.8347 (ttpp) cc_final: 0.8138 (ptmm)
REVERT: A  387 LEU cc_start: 0.8642 (mt) cc_final: 0.8385 (mt)
REVERT: A  424 LYS cc_start: 0.8091 (tmtm) cc_final: 0.7768 (tptp)
REVERT: A  425 LEU cc_start: 0.8843 (tp) cc_final: 0.8506 (tp)
REVERT: A  442 ASP cc_start: 0.8330 (p0) cc_final: 0.7822 (p0)
REVERT: A  452 LEU cc_start: 0.7469 (mp) cc_final: 0.6895 (tt)
REVERT: A  490 PHE cc_start: 0.8158 (t80) cc_final: 0.7894 (t80)
REVERT: A  501 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.7311 (t80)
REVERT: B   29 PHE cc_start: 0.8148 (m-80) cc_final: 0.7553 (m-80)
REVERT: B   38 ARG cc_start: 0.7264 (ttp80) cc_final: 0.6936 (ttp80)
REVERT: B   64 LYS cc_start: 0.8307 (tptt) cc_final: 0.7932 (tptt)
REVERT: B  142 LEU cc_start: 0.8745 (mm) cc_final: 0.7839 (pt)
REVERT: B  158 LEU cc_start: 0.7870 (mm) cc_final: 0.7578 (mt)
REVERT: B  172 MET cc_start: 0.6427 (mpt) cc_final: 0.6208 (mpt)
REVERT: B  189 ILE cc_start: 0.8713 (mm) cc_final: 0.8394 (mm)
REVERT: B  197 TYR cc_start: 0.7046 (m-80) cc_final: 0.6776 (m-80)
REVERT: B  211 ASP cc_start: 0.7983 (t0) cc_final: 0.7596 (t0)
REVERT: B  252 THR cc_start: 0.8207 (t) cc_final: 0.7893 (m)
  outliers start: 32
  outliers final: 24
  residues processed: 219
  average time/residue: 0.2180
  time to fit residues: 60.4569
Evaluate side-chains
  222 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 197
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
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  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
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  389 ASP
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  534 VAL
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  690 GLN
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   37 VAL
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  206 PHE
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:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 67 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0980
   overall best weight:    1.3986

-------------------------------------------------------------------------------
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 280 ASN
** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 519 HIS
A 564 GLN
A 690 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.161624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.130523 restraints weight = 12675.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.135944 restraints weight = 7319.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.139713 restraints weight = 4853.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.5768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6714  Z= 0.192
  Angle     :  0.732   8.697   9140  Z= 0.379
  Chirality :  0.047   0.201   1003
  Planarity :  0.005   0.054   1175
  Dihedral  :  6.967  81.280    930
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 17.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.52 %
    Favored  : 87.48 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 24.23 %
    Favored  : 71.59 %
  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: -1.75 (1.26), residues: 16
  sheet: -2.50 (0.35), residues: 196
  loop : -2.44 (0.23), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.004   TRP B 174 
 HIS   0.016   0.003   HIS A 519 
 PHE   0.028   0.002   PHE A 275 
 TYR   0.017   0.001   TYR A 660 
 ARG   0.006   0.001   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03699 (  112)
  hydrogen bonds       : angle       7.22052 (  264)
  SS BOND              : bond        0.00621 (   11)
  SS BOND              : angle       0.95293 (   22)
  covalent geometry    : bond        0.00409 ( 6703)
  covalent geometry    : angle       0.73123 ( 9118)

*********************** 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
  232 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 202
  time to evaluate  : 0.765 
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: 0.7377 (tp40) cc_final: 0.7087 (tp40)
REVERT: A  169 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8582 (tm-30)
REVERT: A  177 MET cc_start: 0.6517 (mmt) cc_final: 0.6202 (mmt)
REVERT: A  313 TYR cc_start: 0.6393 (m-80) cc_final: 0.5764 (m-80)
REVERT: A  335 LEU cc_start: 0.8204 (tp) cc_final: 0.7946 (tt)
REVERT: A  337 PRO cc_start: 0.8016 (Cg_exo) cc_final: 0.7207 (Cg_endo)
REVERT: A  340 GLU cc_start: 0.8168 (mp0) cc_final: 0.7815 (mp0)
REVERT: A  355 ARG cc_start: 0.8037 (mtp85) cc_final: 0.7773 (mtp85)
REVERT: A  357 ARG cc_start: 0.7718 (ttp80) cc_final: 0.7120 (ttp80)
REVERT: A  360 ASN cc_start: 0.8521 (p0) cc_final: 0.8291 (p0)
REVERT: A  386 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8196 (ptmm)
REVERT: A  387 LEU cc_start: 0.8673 (mt) cc_final: 0.8394 (mt)
REVERT: A  388 ASN cc_start: 0.8331 (p0) cc_final: 0.7798 (t0)
REVERT: A  396 TYR cc_start: 0.7040 (m-80) cc_final: 0.6231 (m-10)
REVERT: A  408 ARG cc_start: 0.7837 (ttp-170) cc_final: 0.7486 (ttp-170)
REVERT: A  424 LYS cc_start: 0.8263 (tmtm) cc_final: 0.7925 (tptp)
REVERT: A  425 LEU cc_start: 0.8848 (tp) cc_final: 0.8548 (tp)
REVERT: A  442 ASP cc_start: 0.8267 (p0) cc_final: 0.7812 (p0)
REVERT: A  452 LEU cc_start: 0.7714 (mp) cc_final: 0.7124 (tt)
REVERT: A  501 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7407 (t80)
REVERT: A  659 SER cc_start: 0.7968 (m) cc_final: 0.7305 (t)
REVERT: B   29 PHE cc_start: 0.8156 (m-80) cc_final: 0.7510 (m-80)
REVERT: B   38 ARG cc_start: 0.7365 (ttp80) cc_final: 0.6981 (ttp80)
REVERT: B   64 LYS cc_start: 0.8362 (tptt) cc_final: 0.8006 (tptt)
REVERT: B  189 ILE cc_start: 0.8762 (mm) cc_final: 0.8404 (mm)
REVERT: B  197 TYR cc_start: 0.7252 (m-80) cc_final: 0.6986 (m-80)
REVERT: B  211 ASP cc_start: 0.8046 (t0) cc_final: 0.7595 (t0)
REVERT: B  234 CYS cc_start: 0.5144 (p) cc_final: 0.4620 (p)
REVERT: B  252 THR cc_start: 0.8174 (t) cc_final: 0.7917 (m)
  outliers start: 30
  outliers final: 26
  residues processed: 221
  average time/residue: 0.2175
  time to fit residues: 61.1875
Evaluate side-chains
  222 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 195
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
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   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  298 GLU
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  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  666 ILE
Chi-restraints excluded: chain A residue  690 GLN
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   66 LEU
Chi-restraints excluded: chain B residue   99 TRP
Chi-restraints excluded: chain B residue  185 TRP
Chi-restraints excluded: chain B residue  188 THR
Chi-restraints excluded: chain B residue  206 PHE
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:    5.9990
   chunk 12 optimal weight:    0.0670
   chunk 35 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0970
   chunk 4 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0050
   chunk 44 optimal weight:    2.9990
   chunk 19 optimal weight:    7.9990
   chunk 56 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.8334

-------------------------------------------------------------------------------
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 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 690 GLN
B 250 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.162917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.131406 restraints weight = 12578.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.136951 restraints weight = 7210.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.140788 restraints weight = 4779.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6863
moved from start:          0.5947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6714  Z= 0.149
  Angle     :  0.775   8.988   9140  Z= 0.394
  Chirality :  0.048   0.223   1003
  Planarity :  0.005   0.055   1175
  Dihedral  :  7.043  81.875    930
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 14.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.41 %
    Favored  : 88.59 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 26.18 %
    Favored  : 69.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -3.38 (0.27), residues: 815
  helix: -1.70 (1.23), residues: 16
  sheet: -2.13 (0.37), residues: 201
  loop : -2.47 (0.23), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.003   TRP B 174 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.021   0.002   PHE A  55 
 TYR   0.015   0.001   TYR A 660 
 ARG   0.005   0.001   ARG A 328 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03233 (  112)
  hydrogen bonds       : angle       7.03419 (  264)
  SS BOND              : bond        0.00381 (   11)
  SS BOND              : angle       2.69953 (   22)
  covalent geometry    : bond        0.00331 ( 6703)
  covalent geometry    : angle       0.76483 ( 9118)

*********************** 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
  225 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 195
  time to evaluate  : 0.671 
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   55 PHE cc_start: 0.7377 (m-80) cc_final: 0.6624 (m-80)
REVERT: A   86 PHE cc_start: 0.8517 (t80) cc_final: 0.7966 (t80)
REVERT: A  177 MET cc_start: 0.6503 (mmt) cc_final: 0.6177 (mmt)
REVERT: A  313 TYR cc_start: 0.6325 (m-80) cc_final: 0.5674 (m-80)
REVERT: A  335 LEU cc_start: 0.8050 (tp) cc_final: 0.7747 (tt)
REVERT: A  337 PRO cc_start: 0.8009 (Cg_exo) cc_final: 0.7195 (Cg_endo)
REVERT: A  340 GLU cc_start: 0.8192 (mp0) cc_final: 0.7655 (mp0)
REVERT: A  355 ARG cc_start: 0.7985 (mtp85) cc_final: 0.7442 (mtp85)
REVERT: A  357 ARG cc_start: 0.7680 (ttp80) cc_final: 0.7163 (ttp80)
REVERT: A  360 ASN cc_start: 0.8553 (p0) cc_final: 0.8296 (p0)
REVERT: A  386 LYS cc_start: 0.8507 (ttpp) cc_final: 0.8226 (ptmm)
REVERT: A  387 LEU cc_start: 0.8581 (mt) cc_final: 0.8292 (mt)
REVERT: A  388 ASN cc_start: 0.8285 (p0) cc_final: 0.7818 (t0)
REVERT: A  396 TYR cc_start: 0.7100 (m-80) cc_final: 0.6433 (m-10)
REVERT: A  408 ARG cc_start: 0.7814 (ttp-170) cc_final: 0.7481 (ttp-170)
REVERT: A  424 LYS cc_start: 0.8151 (tmtm) cc_final: 0.7795 (tptp)
REVERT: A  425 LEU cc_start: 0.8813 (tp) cc_final: 0.8509 (tp)
REVERT: A  442 ASP cc_start: 0.8229 (p0) cc_final: 0.7760 (p0)
REVERT: A  452 LEU cc_start: 0.7599 (mp) cc_final: 0.7015 (tt)
REVERT: A  501 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7259 (t80)
REVERT: A  562 PHE cc_start: 0.6908 (t80) cc_final: 0.6404 (t80)
REVERT: A  577 ARG cc_start: 0.7824 (tpt170) cc_final: 0.7339 (tmt-80)
REVERT: A  578 ASP cc_start: 0.8298 (t0) cc_final: 0.7360 (t0)
REVERT: B   29 PHE cc_start: 0.8122 (m-80) cc_final: 0.7550 (m-80)
REVERT: B   64 LYS cc_start: 0.8311 (tptt) cc_final: 0.7951 (tptt)
REVERT: B   99 TRP cc_start: 0.7700 (OUTLIER) cc_final: 0.7073 (t-100)
REVERT: B  189 ILE cc_start: 0.8714 (mm) cc_final: 0.8364 (mm)
REVERT: B  197 TYR cc_start: 0.7193 (m-80) cc_final: 0.6820 (m-80)
REVERT: B  211 ASP cc_start: 0.8027 (t0) cc_final: 0.7613 (t0)
REVERT: B  217 LEU cc_start: 0.8539 (tt) cc_final: 0.8109 (mp)
REVERT: B  219 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7957 (tp)
REVERT: B  252 THR cc_start: 0.8263 (t) cc_final: 0.8014 (m)
  outliers start: 30
  outliers final: 26
  residues processed: 212
  average time/residue: 0.2236
  time to fit residues: 59.9475
Evaluate side-chains
  214 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
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   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  275 PHE
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  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  666 ILE
Chi-restraints excluded: chain A residue  690 GLN
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   66 LEU
Chi-restraints excluded: chain B residue   99 TRP
Chi-restraints excluded: chain B residue  185 TRP
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  216 THR
Chi-restraints excluded: chain B residue  219 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 72 optimal weight:    8.9990
   chunk 17 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 13 optimal weight:    9.9990
   chunk 70 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0970
   chunk 16 optimal weight:    0.0770
   chunk 48 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 321 GLN
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 690 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.165547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.133783 restraints weight = 12647.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.139528 restraints weight = 7233.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.143410 restraints weight = 4768.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6829
moved from start:          0.6059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6714  Z= 0.137
  Angle     :  0.785   9.574   9140  Z= 0.397
  Chirality :  0.047   0.222   1003
  Planarity :  0.006   0.090   1175
  Dihedral  :  7.140  81.456    930
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.41 %
    Favored  : 88.59 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 26.32 %
    Favored  : 68.25 %
  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: -3.26 (0.27), residues: 815
  helix: -1.60 (1.28), residues: 16
  sheet: -1.98 (0.36), residues: 205
  loop : -2.42 (0.24), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 174 
 HIS   0.016   0.003   HIS A 519 
 PHE   0.040   0.002   PHE A 490 
 TYR   0.017   0.001   TYR B  52 
 ARG   0.010   0.001   ARG B  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03112 (  112)
  hydrogen bonds       : angle       6.94577 (  264)
  SS BOND              : bond        0.00418 (   11)
  SS BOND              : angle       2.42258 (   22)
  covalent geometry    : bond        0.00317 ( 6703)
  covalent geometry    : angle       0.77657 ( 9118)

*********************** 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
  236 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 197
  time to evaluate  : 0.725 
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   55 PHE cc_start: 0.7290 (m-80) cc_final: 0.6501 (m-80)
REVERT: A   86 PHE cc_start: 0.8479 (t80) cc_final: 0.7949 (t80)
REVERT: A  110 LEU cc_start: 0.8029 (mp) cc_final: 0.7535 (pp)
REVERT: A  177 MET cc_start: 0.6536 (mmt) cc_final: 0.6215 (mmt)
REVERT: A  313 TYR cc_start: 0.6124 (m-80) cc_final: 0.5536 (m-80)
REVERT: A  335 LEU cc_start: 0.7901 (tp) cc_final: 0.7551 (tt)
REVERT: A  337 PRO cc_start: 0.7938 (Cg_exo) cc_final: 0.7144 (Cg_endo)
REVERT: A  340 GLU cc_start: 0.8163 (mp0) cc_final: 0.7589 (mp0)
REVERT: A  355 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7377 (mtp85)
REVERT: A  357 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7199 (ttp80)
REVERT: A  359 SER cc_start: 0.8373 (m) cc_final: 0.7937 (t)
REVERT: A  360 ASN cc_start: 0.8571 (p0) cc_final: 0.8358 (p0)
REVERT: A  386 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8201 (ptmm)
REVERT: A  387 LEU cc_start: 0.8536 (mt) cc_final: 0.8290 (mt)
REVERT: A  388 ASN cc_start: 0.8256 (p0) cc_final: 0.7785 (t0)
REVERT: A  390 LEU cc_start: 0.8511 (tp) cc_final: 0.8015 (pp)
REVERT: A  396 TYR cc_start: 0.6984 (m-80) cc_final: 0.6263 (m-10)
REVERT: A  408 ARG cc_start: 0.7766 (ttp-170) cc_final: 0.7432 (ttp-170)
REVERT: A  424 LYS cc_start: 0.8074 (tmtm) cc_final: 0.7766 (tptp)
REVERT: A  442 ASP cc_start: 0.8267 (p0) cc_final: 0.7771 (p0)
REVERT: A  501 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7267 (t80)
REVERT: A  547 LYS cc_start: 0.7510 (mmmt) cc_final: 0.6866 (mmmt)
REVERT: B   29 PHE cc_start: 0.8075 (m-80) cc_final: 0.7575 (m-80)
REVERT: B   38 ARG cc_start: 0.7043 (ttp80) cc_final: 0.6640 (ttp80)
REVERT: B   64 LYS cc_start: 0.8265 (tptt) cc_final: 0.7910 (tptt)
REVERT: B   99 TRP cc_start: 0.7659 (OUTLIER) cc_final: 0.7063 (t-100)
REVERT: B  189 ILE cc_start: 0.8710 (mm) cc_final: 0.8369 (mm)
REVERT: B  197 TYR cc_start: 0.7119 (m-80) cc_final: 0.6737 (m-80)
REVERT: B  211 ASP cc_start: 0.8028 (t0) cc_final: 0.7644 (t0)
REVERT: B  237 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.6123 (ptt180)
REVERT: B  252 THR cc_start: 0.8265 (t) cc_final: 0.8028 (m)
REVERT: B  254 VAL cc_start: 0.9182 (p) cc_final: 0.8874 (m)
  outliers start: 39
  outliers final: 32
  residues processed: 219
  average time/residue: 0.2442
  time to fit residues: 68.6702
Evaluate side-chains
  227 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 192
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
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  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  275 PHE
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  471 GLU
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  666 ILE
Chi-restraints excluded: chain A residue  690 GLN
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   12 VAL
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   99 TRP
Chi-restraints excluded: chain B residue  185 TRP
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
Chi-restraints excluded: chain B residue  234 CYS
Chi-restraints excluded: chain B residue  237 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 80 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 42 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0770
   chunk 9 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.7140

-------------------------------------------------------------------------------
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 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 564 GLN
** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 690 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.164685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.132815 restraints weight = 12806.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.138445 restraints weight = 7329.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.142308 restraints weight = 4864.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6847
moved from start:          0.6178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6714  Z= 0.147
  Angle     :  0.794   9.340   9140  Z= 0.403
  Chirality :  0.047   0.221   1003
  Planarity :  0.006   0.072   1175
  Dihedral  :  6.973  81.579    930
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 16.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.39 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 27.44 %
    Favored  : 67.97 %
  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: -3.19 (0.28), residues: 815
  helix: -1.67 (1.26), residues: 16
  sheet: -2.00 (0.37), residues: 208
  loop : -2.33 (0.24), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP B 174 
 HIS   0.012   0.002   HIS A 519 
 PHE   0.021   0.002   PHE A  55 
 TYR   0.017   0.001   TYR B  52 
 ARG   0.008   0.001   ARG A 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  112)
  hydrogen bonds       : angle       6.96772 (  264)
  SS BOND              : bond        0.00406 (   11)
  SS BOND              : angle       2.32298 (   22)
  covalent geometry    : bond        0.00337 ( 6703)
  covalent geometry    : angle       0.78705 ( 9118)

********************** 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
  233 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 200
  time to evaluate  : 0.635 
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   55 PHE cc_start: 0.7286 (m-80) cc_final: 0.6474 (m-80)
REVERT: A  110 LEU cc_start: 0.8046 (mp) cc_final: 0.7544 (pp)
REVERT: A  177 MET cc_start: 0.6571 (mmt) cc_final: 0.6244 (mmt)
REVERT: A  313 TYR cc_start: 0.6280 (m-80) cc_final: 0.5650 (m-80)
REVERT: A  337 PRO cc_start: 0.7948 (Cg_exo) cc_final: 0.7184 (Cg_endo)
REVERT: A  340 GLU cc_start: 0.8180 (mp0) cc_final: 0.7642 (mp0)
REVERT: A  355 ARG cc_start: 0.8003 (mtp85) cc_final: 0.7687 (mtp85)
REVERT: A  357 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7195 (ttp80)
REVERT: A  359 SER cc_start: 0.8348 (m) cc_final: 0.7932 (t)
REVERT: A  360 ASN cc_start: 0.8630 (p0) cc_final: 0.8383 (p0)
REVERT: A  386 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8223 (ptmm)
REVERT: A  387 LEU cc_start: 0.8586 (mt) cc_final: 0.8320 (mt)
REVERT: A  390 LEU cc_start: 0.8521 (tp) cc_final: 0.8079 (pp)
REVERT: A  396 TYR cc_start: 0.7096 (m-80) cc_final: 0.6293 (m-10)
REVERT: A  408 ARG cc_start: 0.7784 (ttp-170) cc_final: 0.7452 (ttp-170)
REVERT: A  424 LYS cc_start: 0.8067 (tmtm) cc_final: 0.7764 (tptp)
REVERT: A  442 ASP cc_start: 0.8284 (p0) cc_final: 0.7798 (p0)
REVERT: A  501 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.7292 (t80)
REVERT: A  542 ASN cc_start: 0.7841 (m-40) cc_final: 0.7027 (p0)
REVERT: B   29 PHE cc_start: 0.8054 (m-80) cc_final: 0.7573 (m-80)
REVERT: B   64 LYS cc_start: 0.8275 (tptt) cc_final: 0.7885 (tptt)
REVERT: B   99 TRP cc_start: 0.7672 (OUTLIER) cc_final: 0.7162 (t-100)
REVERT: B  189 ILE cc_start: 0.8734 (mm) cc_final: 0.8531 (tp)
REVERT: B  197 TYR cc_start: 0.7310 (m-80) cc_final: 0.6928 (m-80)
REVERT: B  211 ASP cc_start: 0.8040 (t0) cc_final: 0.7635 (t0)
REVERT: B  217 LEU cc_start: 0.8547 (tt) cc_final: 0.8059 (mp)
REVERT: B  252 THR cc_start: 0.8240 (t) cc_final: 0.8004 (m)
  outliers start: 33
  outliers final: 28
  residues processed: 217
  average time/residue: 0.2108
  time to fit residues: 57.7067
Evaluate side-chains
  229 residues out of total 726 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 199
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
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  234 ASN
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  346 ARG
Chi-restraints excluded: chain A residue  362 VAL
Chi-restraints excluded: chain A residue  471 GLU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  501 TYR
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  690 GLN
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   86 ARG
Chi-restraints excluded: chain B residue   99 TRP
Chi-restraints excluded: chain B residue  185 TRP
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
Chi-restraints excluded: chain B residue  234 CYS
Chi-restraints excluded: chain B residue  237 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 46 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 39 optimal weight:    0.0270
   chunk 32 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 66 optimal weight:    9.9990
   chunk 18 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.9644

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

Flipped N/Q/H residues before XYZ refinement:
A 218 GLN
** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 690 GLN
B   3 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.162999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.131086 restraints weight = 13080.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.136634 restraints weight = 7595.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.140505 restraints weight = 5086.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6884
moved from start:          0.6354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6714  Z= 0.161
  Angle     :  0.809   9.715   9140  Z= 0.410
  Chirality :  0.048   0.224   1003
  Planarity :  0.006   0.074   1175
  Dihedral  :  7.049  81.860    928
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.52 %
    Favored  : 87.48 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 27.44 %
    Favored  : 68.25 %
  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: -3.20 (0.28), residues: 815
  helix: -1.79 (1.20), residues: 16
  sheet: -1.97 (0.37), residues: 209
  loop : -2.35 (0.24), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.002   TRP B 174 
 HIS   0.011   0.002   HIS A 519 
 PHE   0.038   0.002   PHE B 165 
 TYR   0.021   0.001   TYR B 243 
 ARG   0.009   0.001   ARG A 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03441 (  112)
  hydrogen bonds       : angle       7.03329 (  264)
  SS BOND              : bond        0.00451 (   11)
  SS BOND              : angle       2.30016 (   22)
  covalent geometry    : bond        0.00363 ( 6703)
  covalent geometry    : angle       0.80166 ( 9118)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2676.19 seconds
wall clock time: 47 minutes 24.72 seconds (2844.72 seconds total)