Starting phenix.real_space_refine
on Tue Mar  3 14:55:03 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rav_24387/03_2026/7rav_24387.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rav_24387/03_2026/7rav_24387.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rav_24387/03_2026/7rav_24387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rav_24387/03_2026/7rav_24387.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rav_24387/03_2026/7rav_24387.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rav_24387/03_2026/7rav_24387.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 40 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      39      5.16       5
     C    3976      2.51       5
     N    1046      2.21       5
     O    1151      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6215
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6184
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 773, 6184
          Classifications: {'peptide': 773}
          Link IDs: {'PTRANS': 26, 'TRANS': 746}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.54, per 1000 atoms: 0.25
  Number of scatterers: 6215
  At special positions: 0
  Unit cell: (74.858, 78.0662, 133.675, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      39     16.00
     P       3     15.00
     O    1151      8.00
     N    1046      7.00
     C    3976      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 124 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 224 " 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: 0.52
  Conformation dependent library (CDL) restraints added in 238.4 milliseconds
  

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1460

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 5 sheets defined
      46.6% alpha, 3.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 64 through 70
      removed outlier: 4.092A  pdb=" N   THR A  69 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 84
    Processing helix  chain 'A' and resid 112 through 121
    Processing helix  chain 'A' and resid 159 through 165
    Processing helix  chain 'A' and resid 177 through 183
    Processing helix  chain 'A' and resid 214 through 221
      removed outlier: 3.511A  pdb=" N   ALA A 218 " --> pdb=" O   TRP A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 231
    Processing helix  chain 'A' and resid 234 through 240
      removed outlier: 3.782A  pdb=" N   GLN A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 280
      removed outlier: 4.022A  pdb=" N   LEU A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 301
      removed outlier: 3.668A  pdb=" N   ARG A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 339
    Processing helix  chain 'A' and resid 343 through 350
      removed outlier: 3.639A  pdb=" N   THR A 347 " --> pdb=" O   VAL A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 418
    Processing helix  chain 'A' and resid 454 through 459
      removed outlier: 3.711A  pdb=" N   PHE A 459 " --> pdb=" O   ILE A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 475 through 489
    Processing helix  chain 'A' and resid 492 through 498
      removed outlier: 3.668A  pdb=" N   LEU A 495 " --> pdb=" O   CYS A 492 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ARG A 497 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 521
    Processing helix  chain 'A' and resid 531 through 542
    Processing helix  chain 'A' and resid 555 through 559
    Processing helix  chain 'A' and resid 560 through 569
    Processing helix  chain 'A' and resid 603 through 615
      removed outlier: 3.541A  pdb=" N   THR A 607 " --> pdb=" O   PRO A 603 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   PHE A 615 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 630
      removed outlier: 3.506A  pdb=" N   ILE A 630 " --> pdb=" O   ILE A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 651
    Processing helix  chain 'A' and resid 652 through 654
      No H-bonds generated for 'chain 'A' and resid 652 through 654'
    Processing helix  chain 'A' and resid 662 through 679
      removed outlier: 3.764A  pdb=" N   THR A 666 " --> pdb=" O   PHE A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 704
      removed outlier: 4.203A  pdb=" N   LEU A 686 " --> pdb=" O   THR A 682 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU A 696 " --> pdb=" O   SER A 692 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA A 697 " --> pdb=" O   CYS A 693 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE A 702 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   SER A 703 " --> pdb=" O   THR A 699 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   SER A 704 " --> pdb=" O   GLY A 700 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 717
      removed outlier: 3.809A  pdb=" N   LEU A 713 " --> pdb=" O   ASN A 709 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA A 714 " --> pdb=" O   SER A 710 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   GLU A 715 " --> pdb=" O   ASP A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 728
      removed outlier: 3.636A  pdb=" N   THR A 726 " --> pdb=" O   LYS A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 763
    Processing helix  chain 'A' and resid 765 through 778
      removed outlier: 4.432A  pdb=" N   LEU A 771 " --> pdb=" O   GLU A 767 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   GLY A 772 " --> pdb=" O   ASP A 768 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLN A 778 " --> pdb=" O   TYR A 774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 788
      removed outlier: 3.607A  pdb=" N   SER A 788 " --> pdb=" O   LYS A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 792 through 797
      removed outlier: 3.945A  pdb=" N   VAL A 796 " --> pdb=" O   PHE A 792 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER A 797 " --> pdb=" O   LEU A 793 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 792 through 797'
    Processing helix  chain 'A' and resid 803 through 814
      removed outlier: 4.569A  pdb=" N   THR A 807 " --> pdb=" O   LYS A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 858 through 878
      removed outlier: 3.993A  pdb=" N   THR A 877 " --> pdb=" O   TYR A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 882 through 887
    Processing helix  chain 'A' and resid 910 through 914
      removed outlier: 3.553A  pdb=" N   LEU A 914 " --> pdb=" O   LEU A 911 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 86 through 88
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188
    Processing sheet with id=AA3, first strand: chain 'A' and resid 305 through 306
    Processing sheet with id=AA4, first strand: chain 'A' and resid 440 through 441
    Processing sheet with id=AA5, first strand: chain 'A' and resid 466 through 468
      removed outlier: 6.714A  pdb=" N   MET A 466 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
      removed outlier: 5.905A  pdb=" N   VAL A 546 " --> pdb=" O   CYS A 576 " (cutoff:3.500A)
      removed outlier: 7.611A  pdb=" N   LEU A 578 " --> pdb=" O   VAL A 546 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   PHE A 548 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   ALA A 580 " --> pdb=" O   PHE A 548 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU A 550 " --> pdb=" O   ALA A 580 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   LEU A 500 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   LEU A 549 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   PHE A 502 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   ASP A 551 " --> pdb=" O   PHE A 502 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   LEU A 504 " --> pdb=" O   ASP A 551 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    199 hydrogen bonds defined for protein.
    555 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.67

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1961
        1.34 -     1.46: 1377
        1.46 -     1.58: 2962
        1.58 -     1.70: 5
        1.70 -     1.83: 52
  Bond restraints: 6357
  Sorted by residual:
  bond pdb=" C4  ATP A1501 "
       pdb=" C5  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.388  1.467 -0.079 1.00e-02 1.00e+04 6.24e+01
  bond pdb=" C5  ATP A1501 "
       pdb=" C6  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.478 -0.069 1.00e-02 1.00e+04 4.79e+01
  bond pdb=" C8  ATP A1501 "
       pdb=" N7  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.310  1.356 -0.046 1.00e-02 1.00e+04 2.11e+01
  bond pdb=" C5  ATP A1501 "
       pdb=" N7  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.387  1.342  0.045 1.00e-02 1.00e+04 2.01e+01
  bond pdb=" C4  ATP A1501 "
       pdb=" N9  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.374  1.331  0.043 1.00e-02 1.00e+04 1.89e+01
  ... (remaining 6352 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.13: 8527
        4.13 -     8.25: 60
        8.25 -    12.38: 4
       12.38 -    16.50: 0
       16.50 -    20.63: 2
  Bond angle restraints: 8593
  Sorted by residual:
  angle pdb=" PB  ATP A1501 "
        pdb=" O3B ATP A1501 "
        pdb=" PG  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     139.87  119.24   20.63 1.00e+00 1.00e+00 4.26e+02
  angle pdb=" PA  ATP A1501 "
        pdb=" O3A ATP A1501 "
        pdb=" PB  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     136.83  118.98   17.85 1.00e+00 1.00e+00 3.19e+02
  angle pdb=" N   GLY A 175 "
        pdb=" CA  GLY A 175 "
        pdb=" C   GLY A 175 "
      ideal   model   delta    sigma   weight residual
     112.73  100.90   11.83 1.20e+00 6.94e-01 9.72e+01
  angle pdb=" C5  ATP A1501 "
        pdb=" C4  ATP A1501 "
        pdb=" N3  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     126.80  118.66    8.14 1.00e+00 1.00e+00 6.62e+01
  angle pdb=" N3  ATP A1501 "
        pdb=" C4  ATP A1501 "
        pdb=" N9  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     127.04  134.79   -7.75 1.15e+00 7.59e-01 4.56e+01
  ... (remaining 8588 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3348
       17.97 -    35.93: 371
       35.93 -    53.90: 71
       53.90 -    71.86: 15
       71.86 -    89.83: 11
  Dihedral angle restraints: 3816
    sinusoidal: 1559
      harmonic: 2257
  Sorted by residual:
  dihedral pdb=" CB  CYS A 100 "
           pdb=" SG  CYS A 100 "
           pdb=" SG  CYS A 124 "
           pdb=" CB  CYS A 124 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   48.56   44.44     1      1.00e+01 1.00e-02 2.75e+01
  dihedral pdb=" CA  HIS A 157 "
           pdb=" C   HIS A 157 "
           pdb=" N   GLU A 158 "
           pdb=" CA  GLU A 158 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.55  -25.45     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" CA  ILE A 135 "
           pdb=" C   ILE A 135 "
           pdb=" N   GLY A 136 "
           pdb=" CA  GLY A 136 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.40   23.60     0      5.00e+00 4.00e-02 2.23e+01
  ... (remaining 3813 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 756
       0.058 -    0.117: 170
       0.117 -    0.175: 18
       0.175 -    0.233: 2
       0.233 -    0.292: 1
  Chirality restraints: 947
  Sorted by residual:
  chirality pdb=" CA  PRO A 340 "
            pdb=" N   PRO A 340 "
            pdb=" C   PRO A 340 "
            pdb=" CB  PRO A 340 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CA  HIS A 174 "
            pdb=" N   HIS A 174 "
            pdb=" C   HIS A 174 "
            pdb=" CB  HIS A 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.05e-01
  chirality pdb=" CA  GLN A 766 "
            pdb=" N   GLN A 766 "
            pdb=" C   GLN A 766 "
            pdb=" CB  GLN A 766 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.68e-01
  ... (remaining 944 not shown)

  Planarity restraints: 1089
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 339 "    0.061 5.00e-02 4.00e+02   9.20e-02 1.36e+01
        pdb=" N   PRO A 340 "   -0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO A 340 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 340 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 492 "   -0.038 5.00e-02 4.00e+02   5.85e-02 5.48e+00
        pdb=" N   PRO A 493 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 493 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 493 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 330 "    0.037 5.00e-02 4.00e+02   5.58e-02 4.97e+00
        pdb=" N   PRO A 331 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "    0.032 5.00e-02 4.00e+02
  ... (remaining 1086 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1067
        2.76 -     3.29: 6528
        3.29 -     3.83: 9907
        3.83 -     4.36: 11611
        4.36 -     4.90: 18876
  Nonbonded interactions: 47989
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 172 "
            pdb=" NH2 ARG A 261 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" NZ  LYS A 723 "
            pdb=" OG1 THR A 725 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" NH1 ARG A 314 "
            pdb=" O   THR A 430 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" OG  SER A 554 "
            pdb=" OG  SER A 558 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   ASN A 900 "
            pdb=" ND2 ASN A 900 "
     model   vdw
     2.248 3.120
  ... (remaining 47984 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.650
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   6359  Z= 0.260
  Angle     :  0.930  20.628   8597  Z= 0.590
  Chirality :  0.049   0.292    947
  Planarity :  0.005   0.092   1089
  Dihedral  : 15.924  89.826   2350
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  : 16.73 %
    Favored  : 82.88 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  0.44 %
    Favored  : 98.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.36 (0.29), residues: 765
  helix: -0.98 (0.29), residues: 313
  sheet: -1.74 (0.75), residues: 37
  loop : -3.46 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  74 
 TYR   0.037   0.002   TYR A 496 
 PHE   0.027   0.002   PHE A 859 
 TRP   0.009   0.001   TRP A 220 
 HIS   0.006   0.001   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 6357)
  covalent geometry    : angle       0.93007 ( 8593)
  SS BOND              : bond        0.00360 (    2)
  SS BOND              : angle       0.96772 (    4)
  hydrogen bonds       : bond        0.18112 (  199)
  hydrogen bonds       : angle       7.18963 (  555)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 225
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7514 (tpp) cc_final: 0.7266 (tpp)
REVERT: A   57 MET cc_start: 0.7615 (ptp) cc_final: 0.7406 (ptp)
REVERT: A  148 MET cc_start: 0.6317 (tmm) cc_final: 0.6110 (tmm)
REVERT: A  160 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7252 (tm-30)
REVERT: A  164 GLU cc_start: 0.7523 (pp20) cc_final: 0.7231 (pp20)
REVERT: A  167 GLU cc_start: 0.7299 (mp0) cc_final: 0.6992 (mp0)
REVERT: A  332 MET cc_start: 0.5342 (pmm) cc_final: 0.5045 (pmm)
REVERT: A  408 ARG cc_start: 0.7768 (tmm-80) cc_final: 0.7233 (tmm-80)
REVERT: A  443 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7908 (mtmm)
REVERT: A  535 LEU cc_start: 0.8698 (tp) cc_final: 0.8469 (tp)
REVERT: A  551 ASP cc_start: 0.7115 (t70) cc_final: 0.6681 (t0)
REVERT: A  598 GLU cc_start: 0.6899 (tt0) cc_final: 0.6650 (tt0)
REVERT: A  630 ILE cc_start: 0.8585 (tp) cc_final: 0.8332 (tp)
REVERT: A  651 ASP cc_start: 0.7321 (t0) cc_final: 0.7086 (t0)
REVERT: A  812 LEU cc_start: 0.8393 (mt) cc_final: 0.8094 (mt)
REVERT: A  814 GLN cc_start: 0.7762 (pp30) cc_final: 0.7405 (pp30)
REVERT: A  865 LEU cc_start: 0.8483 (mm) cc_final: 0.8281 (mm)
REVERT: A  867 LEU cc_start: 0.8955 (pp) cc_final: 0.8365 (pp)
REVERT: A  869 LEU cc_start: 0.8422 (mm) cc_final: 0.8213 (mm)
REVERT: A  871 PHE cc_start: 0.7230 (m-80) cc_final: 0.6856 (m-80)
  outliers start: 8
  outliers final: 0
  residues processed: 228
  average time/residue: 0.0883
  time to fit residues: 25.5926
Evaluate side-chains
  198 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0870
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0010
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4564

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 900 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.156987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.139388 restraints weight = 10471.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 3.72
r_work: 0.3735 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6359  Z= 0.153
  Angle     :  0.759   9.133   8597  Z= 0.396
  Chirality :  0.046   0.176    947
  Planarity :  0.005   0.050   1089
  Dihedral  :  7.747  85.798    871
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 15.56 %
    Favored  : 84.18 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.32 %
    Favored  : 84.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.05 (0.30), residues: 765
  helix: -0.50 (0.30), residues: 324
  sheet: -1.77 (0.76), residues: 37
  loop : -3.53 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 585 
 TYR   0.043   0.003   TYR A 496 
 PHE   0.052   0.002   PHE A 792 
 TRP   0.010   0.001   TRP A 220 
 HIS   0.004   0.001   HIS A 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 6357)
  covalent geometry    : angle       0.75905 ( 8593)
  SS BOND              : bond        0.00353 (    2)
  SS BOND              : angle       1.11694 (    4)
  hydrogen bonds       : bond        0.04364 (  199)
  hydrogen bonds       : angle       5.07130 (  555)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 212
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7646 (tpp) cc_final: 0.7335 (tpp)
REVERT: A   57 MET cc_start: 0.8500 (ptp) cc_final: 0.8286 (ptp)
REVERT: A   62 LYS cc_start: 0.8595 (ttmm) cc_final: 0.8255 (mtmm)
REVERT: A  138 TYR cc_start: 0.6943 (t80) cc_final: 0.6648 (t80)
REVERT: A  148 MET cc_start: 0.6926 (tmm) cc_final: 0.6593 (tmm)
REVERT: A  160 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7670 (tm-30)
REVERT: A  164 GLU cc_start: 0.8031 (pp20) cc_final: 0.7758 (pp20)
REVERT: A  167 GLU cc_start: 0.7907 (mp0) cc_final: 0.7412 (mp0)
REVERT: A  172 TYR cc_start: 0.7319 (m-80) cc_final: 0.7118 (m-80)
REVERT: A  223 LYS cc_start: 0.8585 (mtmm) cc_final: 0.8380 (mtmm)
REVERT: A  226 PHE cc_start: 0.8781 (t80) cc_final: 0.8187 (t80)
REVERT: A  230 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8672 (mmmm)
REVERT: A  332 MET cc_start: 0.6007 (pmm) cc_final: 0.5451 (pmm)
REVERT: A  408 ARG cc_start: 0.8188 (tmm-80) cc_final: 0.7673 (tmm-80)
REVERT: A  443 LYS cc_start: 0.8585 (mtmm) cc_final: 0.7993 (mtmm)
REVERT: A  454 THR cc_start: 0.8340 (p) cc_final: 0.7937 (t)
REVERT: A  455 ILE cc_start: 0.8433 (mm) cc_final: 0.7949 (tp)
REVERT: A  457 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8029 (tm-30)
REVERT: A  551 ASP cc_start: 0.7496 (t70) cc_final: 0.6814 (t0)
REVERT: A  615 PHE cc_start: 0.7469 (m-80) cc_final: 0.7239 (m-80)
REVERT: A  630 ILE cc_start: 0.8720 (tp) cc_final: 0.8402 (tp)
REVERT: A  652 TRP cc_start: 0.6292 (t60) cc_final: 0.6010 (t60)
REVERT: A  709 ASN cc_start: 0.7713 (p0) cc_final: 0.7452 (p0)
REVERT: A  712 ASP cc_start: 0.8379 (m-30) cc_final: 0.8090 (m-30)
REVERT: A  766 GLN cc_start: 0.8425 (tm-30) cc_final: 0.7823 (pp30)
REVERT: A  812 LEU cc_start: 0.8702 (mt) cc_final: 0.8400 (mt)
REVERT: A  814 GLN cc_start: 0.8161 (pp30) cc_final: 0.7749 (pp30)
REVERT: A  863 HIS cc_start: 0.8008 (m90) cc_final: 0.7215 (m90)
REVERT: A  865 LEU cc_start: 0.8605 (mm) cc_final: 0.8373 (mm)
REVERT: A  867 LEU cc_start: 0.9041 (pp) cc_final: 0.8553 (pp)
REVERT: A  871 PHE cc_start: 0.7773 (m-80) cc_final: 0.7292 (m-80)
REVERT: A  873 TYR cc_start: 0.7742 (t80) cc_final: 0.7322 (t80)
  outliers start: 12
  outliers final: 7
  residues processed: 216
  average time/residue: 0.1004
  time to fit residues: 27.0135
Evaluate side-chains
  205 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 198
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  206 ASN
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  779 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0010
   chunk 33 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0670
   chunk 24 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6926

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 107 ASN
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 570 ASN
A 900 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.155200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.137925 restraints weight = 10321.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3861 rms_B_bonded: 3.58
r_work: 0.3714 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.1921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6359  Z= 0.176
  Angle     :  0.729   8.770   8597  Z= 0.381
  Chirality :  0.047   0.189    947
  Planarity :  0.005   0.049   1089
  Dihedral  :  7.487  75.899    871
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 15.82 %
    Favored  : 83.92 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.59 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.98 (0.30), residues: 765
  helix: -0.36 (0.30), residues: 324
  sheet: -1.87 (0.71), residues: 37
  loop : -3.56 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 417 
 TYR   0.045   0.002   TYR A 496 
 PHE   0.035   0.002   PHE A 792 
 TRP   0.011   0.001   TRP A 220 
 HIS   0.006   0.001   HIS A 811 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 6357)
  covalent geometry    : angle       0.72857 ( 8593)
  SS BOND              : bond        0.00265 (    2)
  SS BOND              : angle       1.10694 (    4)
  hydrogen bonds       : bond        0.04018 (  199)
  hydrogen bonds       : angle       4.91014 (  555)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 207
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   47 MET cc_start: 0.7634 (tpp) cc_final: 0.7289 (tpp)
REVERT: A   62 LYS cc_start: 0.8593 (ttmm) cc_final: 0.8241 (mtmm)
REVERT: A  138 TYR cc_start: 0.7147 (t80) cc_final: 0.6705 (t80)
REVERT: A  148 MET cc_start: 0.6955 (tmm) cc_final: 0.6590 (tmm)
REVERT: A  160 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7584 (tm-30)
REVERT: A  164 GLU cc_start: 0.8057 (pp20) cc_final: 0.7712 (pp20)
REVERT: A  167 GLU cc_start: 0.7963 (mp0) cc_final: 0.7446 (mp0)
REVERT: A  172 TYR cc_start: 0.7322 (m-80) cc_final: 0.7088 (m-80)
REVERT: A  208 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7218 (mm-30)
REVERT: A  226 PHE cc_start: 0.8732 (t80) cc_final: 0.8401 (t80)
REVERT: A  282 MET cc_start: 0.7004 (tpt) cc_final: 0.6708 (tpt)
REVERT: A  332 MET cc_start: 0.5903 (pmm) cc_final: 0.5391 (pmm)
REVERT: A  408 ARG cc_start: 0.8145 (tmm-80) cc_final: 0.7720 (tmm-80)
REVERT: A  443 LYS cc_start: 0.8665 (mtmm) cc_final: 0.8089 (mtmm)
REVERT: A  454 THR cc_start: 0.8354 (p) cc_final: 0.8012 (t)
REVERT: A  455 ILE cc_start: 0.8584 (mm) cc_final: 0.8106 (tp)
REVERT: A  457 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7951 (tm-30)
REVERT: A  551 ASP cc_start: 0.7610 (t70) cc_final: 0.7069 (t70)
REVERT: A  585 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8546 (mmm-85)
REVERT: A  624 LYS cc_start: 0.8109 (tptm) cc_final: 0.7763 (tttm)
REVERT: A  630 ILE cc_start: 0.8725 (tp) cc_final: 0.8432 (tp)
REVERT: A  652 TRP cc_start: 0.6077 (t60) cc_final: 0.5849 (t60)
REVERT: A  695 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7857 (tm-30)
REVERT: A  723 LYS cc_start: 0.8101 (tmtt) cc_final: 0.7599 (tmtt)
REVERT: A  766 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8004 (pp30)
REVERT: A  778 GLN cc_start: 0.8145 (mp10) cc_final: 0.7943 (mp10)
REVERT: A  812 LEU cc_start: 0.8633 (mt) cc_final: 0.8353 (mt)
REVERT: A  814 GLN cc_start: 0.8208 (pp30) cc_final: 0.7784 (pp30)
REVERT: A  863 HIS cc_start: 0.7982 (m90) cc_final: 0.7252 (m90)
REVERT: A  865 LEU cc_start: 0.8609 (mm) cc_final: 0.8387 (mm)
REVERT: A  867 LEU cc_start: 0.9022 (pp) cc_final: 0.8532 (pp)
REVERT: A  871 PHE cc_start: 0.7717 (m-80) cc_final: 0.7245 (m-80)
REVERT: A  873 TYR cc_start: 0.7670 (t80) cc_final: 0.7210 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 216
  average time/residue: 0.0911
  time to fit residues: 24.8784
Evaluate side-chains
  210 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 200
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 PHE
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  771 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0970
   chunk 3 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 4 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 ASN
A 900 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.156394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.139177 restraints weight = 10363.720|
|-----------------------------------------------------------------------------|
r_work (start): 0.3868 rms_B_bonded: 3.60
r_work: 0.3719 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6359  Z= 0.156
  Angle     :  0.720   8.908   8597  Z= 0.371
  Chirality :  0.047   0.236    947
  Planarity :  0.005   0.054   1089
  Dihedral  :  7.354  74.813    871
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 16.08 %
    Favored  : 83.79 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 21.52 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.88 (0.30), residues: 765
  helix: -0.27 (0.30), residues: 324
  sheet: -1.95 (0.71), residues: 37
  loop : -3.48 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 417 
 TYR   0.031   0.002   TYR A 496 
 PHE   0.027   0.002   PHE A 792 
 TRP   0.009   0.001   TRP A 220 
 HIS   0.004   0.001   HIS A 811 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 6357)
  covalent geometry    : angle       0.72029 ( 8593)
  SS BOND              : bond        0.00240 (    2)
  SS BOND              : angle       0.98789 (    4)
  hydrogen bonds       : bond        0.03702 (  199)
  hydrogen bonds       : angle       4.78467 (  555)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 209
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7671 (tpp) cc_final: 0.7328 (tpp)
REVERT: A  148 MET cc_start: 0.6950 (tmm) cc_final: 0.6557 (tmm)
REVERT: A  160 GLU cc_start: 0.8115 (tm-30) cc_final: 0.7664 (tm-30)
REVERT: A  172 TYR cc_start: 0.7435 (m-80) cc_final: 0.7096 (m-80)
REVERT: A  206 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8335 (m110)
REVERT: A  208 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7229 (mm-30)
REVERT: A  226 PHE cc_start: 0.8712 (t80) cc_final: 0.8344 (t80)
REVERT: A  282 MET cc_start: 0.7112 (tpt) cc_final: 0.6786 (tpt)
REVERT: A  332 MET cc_start: 0.5736 (pmm) cc_final: 0.5225 (pmm)
REVERT: A  408 ARG cc_start: 0.8133 (tmm-80) cc_final: 0.7755 (tmm-80)
REVERT: A  443 LYS cc_start: 0.8471 (mtmm) cc_final: 0.8061 (mtmm)
REVERT: A  455 ILE cc_start: 0.8597 (mm) cc_final: 0.8159 (tp)
REVERT: A  457 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7780 (tm-30)
REVERT: A  532 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7698 (mm-30)
REVERT: A  551 ASP cc_start: 0.7609 (t70) cc_final: 0.7090 (t70)
REVERT: A  624 LYS cc_start: 0.8098 (tptm) cc_final: 0.7727 (tttm)
REVERT: A  630 ILE cc_start: 0.8707 (tp) cc_final: 0.8430 (tp)
REVERT: A  695 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7830 (tm-30)
REVERT: A  723 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7554 (tmtt)
REVERT: A  747 LEU cc_start: 0.8405 (mm) cc_final: 0.8167 (mm)
REVERT: A  766 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8063 (pp30)
REVERT: A  778 GLN cc_start: 0.8212 (mp10) cc_final: 0.7907 (mp10)
REVERT: A  812 LEU cc_start: 0.8602 (mt) cc_final: 0.8317 (mt)
REVERT: A  814 GLN cc_start: 0.8209 (pp30) cc_final: 0.7765 (pp30)
REVERT: A  863 HIS cc_start: 0.8025 (m90) cc_final: 0.7270 (m90)
REVERT: A  865 LEU cc_start: 0.8673 (mm) cc_final: 0.8342 (mt)
REVERT: A  867 LEU cc_start: 0.9037 (pp) cc_final: 0.8561 (pp)
REVERT: A  871 PHE cc_start: 0.7804 (m-80) cc_final: 0.7365 (m-80)
REVERT: A  873 TYR cc_start: 0.7607 (t80) cc_final: 0.7210 (t80)
  outliers start: 20
  outliers final: 11
  residues processed: 217
  average time/residue: 0.0953
  time to fit residues: 25.9707
Evaluate side-chains
  207 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 195
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 ASN
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  705 CYS
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  779 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 74 optimal weight:    0.1980
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0870
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 606 ASN
A 887 GLN
A 900 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.156075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.138773 restraints weight = 10497.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 3.60
r_work: 0.3720 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6359  Z= 0.150
  Angle     :  0.731  11.731   8597  Z= 0.372
  Chirality :  0.048   0.392    947
  Planarity :  0.005   0.052   1089
  Dihedral  :  7.258  73.474    871
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.42 %
    Favored  : 84.44 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 22.25 %
    Favored  : 74.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.76 (0.30), residues: 765
  helix: -0.09 (0.30), residues: 313
  sheet: -1.92 (0.70), residues: 37
  loop : -3.43 (0.28), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  92 
 TYR   0.026   0.002   TYR A 496 
 PHE   0.021   0.001   PHE A 792 
 TRP   0.008   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 811 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6357)
  covalent geometry    : angle       0.73136 ( 8593)
  SS BOND              : bond        0.00216 (    2)
  SS BOND              : angle       0.86319 (    4)
  hydrogen bonds       : bond        0.03607 (  199)
  hydrogen bonds       : angle       4.77367 (  555)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 204
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7662 (tpp) cc_final: 0.7329 (tpp)
REVERT: A  148 MET cc_start: 0.6940 (tmm) cc_final: 0.6542 (tmm)
REVERT: A  160 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7652 (tm-30)
REVERT: A  164 GLU cc_start: 0.8315 (pp20) cc_final: 0.7931 (pp20)
REVERT: A  167 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7922 (mm-30)
REVERT: A  172 TYR cc_start: 0.7484 (m-80) cc_final: 0.7128 (m-80)
REVERT: A  208 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7190 (mm-30)
REVERT: A  226 PHE cc_start: 0.8722 (t80) cc_final: 0.8304 (t80)
REVERT: A  260 ARG cc_start: 0.7116 (mpp-170) cc_final: 0.6845 (mpp-170)
REVERT: A  282 MET cc_start: 0.7119 (tpt) cc_final: 0.6786 (tpt)
REVERT: A  332 MET cc_start: 0.5690 (pmm) cc_final: 0.5182 (pmm)
REVERT: A  408 ARG cc_start: 0.8128 (tmm-80) cc_final: 0.7773 (tmm-80)
REVERT: A  443 LYS cc_start: 0.8549 (mtmm) cc_final: 0.8178 (mtmm)
REVERT: A  457 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7855 (tm-30)
REVERT: A  532 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7726 (mm-30)
REVERT: A  551 ASP cc_start: 0.7624 (t70) cc_final: 0.7123 (t70)
REVERT: A  624 LYS cc_start: 0.8118 (tptm) cc_final: 0.7745 (tttm)
REVERT: A  630 ILE cc_start: 0.8692 (tp) cc_final: 0.8422 (tp)
REVERT: A  674 TYR cc_start: 0.8487 (t80) cc_final: 0.7903 (t80)
REVERT: A  695 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7768 (tm-30)
REVERT: A  712 ASP cc_start: 0.8394 (m-30) cc_final: 0.8010 (m-30)
REVERT: A  723 LYS cc_start: 0.8081 (tmtt) cc_final: 0.7567 (tmtt)
REVERT: A  747 LEU cc_start: 0.8408 (mm) cc_final: 0.8160 (mm)
REVERT: A  766 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8102 (tm-30)
REVERT: A  812 LEU cc_start: 0.8571 (mt) cc_final: 0.8275 (mt)
REVERT: A  814 GLN cc_start: 0.8177 (pp30) cc_final: 0.7736 (pp30)
REVERT: A  865 LEU cc_start: 0.8674 (mm) cc_final: 0.8351 (mt)
REVERT: A  867 LEU cc_start: 0.9044 (pp) cc_final: 0.8580 (pp)
REVERT: A  871 PHE cc_start: 0.7685 (m-80) cc_final: 0.7309 (m-80)
REVERT: A  873 TYR cc_start: 0.7542 (t80) cc_final: 0.7104 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 213
  average time/residue: 0.0948
  time to fit residues: 25.3056
Evaluate side-chains
  214 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 198
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  206 ASN
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  705 CYS
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  887 GLN
Chi-restraints excluded: chain A residue  900 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0060
   chunk 75 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
A 206 ASN
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 517 ASN
A 887 GLN
A 900 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.154808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.137421 restraints weight = 10406.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 3.62
r_work: 0.3700 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6359  Z= 0.170
  Angle     :  0.738  12.693   8597  Z= 0.378
  Chirality :  0.048   0.396    947
  Planarity :  0.005   0.050   1089
  Dihedral  :  7.232  70.006    871
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.82 %
    Favored  : 84.05 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 22.11 %
    Favored  : 74.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.85 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.70 (0.30), residues: 765
  helix: -0.05 (0.30), residues: 314
  sheet: -1.40 (1.01), residues: 25
  loop : -3.40 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 417 
 TYR   0.022   0.002   TYR A 496 
 PHE   0.021   0.001   PHE A 792 
 TRP   0.008   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 432 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 6357)
  covalent geometry    : angle       0.73806 ( 8593)
  SS BOND              : bond        0.00190 (    2)
  SS BOND              : angle       0.90335 (    4)
  hydrogen bonds       : bond        0.03643 (  199)
  hydrogen bonds       : angle       4.80934 (  555)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 199
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7671 (tpp) cc_final: 0.7340 (tpp)
REVERT: A   74 ARG cc_start: 0.8223 (ttm-80) cc_final: 0.8004 (ttm110)
REVERT: A   92 ARG cc_start: 0.7855 (mtm110) cc_final: 0.7544 (ttp80)
REVERT: A  119 LYS cc_start: 0.8821 (tppp) cc_final: 0.8430 (tppp)
REVERT: A  148 MET cc_start: 0.6935 (tmm) cc_final: 0.6534 (tmm)
REVERT: A  160 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7660 (tm-30)
REVERT: A  172 TYR cc_start: 0.7551 (m-80) cc_final: 0.7162 (m-80)
REVERT: A  208 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7340 (mm-30)
REVERT: A  226 PHE cc_start: 0.8716 (t80) cc_final: 0.8336 (t80)
REVERT: A  235 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7687 (pm20)
REVERT: A  282 MET cc_start: 0.7178 (tpt) cc_final: 0.6849 (tpt)
REVERT: A  332 MET cc_start: 0.5682 (pmm) cc_final: 0.5187 (pmm)
REVERT: A  408 ARG cc_start: 0.8144 (tmm-80) cc_final: 0.7775 (tmm-80)
REVERT: A  441 ILE cc_start: 0.8405 (OUTLIER) cc_final: 0.8186 (mm)
REVERT: A  457 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7830 (tm-30)
REVERT: A  532 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7694 (mm-30)
REVERT: A  551 ASP cc_start: 0.7666 (t70) cc_final: 0.7147 (t70)
REVERT: A  624 LYS cc_start: 0.8133 (tptm) cc_final: 0.7780 (tttm)
REVERT: A  630 ILE cc_start: 0.8692 (tp) cc_final: 0.8421 (tp)
REVERT: A  723 LYS cc_start: 0.8118 (tmtt) cc_final: 0.7664 (tmtt)
REVERT: A  747 LEU cc_start: 0.8418 (mm) cc_final: 0.8172 (mm)
REVERT: A  766 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8137 (tm-30)
REVERT: A  812 LEU cc_start: 0.8595 (mt) cc_final: 0.8301 (mt)
REVERT: A  814 GLN cc_start: 0.8243 (pp30) cc_final: 0.7778 (pp30)
REVERT: A  865 LEU cc_start: 0.8728 (mm) cc_final: 0.8399 (mt)
REVERT: A  867 LEU cc_start: 0.9081 (pp) cc_final: 0.8637 (pp)
REVERT: A  871 PHE cc_start: 0.7743 (m-80) cc_final: 0.7380 (m-80)
REVERT: A  873 TYR cc_start: 0.7529 (t80) cc_final: 0.7090 (t80)
  outliers start: 26
  outliers final: 16
  residues processed: 212
  average time/residue: 0.0975
  time to fit residues: 25.9664
Evaluate side-chains
  222 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 204
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  705 CYS
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  887 GLN
Chi-restraints excluded: chain A residue  900 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0770
   chunk 67 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 2 optimal weight:    0.3980
   chunk 35 optimal weight:    0.0040
   chunk 38 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.4150

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 863 HIS
A 887 GLN
A 900 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.156411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.139152 restraints weight = 10309.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 3.62
r_work: 0.3729 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6359  Z= 0.141
  Angle     :  0.734  13.362   8597  Z= 0.373
  Chirality :  0.048   0.415    947
  Planarity :  0.005   0.051   1089
  Dihedral  :  7.101  71.436    871
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 15.29 %
    Favored  : 84.58 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 23.28 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.30), residues: 765
  helix: -0.05 (0.30), residues: 315
  sheet: -1.78 (0.73), residues: 37
  loop : -3.35 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 141 
 TYR   0.020   0.002   TYR A 496 
 PHE   0.018   0.001   PHE A 629 
 TRP   0.007   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 544 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6357)
  covalent geometry    : angle       0.73435 ( 8593)
  SS BOND              : bond        0.00219 (    2)
  SS BOND              : angle       0.80924 (    4)
  hydrogen bonds       : bond        0.03577 (  199)
  hydrogen bonds       : angle       4.74050 (  555)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 211
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7612 (tpp) cc_final: 0.7312 (tpp)
REVERT: A   92 ARG cc_start: 0.7789 (mtm110) cc_final: 0.7475 (mtm110)
REVERT: A  119 LYS cc_start: 0.8805 (tppp) cc_final: 0.8410 (tppp)
REVERT: A  148 MET cc_start: 0.6892 (tmm) cc_final: 0.6493 (tmm)
REVERT: A  158 GLU cc_start: 0.7684 (tp30) cc_final: 0.7426 (tp30)
REVERT: A  160 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7626 (tm-30)
REVERT: A  168 ASP cc_start: 0.7880 (p0) cc_final: 0.7333 (p0)
REVERT: A  208 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7371 (mm-30)
REVERT: A  226 PHE cc_start: 0.8693 (t80) cc_final: 0.8305 (t80)
REVERT: A  262 GLU cc_start: 0.7586 (pm20) cc_final: 0.7108 (pm20)
REVERT: A  282 MET cc_start: 0.7310 (tpt) cc_final: 0.6967 (tpt)
REVERT: A  332 MET cc_start: 0.5654 (pmm) cc_final: 0.5153 (pmm)
REVERT: A  408 ARG cc_start: 0.8124 (tmm-80) cc_final: 0.7723 (tmm-80)
REVERT: A  409 ASP cc_start: 0.7801 (t0) cc_final: 0.7458 (t0)
REVERT: A  441 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8178 (mm)
REVERT: A  443 LYS cc_start: 0.8513 (mtmm) cc_final: 0.7942 (mtmm)
REVERT: A  457 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7811 (tm-30)
REVERT: A  532 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7658 (mm-30)
REVERT: A  551 ASP cc_start: 0.7553 (t70) cc_final: 0.7037 (t70)
REVERT: A  624 LYS cc_start: 0.8085 (tptm) cc_final: 0.7721 (tttm)
REVERT: A  630 ILE cc_start: 0.8684 (tp) cc_final: 0.8409 (tp)
REVERT: A  669 GLN cc_start: 0.8270 (tp40) cc_final: 0.8063 (tp40)
REVERT: A  695 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7698 (tm-30)
REVERT: A  723 LYS cc_start: 0.8212 (tmtt) cc_final: 0.7715 (tmtt)
REVERT: A  747 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8159 (mm)
REVERT: A  766 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8307 (tm-30)
REVERT: A  812 LEU cc_start: 0.8587 (mt) cc_final: 0.8291 (mt)
REVERT: A  814 GLN cc_start: 0.8213 (pp30) cc_final: 0.7747 (pp30)
REVERT: A  865 LEU cc_start: 0.8716 (mm) cc_final: 0.8390 (mt)
REVERT: A  867 LEU cc_start: 0.9065 (pp) cc_final: 0.8621 (pp)
REVERT: A  871 PHE cc_start: 0.7723 (m-80) cc_final: 0.7365 (m-80)
REVERT: A  873 TYR cc_start: 0.7535 (t80) cc_final: 0.7098 (t80)
  outliers start: 25
  outliers final: 18
  residues processed: 220
  average time/residue: 0.0894
  time to fit residues: 24.8168
Evaluate side-chains
  222 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 202
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  705 CYS
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  887 GLN
Chi-restraints excluded: chain A residue  911 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 9 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 75 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 887 GLN
A 900 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.155622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.138484 restraints weight = 10409.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 3.59
r_work: 0.3710 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6359  Z= 0.170
  Angle     :  0.738  12.208   8597  Z= 0.379
  Chirality :  0.049   0.399    947
  Planarity :  0.005   0.049   1089
  Dihedral  :  7.127  67.748    871
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 16.21 %
    Favored  : 83.66 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 24.30 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.66 (0.30), residues: 765
  helix: -0.05 (0.30), residues: 314
  sheet: -1.29 (1.04), residues: 25
  loop : -3.35 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 417 
 TYR   0.054   0.002   TYR A 496 
 PHE   0.018   0.001   PHE A 629 
 TRP   0.008   0.001   TRP A 220 
 HIS   0.005   0.001   HIS A 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 6357)
  covalent geometry    : angle       0.73786 ( 8593)
  SS BOND              : bond        0.00180 (    2)
  SS BOND              : angle       0.85017 (    4)
  hydrogen bonds       : bond        0.03658 (  199)
  hydrogen bonds       : angle       4.77227 (  555)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 206
  time to evaluate  : 0.216 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7620 (tpp) cc_final: 0.7328 (tpp)
REVERT: A   58 ARG cc_start: 0.7086 (tpp-160) cc_final: 0.6812 (tpp-160)
REVERT: A   79 GLN cc_start: 0.8253 (mp10) cc_final: 0.7970 (mm-40)
REVERT: A   92 ARG cc_start: 0.7833 (mtm110) cc_final: 0.7609 (mtm110)
REVERT: A  119 LYS cc_start: 0.8788 (tppp) cc_final: 0.8403 (tppp)
REVERT: A  148 MET cc_start: 0.6877 (tmm) cc_final: 0.6461 (tmm)
REVERT: A  158 GLU cc_start: 0.7719 (tp30) cc_final: 0.7501 (tp30)
REVERT: A  168 ASP cc_start: 0.7891 (p0) cc_final: 0.7362 (p0)
REVERT: A  208 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7355 (mm-30)
REVERT: A  226 PHE cc_start: 0.8738 (t80) cc_final: 0.8381 (t80)
REVERT: A  262 GLU cc_start: 0.7566 (pm20) cc_final: 0.7264 (pm20)
REVERT: A  282 MET cc_start: 0.7276 (tpt) cc_final: 0.6883 (tpt)
REVERT: A  332 MET cc_start: 0.5618 (pmm) cc_final: 0.5127 (pmm)
REVERT: A  408 ARG cc_start: 0.8122 (tmm-80) cc_final: 0.7710 (tmm-80)
REVERT: A  441 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8204 (mm)
REVERT: A  457 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7789 (tm-30)
REVERT: A  532 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7630 (mm-30)
REVERT: A  551 ASP cc_start: 0.7520 (t70) cc_final: 0.7029 (t70)
REVERT: A  624 LYS cc_start: 0.8118 (tptm) cc_final: 0.7758 (tttm)
REVERT: A  630 ILE cc_start: 0.8699 (tp) cc_final: 0.8420 (tp)
REVERT: A  669 GLN cc_start: 0.8323 (tp40) cc_final: 0.8109 (tp40)
REVERT: A  695 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7752 (tm-30)
REVERT: A  747 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8220 (mm)
REVERT: A  766 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8321 (tm-30)
REVERT: A  808 VAL cc_start: 0.8780 (p) cc_final: 0.8435 (t)
REVERT: A  812 LEU cc_start: 0.8583 (mt) cc_final: 0.8298 (mt)
REVERT: A  814 GLN cc_start: 0.8235 (pp30) cc_final: 0.7737 (pp30)
REVERT: A  865 LEU cc_start: 0.8717 (mm) cc_final: 0.8393 (mt)
REVERT: A  867 LEU cc_start: 0.9080 (pp) cc_final: 0.8654 (pp)
REVERT: A  871 PHE cc_start: 0.7782 (m-80) cc_final: 0.7446 (m-80)
REVERT: A  873 TYR cc_start: 0.7457 (t80) cc_final: 0.7047 (t80)
  outliers start: 23
  outliers final: 19
  residues processed: 216
  average time/residue: 0.0882
  time to fit residues: 24.1293
Evaluate side-chains
  217 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  300 VAL
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  705 CYS
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  747 LEU
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  887 GLN
Chi-restraints excluded: chain A residue  900 ASN
Chi-restraints excluded: chain A residue  911 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 2 optimal weight:    0.0370
   chunk 52 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0470
   chunk 60 optimal weight:    0.0030
   chunk 16 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0980
   chunk 72 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0170
   overall best weight:    0.0404

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

Flipped N/Q/H residues before XYZ refinement:
A  88 HIS
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 887 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.159888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.142327 restraints weight = 10525.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 3.76
r_work: 0.3773 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7188
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6359  Z= 0.128
  Angle     :  0.742  11.951   8597  Z= 0.373
  Chirality :  0.047   0.391    947
  Planarity :  0.005   0.054   1089
  Dihedral  :  6.898  72.362    871
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 13.59 %
    Favored  : 86.27 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 25.62 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.55 (0.30), residues: 765
  helix:  0.07 (0.30), residues: 307
  sheet: -1.76 (0.73), residues: 37
  loop : -3.25 (0.29), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 574 
 TYR   0.036   0.002   TYR A 553 
 PHE   0.022   0.001   PHE A 888 
 TRP   0.004   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 544 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6357)
  covalent geometry    : angle       0.74226 ( 8593)
  SS BOND              : bond        0.00263 (    2)
  SS BOND              : angle       0.64990 (    4)
  hydrogen bonds       : bond        0.03381 (  199)
  hydrogen bonds       : angle       4.71781 (  555)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 202
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7652 (tpp) cc_final: 0.7419 (tpp)
REVERT: A   58 ARG cc_start: 0.6996 (tpp-160) cc_final: 0.6716 (tpp-160)
REVERT: A   92 ARG cc_start: 0.7805 (mtm110) cc_final: 0.7488 (ttp80)
REVERT: A  119 LYS cc_start: 0.8801 (tppp) cc_final: 0.8384 (tppp)
REVERT: A  148 MET cc_start: 0.6778 (tmm) cc_final: 0.6419 (tmm)
REVERT: A  158 GLU cc_start: 0.7645 (tp30) cc_final: 0.7344 (tp30)
REVERT: A  166 PHE cc_start: 0.8747 (m-10) cc_final: 0.8305 (m-80)
REVERT: A  168 ASP cc_start: 0.7725 (p0) cc_final: 0.7143 (p0)
REVERT: A  208 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7368 (mm-30)
REVERT: A  226 PHE cc_start: 0.8664 (t80) cc_final: 0.8277 (t80)
REVERT: A  262 GLU cc_start: 0.7580 (pm20) cc_final: 0.7373 (pm20)
REVERT: A  282 MET cc_start: 0.7263 (tpt) cc_final: 0.6832 (tpt)
REVERT: A  332 MET cc_start: 0.5519 (pmm) cc_final: 0.4983 (pmm)
REVERT: A  408 ARG cc_start: 0.8118 (tmm-80) cc_final: 0.7733 (tmm-80)
REVERT: A  409 ASP cc_start: 0.7817 (t0) cc_final: 0.7559 (t0)
REVERT: A  441 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8141 (mm)
REVERT: A  443 LYS cc_start: 0.8429 (mtmm) cc_final: 0.8057 (mtmm)
REVERT: A  457 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7676 (tm-30)
REVERT: A  499 GLN cc_start: 0.7249 (mm-40) cc_final: 0.7014 (mm-40)
REVERT: A  532 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7600 (mm-30)
REVERT: A  551 ASP cc_start: 0.7456 (t70) cc_final: 0.7020 (t0)
REVERT: A  624 LYS cc_start: 0.8004 (tptm) cc_final: 0.7605 (tttm)
REVERT: A  630 ILE cc_start: 0.8656 (tp) cc_final: 0.8351 (tp)
REVERT: A  645 VAL cc_start: 0.8509 (t) cc_final: 0.8169 (p)
REVERT: A  669 GLN cc_start: 0.8217 (tp40) cc_final: 0.8001 (tp40)
REVERT: A  674 TYR cc_start: 0.8369 (t80) cc_final: 0.7953 (t80)
REVERT: A  695 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7532 (tm-30)
REVERT: A  715 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8294 (tm-30)
REVERT: A  766 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: A  808 VAL cc_start: 0.8799 (p) cc_final: 0.8437 (t)
REVERT: A  812 LEU cc_start: 0.8627 (mt) cc_final: 0.8402 (mt)
REVERT: A  814 GLN cc_start: 0.8171 (pp30) cc_final: 0.7764 (pp30)
REVERT: A  865 LEU cc_start: 0.8688 (mm) cc_final: 0.8381 (mt)
REVERT: A  867 LEU cc_start: 0.9081 (pp) cc_final: 0.8644 (pp)
REVERT: A  871 PHE cc_start: 0.7807 (m-80) cc_final: 0.7447 (m-80)
REVERT: A  873 TYR cc_start: 0.7482 (t80) cc_final: 0.7082 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 210
  average time/residue: 0.0950
  time to fit residues: 25.2391
Evaluate side-chains
  211 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 196
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  206 ASN
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  691 SER
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  729 MET
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0040
   chunk 43 optimal weight:    0.2980
   chunk 67 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.4792

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 900 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.157429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.140291 restraints weight = 10404.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 3.63
r_work: 0.3743 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7238
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6359  Z= 0.151
  Angle     :  0.758  11.450   8597  Z= 0.385
  Chirality :  0.048   0.381    947
  Planarity :  0.005   0.055   1089
  Dihedral  :  6.914  68.390    871
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.51 %
    Favored  : 85.36 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 27.23 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.30), residues: 765
  helix:  0.13 (0.30), residues: 309
  sheet: -1.61 (0.75), residues: 37
  loop : -3.28 (0.29), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  74 
 TYR   0.018   0.002   TYR A 605 
 PHE   0.017   0.001   PHE A 629 
 TRP   0.007   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 811 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6357)
  covalent geometry    : angle       0.75766 ( 8593)
  SS BOND              : bond        0.00208 (    2)
  SS BOND              : angle       0.64954 (    4)
  hydrogen bonds       : bond        0.03392 (  199)
  hydrogen bonds       : angle       4.72516 (  555)

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

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

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1530 Ramachandran restraints generated.
    765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 201
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7646 (tpp) cc_final: 0.7417 (tpp)
REVERT: A   58 ARG cc_start: 0.7000 (tpp-160) cc_final: 0.6756 (tpp-160)
REVERT: A  119 LYS cc_start: 0.8785 (tppp) cc_final: 0.8381 (tppp)
REVERT: A  148 MET cc_start: 0.6773 (tmm) cc_final: 0.6405 (tmm)
REVERT: A  150 ARG cc_start: 0.7232 (ptp-110) cc_final: 0.6846 (ptp-110)
REVERT: A  158 GLU cc_start: 0.7634 (tp30) cc_final: 0.7354 (tp30)
REVERT: A  166 PHE cc_start: 0.8797 (m-10) cc_final: 0.8457 (m-80)
REVERT: A  168 ASP cc_start: 0.7761 (p0) cc_final: 0.7172 (p0)
REVERT: A  208 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7322 (mm-30)
REVERT: A  226 PHE cc_start: 0.8690 (t80) cc_final: 0.8318 (t80)
REVERT: A  262 GLU cc_start: 0.7552 (pm20) cc_final: 0.7315 (pm20)
REVERT: A  282 MET cc_start: 0.7269 (tpt) cc_final: 0.6844 (tpt)
REVERT: A  332 MET cc_start: 0.5487 (pmm) cc_final: 0.4975 (pmm)
REVERT: A  408 ARG cc_start: 0.8101 (tmm-80) cc_final: 0.7741 (tmm-80)
REVERT: A  409 ASP cc_start: 0.7835 (t0) cc_final: 0.7578 (t0)
REVERT: A  441 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8188 (mm)
REVERT: A  457 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7717 (tm-30)
REVERT: A  499 GLN cc_start: 0.7431 (mm-40) cc_final: 0.7087 (mm-40)
REVERT: A  532 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7566 (mm-30)
REVERT: A  551 ASP cc_start: 0.7438 (t70) cc_final: 0.7082 (t0)
REVERT: A  624 LYS cc_start: 0.8076 (tptm) cc_final: 0.7682 (tttm)
REVERT: A  630 ILE cc_start: 0.8678 (tp) cc_final: 0.8372 (tp)
REVERT: A  645 VAL cc_start: 0.8568 (t) cc_final: 0.8272 (p)
REVERT: A  669 GLN cc_start: 0.8282 (tp40) cc_final: 0.8074 (tp40)
REVERT: A  674 TYR cc_start: 0.8351 (t80) cc_final: 0.7932 (t80)
REVERT: A  675 LEU cc_start: 0.8802 (mp) cc_final: 0.8582 (mp)
REVERT: A  695 GLN cc_start: 0.7950 (tm-30) cc_final: 0.7651 (tm-30)
REVERT: A  715 GLU cc_start: 0.8490 (tm-30) cc_final: 0.8286 (tm-30)
REVERT: A  766 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8186 (pp30)
REVERT: A  808 VAL cc_start: 0.8817 (p) cc_final: 0.8476 (t)
REVERT: A  812 LEU cc_start: 0.8643 (mt) cc_final: 0.8386 (mt)
REVERT: A  814 GLN cc_start: 0.8203 (pp30) cc_final: 0.7783 (pp30)
REVERT: A  865 LEU cc_start: 0.8667 (mm) cc_final: 0.8363 (mt)
REVERT: A  867 LEU cc_start: 0.9095 (pp) cc_final: 0.8682 (pp)
REVERT: A  871 PHE cc_start: 0.7735 (m-80) cc_final: 0.7398 (m-80)
REVERT: A  873 TYR cc_start: 0.7458 (t80) cc_final: 0.7068 (t80)
  outliers start: 15
  outliers final: 10
  residues processed: 208
  average time/residue: 0.0881
  time to fit residues: 23.2035
Evaluate side-chains
  210 residues out of total 683 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 199
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 HIS
Chi-restraints excluded: chain A residue  206 ASN
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  441 ILE
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  509 ILE
Chi-restraints excluded: chain A residue  596 SER
Chi-restraints excluded: chain A residue  650 THR
Chi-restraints excluded: chain A residue  725 THR
Chi-restraints excluded: chain A residue  771 LEU
Chi-restraints excluded: chain A residue  779 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 17 optimal weight:    0.3980
   chunk 52 optimal weight:    0.7980
   chunk 33 optimal weight:    0.3980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.156356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.138900 restraints weight = 10371.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 3.70
r_work: 0.3729 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   6359  Z= 0.161
  Angle     :  0.766  10.889   8597  Z= 0.391
  Chirality :  0.049   0.379    947
  Planarity :  0.005   0.055   1089
  Dihedral  :  7.044  65.813    871
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 14.90 %
    Favored  : 84.97 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 27.53 %
    Favored  : 70.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.52 (0.30), residues: 765
  helix:  0.09 (0.30), residues: 315
  sheet: -1.68 (0.73), residues: 37
  loop : -3.29 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  92 
 TYR   0.026   0.002   TYR A 553 
 PHE   0.017   0.001   PHE A 629 
 TRP   0.005   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 811 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 6357)
  covalent geometry    : angle       0.76575 ( 8593)
  SS BOND              : bond        0.00211 (    2)
  SS BOND              : angle       0.71052 (    4)
  hydrogen bonds       : bond        0.03579 (  199)
  hydrogen bonds       : angle       4.76783 (  555)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1546.32 seconds
wall clock time: 27 minutes 16.99 seconds (1636.99 seconds total)