Starting phenix.real_space_refine
on Tue Mar  3 16:32:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w88_32353/03_2026/7w88_32353.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w88_32353/03_2026/7w88_32353.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w88_32353/03_2026/7w88_32353.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w88_32353/03_2026/7w88_32353.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w88_32353/03_2026/7w88_32353.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w88_32353/03_2026/7w88_32353.cif"
  }
  resolution = 3.5
  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=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      45      5.16       5
     C    4541      2.51       5
     N    1241      2.21       5
     O    1311      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 43 residue(s): 0.00s

  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: 7138
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7138
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 896, 7138
          Classifications: {'peptide': 896}
          Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 854}
          Chain breaks: 7
  Time building chain proxies: 1.64, per 1000 atoms: 0.23
  Number of scatterers: 7138
  At special positions: 0
  Unit cell: (79.18, 94.72, 105.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      45     16.00
     O    1311      8.00
     N    1241      7.00
     C    4541      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 728 " - pdb=" SG  CYS A 805 " distance=2.04

  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: 0.66
  Conformation dependent library (CDL) restraints added in 301.9 milliseconds
  

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1688

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      31.4% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 141 through 143
      No H-bonds generated for 'chain 'A' and resid 141 through 143'
    Processing helix  chain 'A' and resid 290 through 304
      removed outlier: 3.525A  pdb=" N   LEU A 294 " --> pdb=" O   PRO A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 319
    Processing helix  chain 'A' and resid 323 through 335
      removed outlier: 3.790A  pdb=" N   LEU A 327 " --> pdb=" O   SER A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 353
    Processing helix  chain 'A' and resid 395 through 401
    Processing helix  chain 'A' and resid 402 through 408
      removed outlier: 4.260A  pdb=" N   SER A 406 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 427
      removed outlier: 3.781A  pdb=" N   LEU A 426 " --> pdb=" O   SER A 422 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   SER A 427 " --> pdb=" O   PRO A 423 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 422 through 427'
    Processing helix  chain 'A' and resid 441 through 453
      removed outlier: 4.075A  pdb=" N   HIS A 445 " --> pdb=" O   THR A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 496
      removed outlier: 3.948A  pdb=" N   GLY A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 510
      removed outlier: 3.647A  pdb=" N   CYS A 507 " --> pdb=" O   SER A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'
    Processing helix  chain 'A' and resid 554 through 566
      removed outlier: 3.771A  pdb=" N   LYS A 563 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU A 564 " --> pdb=" O   GLN A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 636
    Processing helix  chain 'A' and resid 641 through 651
      removed outlier: 4.990A  pdb=" N   MET A 647 " --> pdb=" O   VAL A 643 " (cutoff:3.500A)
      removed outlier: 4.994A  pdb=" N   GLN A 648 " --> pdb=" O   PHE A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 670
    Processing helix  chain 'A' and resid 671 through 673
      No H-bonds generated for 'chain 'A' and resid 671 through 673'
    Processing helix  chain 'A' and resid 694 through 715
    Processing helix  chain 'A' and resid 747 through 752
    Processing helix  chain 'A' and resid 794 through 800
    Processing helix  chain 'A' and resid 815 through 821
      removed outlier: 4.410A  pdb=" N   SER A 821 " --> pdb=" O   PRO A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 874
      removed outlier: 3.673A  pdb=" N   MET A 874 " --> pdb=" O   PHE A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 892
      removed outlier: 3.503A  pdb=" N   ILE A 882 " --> pdb=" O   THR A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 909
      removed outlier: 3.807A  pdb=" N   VAL A 903 " --> pdb=" O   SER A 899 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 950 through 956
    Processing helix  chain 'A' and resid 997 through 1009
    Processing helix  chain 'A' and resid 1017 through 1022
    Processing helix  chain 'A' and resid 1039 through 1060
    Processing helix  chain 'A' and resid 1073 through 1078
    Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 131
      removed outlier: 3.562A  pdb=" N   ALA A 129 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   LEU A 117 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   SER A 131 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 6.677A  pdb=" N   LEU A 115 " --> pdb=" O   SER A 131 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A 238 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 140
    Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168
      removed outlier: 7.266A  pdb=" N   GLN A 183 " --> pdb=" O   ASN A 167 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 191 through 192
    Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 374
      removed outlier: 3.567A  pdb=" N   GLU A 390 " --> pdb=" O   CYS A 374 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 384 through 386
      removed outlier: 7.036A  pdb=" N   TRP A 478 " --> pdb=" O   LEU A 465 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   PHE A 455 " --> pdb=" O   TYR A 462 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 529 through 530
    Processing sheet with id=AA8, first strand: chain 'A' and resid 537 through 539
    Processing sheet with id=AA9, first strand: chain 'A' and resid 575 through 576
      removed outlier: 3.504A  pdb=" N   PHE A 576 " --> pdb=" O   ILE A 587 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 726 through 727
      removed outlier: 7.404A  pdb=" N   ILE A 726 " --> pdb=" O   VAL A 806 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 740
      removed outlier: 3.599A  pdb=" N   VAL A 740 " --> pdb=" O   GLU A 790 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU A 789 " --> pdb=" O   VAL A 773 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR A 776 " --> pdb=" O   PHE A 831 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 744 through 745
      removed outlier: 3.618A  pdb=" N   ILE A 744 " --> pdb=" O   ALA A 767 " (cutoff:3.500A)

    195 hydrogen bonds defined for protein.
    540 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 0.88 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: 2334
        1.34 -     1.46: 1638
        1.46 -     1.58: 3252
        1.58 -     1.70: 0
        1.70 -     1.82: 69
  Bond restraints: 7293
  Sorted by residual:
  bond pdb=" N   GLU A 391 "
       pdb=" CA  GLU A 391 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.038 1.23e-02 6.61e+03 9.43e+00
  bond pdb=" N   GLU A 390 "
       pdb=" CA  GLU A 390 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.29e-02 6.01e+03 6.58e+00
  bond pdb=" N   ASP A 590 "
       pdb=" CA  ASP A 590 "
    ideal  model  delta    sigma   weight residual
    1.457  1.486 -0.030 1.41e-02 5.03e+03 4.40e+00
  bond pdb=" N   GLU A 938 "
       pdb=" CA  GLU A 938 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.016 1.29e-02 6.01e+03 1.60e+00
  bond pdb=" CA  VAL A 529 "
       pdb=" CB  VAL A 529 "
    ideal  model  delta    sigma   weight residual
    1.528  1.544 -0.016 1.34e-02 5.57e+03 1.49e+00
  ... (remaining 7288 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 9530
        1.77 -     3.53: 278
        3.53 -     5.30: 34
        5.30 -     7.06: 6
        7.06 -     8.83: 2
  Bond angle restraints: 9850
  Sorted by residual:
  angle pdb=" C   ARG A 898 "
        pdb=" N   SER A 899 "
        pdb=" CA  SER A 899 "
      ideal   model   delta    sigma   weight residual
     120.49  114.60    5.89 1.42e+00 4.96e-01 1.72e+01
  angle pdb=" N   VAL A 247 "
        pdb=" CA  VAL A 247 "
        pdb=" C   VAL A 247 "
      ideal   model   delta    sigma   weight residual
     113.71  110.18    3.53 9.50e-01 1.11e+00 1.38e+01
  angle pdb=" N   GLY A 638 "
        pdb=" CA  GLY A 638 "
        pdb=" C   GLY A 638 "
      ideal   model   delta    sigma   weight residual
     113.18  120.68   -7.50 2.37e+00 1.78e-01 1.00e+01
  angle pdb=" N   SER A 339 "
        pdb=" CA  SER A 339 "
        pdb=" C   SER A 339 "
      ideal   model   delta    sigma   weight residual
     108.32  113.51   -5.19 1.64e+00 3.72e-01 1.00e+01
  angle pdb=" N   LYS A 640 "
        pdb=" CA  LYS A 640 "
        pdb=" C   LYS A 640 "
      ideal   model   delta    sigma   weight residual
     110.80  117.23   -6.43 2.13e+00 2.20e-01 9.10e+00
  ... (remaining 9845 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 3779
       17.99 -    35.98: 492
       35.98 -    53.97: 122
       53.97 -    71.96: 20
       71.96 -    89.95: 5
  Dihedral angle restraints: 4418
    sinusoidal: 1806
      harmonic: 2612
  Sorted by residual:
  dihedral pdb=" CA  SER A 547 "
           pdb=" C   SER A 547 "
           pdb=" N   ASP A 548 "
           pdb=" CA  ASP A 548 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.59   27.41     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CA  MET A1009 "
           pdb=" C   MET A1009 "
           pdb=" N   THR A1010 "
           pdb=" CA  THR A1010 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.54   22.46     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  ALA A1108 "
           pdb=" C   ALA A1108 "
           pdb=" N   ARG A1109 "
           pdb=" CA  ARG A1109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.18   21.82     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 4415 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 738
       0.039 -    0.078: 246
       0.078 -    0.118: 82
       0.118 -    0.157: 17
       0.157 -    0.196: 1
  Chirality restraints: 1084
  Sorted by residual:
  chirality pdb=" CB  VAL A 740 "
            pdb=" CA  VAL A 740 "
            pdb=" CG1 VAL A 740 "
            pdb=" CG2 VAL A 740 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.60e-01
  chirality pdb=" CB  ILE A 265 "
            pdb=" CA  ILE A 265 "
            pdb=" CG1 ILE A 265 "
            pdb=" CG2 ILE A 265 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 4.99e-01
  chirality pdb=" CA  ILE A 377 "
            pdb=" N   ILE A 377 "
            pdb=" C   ILE A 377 "
            pdb=" CB  ILE A 377 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.79e-01
  ... (remaining 1081 not shown)

  Planarity restraints: 1260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 589 "   -0.014 2.00e-02 2.50e+03   2.82e-02 7.98e+00
        pdb=" C   ILE A 589 "    0.049 2.00e-02 2.50e+03
        pdb=" O   ILE A 589 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASP A 590 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 380 "    0.035 5.00e-02 4.00e+02   5.27e-02 4.45e+00
        pdb=" N   PRO A 381 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 381 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 381 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 933 "    0.030 5.00e-02 4.00e+02   4.57e-02 3.35e+00
        pdb=" N   PRO A 934 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO A 934 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 934 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1257 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1190
        2.76 -     3.29: 6891
        3.29 -     3.83: 11142
        3.83 -     4.36: 12501
        4.36 -     4.90: 21855
  Nonbonded interactions: 53579
  Sorted by model distance:
  nonbonded pdb=" O   MET A 603 "
            pdb=" NZ  LYS A 605 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" N   ASP A 165 "
            pdb=" OD1 ASP A 165 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" OE2 GLU A 642 "
            pdb=" NZ  LYS A 837 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   CYS A 624 "
            pdb=" ND1 HIS A 718 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" NH2 ARG A 519 "
            pdb=" O   ILE A 565 "
     model   vdw
     2.263 3.120
  ... (remaining 53574 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.550
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6866
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      :  0.003   0.038   7294  Z= 0.164
  Angle     :  0.705   8.829   9852  Z= 0.406
  Chirality :  0.045   0.196   1084
  Planarity :  0.004   0.053   1260
  Dihedral  : 16.867  89.950   2727
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 15.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.23 %
    Favored  : 84.77 %
  Rotamer:
    Outliers :  8.23 %
    Allowed  : 23.26 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -5.15 (0.23), residues: 880
  helix: -1.89 (0.28), residues: 236
  sheet: -4.61 (0.35), residues: 129
  loop : -4.04 (0.23), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 929 
 TYR   0.012   0.001   TYR A 695 
 PHE   0.012   0.001   PHE A 464 
 TRP   0.008   0.001   TRP A1096 
 HIS   0.005   0.001   HIS A 718 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7293)
  covalent geometry    : angle       0.70543 ( 9850)
  SS BOND              : bond        0.00921 (    1)
  SS BOND              : angle       0.66447 (    2)
  hydrogen bonds       : bond        0.18228 (  195)
  hydrogen bonds       : angle       7.48859 (  540)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 114
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7529 (ptpt) cc_final: 0.7271 (ptmt)
REVERT: A  329 ARG cc_start: 0.7495 (mpp80) cc_final: 0.6665 (mpp80)
REVERT: A  446 ARG cc_start: 0.7242 (OUTLIER) cc_final: 0.5784 (ttt-90)
REVERT: A  519 ARG cc_start: 0.7342 (mtp180) cc_final: 0.7083 (ptp-110)
REVERT: A  606 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7621 (p90)
REVERT: A  630 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6570 (mp)
REVERT: A  708 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7391 (mt)
REVERT: A  942 ARG cc_start: 0.1644 (OUTLIER) cc_final: -0.0979 (ptt-90)
  outliers start: 64
  outliers final: 35
  residues processed: 166
  average time/residue: 0.0969
  time to fit residues: 21.0840
Evaluate side-chains
  130 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 90
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  174 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  437 LYS
Chi-restraints excluded: chain A residue  446 ARG
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  606 PHE
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  660 THR
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  715 CYS
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  942 ARG
Chi-restraints excluded: chain A residue  997 ARG
Chi-restraints excluded: chain A residue  998 TYR
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1081 TYR
Chi-restraints excluded: chain A residue 1084 ASP
Chi-restraints excluded: chain A residue 1101 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.0980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0270
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0670
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 276 ASN
A 560 GLN
A 686 GLN
A 778 ASN
** A 869 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1024 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.216933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.184636 restraints weight = 9479.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.186587 restraints weight = 6078.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.187904 restraints weight = 5287.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.189085 restraints weight = 3620.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.190326 restraints weight = 3334.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.4386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6795
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7294  Z= 0.131
  Angle     :  0.661   7.567   9852  Z= 0.338
  Chirality :  0.044   0.141   1084
  Planarity :  0.005   0.056   1260
  Dihedral  :  9.216  57.120   1063
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.11 %
    Favored  : 84.89 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 24.04 %
    Favored  : 69.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -4.20 (0.26), residues: 880
  helix: -0.89 (0.31), residues: 244
  sheet: -4.13 (0.35), residues: 134
  loop : -3.54 (0.25), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 579 
 TYR   0.022   0.001   TYR A1001 
 PHE   0.012   0.001   PHE A 759 
 TRP   0.008   0.001   TRP A 940 
 HIS   0.006   0.001   HIS A 718 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7293)
  covalent geometry    : angle       0.66096 ( 9850)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       1.42440 (    2)
  hydrogen bonds       : bond        0.04161 (  195)
  hydrogen bonds       : angle       5.72654 (  540)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 102
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 HIS cc_start: 0.5992 (OUTLIER) cc_final: 0.5367 (m-70)
REVERT: A  329 ARG cc_start: 0.7488 (mpp80) cc_final: 0.7182 (mpp80)
REVERT: A  332 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6601 (mt-10)
REVERT: A  506 LYS cc_start: 0.7809 (mtpp) cc_final: 0.6894 (mmmt)
REVERT: A  617 ASN cc_start: 0.7263 (t0) cc_final: 0.6925 (m-40)
REVERT: A  630 ILE cc_start: 0.6709 (mp) cc_final: 0.6268 (mp)
REVERT: A  708 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.6826 (pp)
  outliers start: 54
  outliers final: 30
  residues processed: 146
  average time/residue: 0.0996
  time to fit residues: 19.0206
Evaluate side-chains
  121 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  437 LYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  728 CYS
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  997 ARG
Chi-restraints excluded: chain A residue  998 TYR
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1084 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 88 optimal weight:    0.0870
   chunk 35 optimal weight:    3.9990
   chunk 86 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9980
   chunk 43 optimal weight:    0.3980
   chunk 79 optimal weight:    0.7980
   chunk 7 optimal weight:    7.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 560 GLN
A 869 HIS
A 948 ASN
A1036 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4669 r_free = 0.4669 target = 0.219113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.185564 restraints weight = 9497.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.189579 restraints weight = 6125.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.190857 restraints weight = 3946.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.191409 restraints weight = 3265.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.191764 restraints weight = 2972.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.4399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6774
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7294  Z= 0.118
  Angle     :  0.627   8.029   9852  Z= 0.319
  Chirality :  0.043   0.178   1084
  Planarity :  0.005   0.053   1260
  Dihedral  :  7.830  59.838   1022
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.32 %
    Favored  : 85.68 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 25.06 %
    Favored  : 67.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -3.66 (0.27), residues: 880
  helix: -0.34 (0.33), residues: 245
  sheet: -3.86 (0.36), residues: 132
  loop : -3.26 (0.26), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 145 
 TYR   0.015   0.001   TYR A 695 
 PHE   0.012   0.001   PHE A 759 
 TRP   0.009   0.001   TRP A 618 
 HIS   0.007   0.001   HIS A 718 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 7293)
  covalent geometry    : angle       0.62709 ( 9850)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.84554 (    2)
  hydrogen bonds       : bond        0.03524 (  195)
  hydrogen bonds       : angle       5.45606 (  540)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 98
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7534 (ptmt) cc_final: 0.7016 (mptt)
REVERT: A  173 HIS cc_start: 0.5985 (OUTLIER) cc_final: 0.5451 (m-70)
REVERT: A  329 ARG cc_start: 0.7508 (mpp80) cc_final: 0.7097 (mpp80)
REVERT: A  506 LYS cc_start: 0.7841 (mtpp) cc_final: 0.6866 (mmmt)
REVERT: A  630 ILE cc_start: 0.6684 (OUTLIER) cc_final: 0.6262 (mp)
REVERT: A  708 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7232 (mt)
REVERT: A  942 ARG cc_start: 0.1213 (OUTLIER) cc_final: -0.1625 (ptt-90)
  outliers start: 59
  outliers final: 30
  residues processed: 149
  average time/residue: 0.1029
  time to fit residues: 19.7911
Evaluate side-chains
  129 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  437 LYS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  547 SER
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  942 ARG
Chi-restraints excluded: chain A residue  997 ARG
Chi-restraints excluded: chain A residue  998 TYR
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1084 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 20 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 69 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 14 optimal weight:    6.9990
   chunk 68 optimal weight:    0.0070
   overall best weight:    1.0600

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A1036 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4659 r_free = 0.4659 target = 0.217883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.185303 restraints weight = 9457.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.185494 restraints weight = 6243.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.187609 restraints weight = 5605.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.188698 restraints weight = 3710.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.189252 restraints weight = 3344.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6818
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7294  Z= 0.135
  Angle     :  0.629   7.807   9852  Z= 0.321
  Chirality :  0.043   0.168   1084
  Planarity :  0.005   0.053   1260
  Dihedral  :  7.678  57.677   1017
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.91 %
    Favored  : 84.09 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 24.55 %
    Favored  : 67.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -3.55 (0.27), residues: 880
  helix: -0.23 (0.33), residues: 247
  sheet: -3.72 (0.35), residues: 144
  loop : -3.18 (0.26), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 142 
 TYR   0.016   0.001   TYR A 695 
 PHE   0.015   0.001   PHE A 464 
 TRP   0.015   0.001   TRP A 618 
 HIS   0.004   0.001   HIS A 703 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7293)
  covalent geometry    : angle       0.62951 ( 9850)
  SS BOND              : bond        0.00350 (    1)
  SS BOND              : angle       0.18033 (    2)
  hydrogen bonds       : bond        0.03541 (  195)
  hydrogen bonds       : angle       5.37370 (  540)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 100
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7508 (ptmt) cc_final: 0.7038 (mptt)
REVERT: A  173 HIS cc_start: 0.6164 (OUTLIER) cc_final: 0.5597 (m-70)
REVERT: A  329 ARG cc_start: 0.7490 (mpp80) cc_final: 0.6730 (mpp80)
REVERT: A  506 LYS cc_start: 0.7843 (mtpp) cc_final: 0.6935 (mmmt)
REVERT: A  630 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6333 (mp)
REVERT: A  708 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7195 (mt)
REVERT: A  942 ARG cc_start: 0.1203 (OUTLIER) cc_final: -0.1662 (ptt-90)
REVERT: A  944 MET cc_start: 0.1812 (mtm) cc_final: 0.1525 (mtt)
REVERT: A 1003 GLU cc_start: 0.8572 (tt0) cc_final: 0.8371 (mm-30)
REVERT: A 1081 TYR cc_start: 0.3989 (OUTLIER) cc_final: 0.3464 (m-80)
  outliers start: 59
  outliers final: 36
  residues processed: 149
  average time/residue: 0.0862
  time to fit residues: 17.1000
Evaluate side-chains
  132 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 91
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  276 ASN
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  437 LYS
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  547 SER
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  942 ARG
Chi-restraints excluded: chain A residue  997 ARG
Chi-restraints excluded: chain A residue  998 TYR
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1081 TYR
Chi-restraints excluded: chain A residue 1084 ASP
Chi-restraints excluded: chain A residue 1091 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 88 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 85 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 87 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 74 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 560 GLN
** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.215473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.182012 restraints weight = 9434.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.182908 restraints weight = 6300.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.185529 restraints weight = 4918.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.185782 restraints weight = 3482.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.186123 restraints weight = 3525.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6866
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7294  Z= 0.155
  Angle     :  0.656  10.460   9852  Z= 0.333
  Chirality :  0.044   0.207   1084
  Planarity :  0.005   0.055   1260
  Dihedral  :  7.760  59.960   1017
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.36 %
    Favored  : 83.64 %
  Rotamer:
    Outliers :  8.74 %
    Allowed  : 24.16 %
    Favored  : 67.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -3.55 (0.27), residues: 880
  helix: -0.34 (0.32), residues: 254
  sheet: -3.68 (0.36), residues: 138
  loop : -3.19 (0.26), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 579 
 TYR   0.016   0.001   TYR A 695 
 PHE   0.016   0.002   PHE A 464 
 TRP   0.019   0.001   TRP A 618 
 HIS   0.003   0.001   HIS A 718 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 7293)
  covalent geometry    : angle       0.65645 ( 9850)
  SS BOND              : bond        0.00547 (    1)
  SS BOND              : angle       0.15377 (    2)
  hydrogen bonds       : bond        0.03627 (  195)
  hydrogen bonds       : angle       5.42953 (  540)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 97
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7523 (ptmt) cc_final: 0.7054 (mptt)
REVERT: A  173 HIS cc_start: 0.6203 (OUTLIER) cc_final: 0.5615 (m-70)
REVERT: A  329 ARG cc_start: 0.7483 (mpp80) cc_final: 0.7008 (mpp80)
REVERT: A  506 LYS cc_start: 0.7872 (mtpp) cc_final: 0.6950 (mmmt)
REVERT: A  630 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6394 (mp)
REVERT: A  708 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7186 (mt)
REVERT: A  942 ARG cc_start: 0.1253 (OUTLIER) cc_final: -0.1686 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.3988 (OUTLIER) cc_final: 0.3450 (m-80)
  outliers start: 68
  outliers final: 41
  residues processed: 152
  average time/residue: 0.0860
  time to fit residues: 17.3736
Evaluate side-chains
  136 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 90
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  547 SER
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  942 ARG
Chi-restraints excluded: chain A residue  997 ARG
Chi-restraints excluded: chain A residue  998 TYR
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1081 TYR
Chi-restraints excluded: chain A residue 1084 ASP
Chi-restraints excluded: chain A residue 1091 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0770
   chunk 21 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   overall best weight:    0.8740

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 560 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.217488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.184221 restraints weight = 9332.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.184045 restraints weight = 6154.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.186978 restraints weight = 4888.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.187290 restraints weight = 3463.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.188382 restraints weight = 3191.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.4365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6822
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7294  Z= 0.126
  Angle     :  0.639   9.244   9852  Z= 0.325
  Chirality :  0.044   0.173   1084
  Planarity :  0.005   0.059   1260
  Dihedral  :  7.483  57.733   1013
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.00 %
    Favored  : 85.00 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 25.45 %
    Favored  : 66.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -3.37 (0.27), residues: 880
  helix: -0.15 (0.33), residues: 253
  sheet: -3.52 (0.37), residues: 136
  loop : -3.13 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 142 
 TYR   0.015   0.001   TYR A 695 
 PHE   0.013   0.001   PHE A 464 
 TRP   0.019   0.001   TRP A 618 
 HIS   0.003   0.001   HIS A 718 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7293)
  covalent geometry    : angle       0.63940 ( 9850)
  SS BOND              : bond        0.00412 (    1)
  SS BOND              : angle       0.01724 (    2)
  hydrogen bonds       : bond        0.03364 (  195)
  hydrogen bonds       : angle       5.37217 (  540)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 99
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7497 (ptmt) cc_final: 0.7085 (mptt)
REVERT: A  173 HIS cc_start: 0.6304 (OUTLIER) cc_final: 0.5714 (m-70)
REVERT: A  506 LYS cc_start: 0.7923 (mtpp) cc_final: 0.6962 (mmmt)
REVERT: A  630 ILE cc_start: 0.6746 (OUTLIER) cc_final: 0.6292 (mp)
REVERT: A  647 MET cc_start: 0.6462 (mpt) cc_final: 0.6140 (mpt)
REVERT: A  708 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7225 (mt)
REVERT: A  942 ARG cc_start: 0.1166 (OUTLIER) cc_final: -0.0483 (ptt-90)
REVERT: A  944 MET cc_start: 0.2210 (mtm) cc_final: 0.1930 (mtt)
REVERT: A 1081 TYR cc_start: 0.3999 (OUTLIER) cc_final: 0.3491 (m-80)
  outliers start: 59
  outliers final: 43
  residues processed: 146
  average time/residue: 0.0933
  time to fit residues: 17.9778
Evaluate side-chains
  141 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 93
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  437 LYS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  547 SER
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  942 ARG
Chi-restraints excluded: chain A residue  997 ARG
Chi-restraints excluded: chain A residue  998 TYR
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1081 TYR
Chi-restraints excluded: chain A residue 1084 ASP
Chi-restraints excluded: chain A residue 1091 PHE
Chi-restraints excluded: chain A residue 1100 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    0.0970
   chunk 80 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 83 optimal weight:    1.9990
   chunk 74 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0170
   chunk 56 optimal weight:    0.9990
   overall best weight:    0.7820

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

Flipped N/Q/H residues before XYZ refinement:
A 560 GLN
** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 HIS
A1036 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4671 r_free = 0.4671 target = 0.219743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.186574 restraints weight = 9429.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.186675 restraints weight = 6048.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.189293 restraints weight = 4813.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.189723 restraints weight = 3482.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.190727 restraints weight = 3191.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6806
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7294  Z= 0.121
  Angle     :  0.637   8.718   9852  Z= 0.323
  Chirality :  0.043   0.167   1084
  Planarity :  0.005   0.058   1260
  Dihedral  :  7.303  54.409   1013
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.77 %
    Favored  : 85.23 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 25.58 %
    Favored  : 66.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -3.29 (0.27), residues: 880
  helix: -0.08 (0.33), residues: 254
  sheet: -3.45 (0.37), residues: 136
  loop : -3.09 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 446 
 TYR   0.022   0.001   TYR A 695 
 PHE   0.013   0.001   PHE A 464 
 TRP   0.025   0.001   TRP A 618 
 HIS   0.005   0.001   HIS A 909 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7293)
  covalent geometry    : angle       0.63689 ( 9850)
  SS BOND              : bond        0.00387 (    1)
  SS BOND              : angle       0.05648 (    2)
  hydrogen bonds       : bond        0.03242 (  195)
  hydrogen bonds       : angle       5.27055 (  540)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 101
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7479 (ptmt) cc_final: 0.7081 (mptt)
REVERT: A  173 HIS cc_start: 0.6306 (OUTLIER) cc_final: 0.5709 (m-70)
REVERT: A  240 LYS cc_start: 0.8377 (ttmm) cc_final: 0.7872 (tttm)
REVERT: A  241 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8351 (tt)
REVERT: A  506 LYS cc_start: 0.7897 (mtpp) cc_final: 0.6960 (mmmt)
REVERT: A  630 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6279 (mp)
REVERT: A  647 MET cc_start: 0.6559 (mpt) cc_final: 0.6188 (mpt)
REVERT: A  708 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7273 (mt)
REVERT: A  909 HIS cc_start: 0.6704 (m90) cc_final: 0.5806 (m170)
REVERT: A  924 MET cc_start: 0.7805 (mpp) cc_final: 0.7316 (mpp)
REVERT: A  941 GLU cc_start: 0.2596 (OUTLIER) cc_final: 0.1717 (pm20)
REVERT: A  942 ARG cc_start: 0.1087 (OUTLIER) cc_final: -0.0064 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.3931 (OUTLIER) cc_final: 0.3411 (m-80)
  outliers start: 61
  outliers final: 42
  residues processed: 152
  average time/residue: 0.0886
  time to fit residues: 17.9295
Evaluate side-chains
  142 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 93
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  437 LYS
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  547 SER
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  941 GLU
Chi-restraints excluded: chain A residue  942 ARG
Chi-restraints excluded: chain A residue  997 ARG
Chi-restraints excluded: chain A residue  998 TYR
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1081 TYR
Chi-restraints excluded: chain A residue 1084 ASP
Chi-restraints excluded: chain A residue 1091 PHE
Chi-restraints excluded: chain A residue 1100 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 6 optimal weight:    8.9990
   chunk 81 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 560 GLN
** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 706 ASN
A1036 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.215843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.182041 restraints weight = 9402.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.184131 restraints weight = 6395.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.186392 restraints weight = 4930.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.187074 restraints weight = 3452.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.188045 restraints weight = 3134.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6850
moved from start:          0.2500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7294  Z= 0.170
  Angle     :  0.702  10.311   9852  Z= 0.357
  Chirality :  0.045   0.165   1084
  Planarity :  0.005   0.057   1260
  Dihedral  :  7.515  53.614   1013
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.36 %
    Favored  : 83.64 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 25.96 %
    Favored  : 66.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -3.44 (0.27), residues: 880
  helix: -0.32 (0.32), residues: 254
  sheet: -3.39 (0.39), residues: 128
  loop : -3.18 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 704 
 TYR   0.023   0.002   TYR A 695 
 PHE   0.018   0.002   PHE A 464 
 TRP   0.016   0.001   TRP A 618 
 HIS   0.003   0.001   HIS A 718 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 7293)
  covalent geometry    : angle       0.70219 ( 9850)
  SS BOND              : bond        0.00759 (    1)
  SS BOND              : angle       0.50488 (    2)
  hydrogen bonds       : bond        0.03802 (  195)
  hydrogen bonds       : angle       5.43985 (  540)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 95
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7552 (ptmt) cc_final: 0.7040 (mptt)
REVERT: A  173 HIS cc_start: 0.6424 (OUTLIER) cc_final: 0.5760 (m-70)
REVERT: A  240 LYS cc_start: 0.8429 (ttmm) cc_final: 0.7925 (tttm)
REVERT: A  241 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8341 (tt)
REVERT: A  630 ILE cc_start: 0.6789 (OUTLIER) cc_final: 0.6345 (mp)
REVERT: A  708 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7417 (mt)
REVERT: A  909 HIS cc_start: 0.6818 (m90) cc_final: 0.6098 (m170)
REVERT: A  924 MET cc_start: 0.7845 (mpp) cc_final: 0.7293 (mpp)
REVERT: A  941 GLU cc_start: 0.2755 (OUTLIER) cc_final: 0.1649 (pm20)
REVERT: A  942 ARG cc_start: 0.1245 (OUTLIER) cc_final: -0.0922 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4119 (OUTLIER) cc_final: 0.3451 (m-80)
  outliers start: 56
  outliers final: 45
  residues processed: 141
  average time/residue: 0.0902
  time to fit residues: 16.6415
Evaluate side-chains
  145 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 93
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  336 LYS
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  437 LYS
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  545 ILE
Chi-restraints excluded: chain A residue  547 SER
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  941 GLU
Chi-restraints excluded: chain A residue  942 ARG
Chi-restraints excluded: chain A residue  997 ARG
Chi-restraints excluded: chain A residue  998 TYR
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1081 TYR
Chi-restraints excluded: chain A residue 1084 ASP
Chi-restraints excluded: chain A residue 1091 PHE
Chi-restraints excluded: chain A residue 1100 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 59 optimal weight:    0.0970
   chunk 51 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0770
   chunk 6 optimal weight:   10.0000
   chunk 3 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.9740

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

Flipped N/Q/H residues before XYZ refinement:
A 560 GLN
A 859 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.218485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.184915 restraints weight = 9302.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.185053 restraints weight = 6092.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.187994 restraints weight = 4740.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.188711 restraints weight = 3421.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.189193 restraints weight = 3108.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.4354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6822
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7294  Z= 0.135
  Angle     :  0.682  10.281   9852  Z= 0.343
  Chirality :  0.044   0.168   1084
  Planarity :  0.005   0.058   1260
  Dihedral  :  7.350  52.486   1013
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.00 %
    Favored  : 85.00 %
  Rotamer:
    Outliers :  7.33 %
    Allowed  : 26.61 %
    Favored  : 66.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -3.32 (0.27), residues: 880
  helix: -0.21 (0.32), residues: 255
  sheet: -3.26 (0.40), residues: 126
  loop : -3.15 (0.26), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 142 
 TYR   0.020   0.001   TYR A 695 
 PHE   0.013   0.001   PHE A 464 
 TRP   0.013   0.001   TRP A 618 
 HIS   0.005   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7293)
  covalent geometry    : angle       0.68197 ( 9850)
  SS BOND              : bond        0.00480 (    1)
  SS BOND              : angle       0.13080 (    2)
  hydrogen bonds       : bond        0.03411 (  195)
  hydrogen bonds       : angle       5.31765 (  540)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 96
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7523 (ptmt) cc_final: 0.7014 (mptt)
REVERT: A  165 ASP cc_start: 0.6875 (OUTLIER) cc_final: 0.6481 (p0)
REVERT: A  173 HIS cc_start: 0.6408 (OUTLIER) cc_final: 0.5750 (m-70)
REVERT: A  240 LYS cc_start: 0.8412 (ttmm) cc_final: 0.7911 (tttm)
REVERT: A  241 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8260 (tt)
REVERT: A  506 LYS cc_start: 0.7879 (mtpp) cc_final: 0.6956 (mmmt)
REVERT: A  630 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6246 (mp)
REVERT: A  708 LEU cc_start: 0.7903 (mp) cc_final: 0.7371 (mt)
REVERT: A  909 HIS cc_start: 0.6852 (m90) cc_final: 0.6189 (m170)
REVERT: A  924 MET cc_start: 0.7837 (mpp) cc_final: 0.7369 (mpp)
REVERT: A  941 GLU cc_start: 0.2599 (OUTLIER) cc_final: 0.1631 (pm20)
REVERT: A  942 ARG cc_start: 0.1064 (OUTLIER) cc_final: -0.0017 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4072 (OUTLIER) cc_final: 0.3477 (m-80)
REVERT: A 1110 ARG cc_start: 0.4325 (OUTLIER) cc_final: 0.4102 (ptt-90)
  outliers start: 57
  outliers final: 44
  residues processed: 143
  average time/residue: 0.0955
  time to fit residues: 17.8934
Evaluate side-chains
  146 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 94
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  437 LYS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  545 ILE
Chi-restraints excluded: chain A residue  547 SER
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  941 GLU
Chi-restraints excluded: chain A residue  942 ARG
Chi-restraints excluded: chain A residue  997 ARG
Chi-restraints excluded: chain A residue  998 TYR
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1081 TYR
Chi-restraints excluded: chain A residue 1084 ASP
Chi-restraints excluded: chain A residue 1091 PHE
Chi-restraints excluded: chain A residue 1100 ASP
Chi-restraints excluded: chain A residue 1110 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 71 optimal weight:    2.9990
   chunk 86 optimal weight:    7.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 560 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.220198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.188203 restraints weight = 9341.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.190190 restraints weight = 6111.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.191186 restraints weight = 5332.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.191980 restraints weight = 3956.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.192632 restraints weight = 3420.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.4415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6806
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7294  Z= 0.126
  Angle     :  0.672   9.732   9852  Z= 0.337
  Chirality :  0.044   0.167   1084
  Planarity :  0.005   0.079   1260
  Dihedral  :  7.041  52.166   1011
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.11 %
    Favored  : 84.89 %
  Rotamer:
    Outliers :  7.07 %
    Allowed  : 26.86 %
    Favored  : 66.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -3.20 (0.27), residues: 880
  helix:  0.05 (0.33), residues: 248
  sheet: -3.36 (0.38), residues: 135
  loop : -3.04 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 142 
 TYR   0.019   0.001   TYR A 695 
 PHE   0.013   0.001   PHE A 464 
 TRP   0.017   0.001   TRP A 618 
 HIS   0.004   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7293)
  covalent geometry    : angle       0.67247 ( 9850)
  SS BOND              : bond        0.00461 (    1)
  SS BOND              : angle       0.09726 (    2)
  hydrogen bonds       : bond        0.03289 (  195)
  hydrogen bonds       : angle       5.20516 (  540)

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 96
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7506 (ptmt) cc_final: 0.7094 (mptt)
REVERT: A  173 HIS cc_start: 0.6301 (OUTLIER) cc_final: 0.5706 (m-70)
REVERT: A  240 LYS cc_start: 0.8300 (ttmm) cc_final: 0.7895 (tttm)
REVERT: A  241 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8195 (tt)
REVERT: A  506 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7127 (mmmt)
REVERT: A  630 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6400 (mp)
REVERT: A  708 LEU cc_start: 0.7989 (mp) cc_final: 0.7463 (mt)
REVERT: A  909 HIS cc_start: 0.6758 (m90) cc_final: 0.6207 (m170)
REVERT: A  924 MET cc_start: 0.7841 (mpp) cc_final: 0.7436 (mpp)
REVERT: A  941 GLU cc_start: 0.2508 (OUTLIER) cc_final: 0.1618 (pm20)
REVERT: A  942 ARG cc_start: 0.1052 (OUTLIER) cc_final: -0.0036 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.3988 (OUTLIER) cc_final: 0.3396 (m-80)
REVERT: A 1110 ARG cc_start: 0.4227 (OUTLIER) cc_final: 0.3984 (ptt-90)
  outliers start: 55
  outliers final: 44
  residues processed: 142
  average time/residue: 0.1011
  time to fit residues: 18.6586
Evaluate side-chains
  148 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 97
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  437 LYS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  542 THR
Chi-restraints excluded: chain A residue  545 ILE
Chi-restraints excluded: chain A residue  547 SER
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  587 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  941 GLU
Chi-restraints excluded: chain A residue  942 ARG
Chi-restraints excluded: chain A residue  997 ARG
Chi-restraints excluded: chain A residue  998 TYR
Chi-restraints excluded: chain A residue 1030 VAL
Chi-restraints excluded: chain A residue 1081 TYR
Chi-restraints excluded: chain A residue 1084 ASP
Chi-restraints excluded: chain A residue 1091 PHE
Chi-restraints excluded: chain A residue 1100 ASP
Chi-restraints excluded: chain A residue 1110 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 52 optimal weight:    0.0270
   chunk 68 optimal weight:    8.9990
   chunk 48 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.7438

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

Flipped N/Q/H residues before XYZ refinement:
A 560 GLN
A1036 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.220094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.186514 restraints weight = 9362.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.186829 restraints weight = 6287.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.188160 restraints weight = 5632.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.190048 restraints weight = 3906.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.190909 restraints weight = 3243.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.4386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6782
moved from start:          0.2800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7294  Z= 0.122
  Angle     :  0.669   9.795   9852  Z= 0.334
  Chirality :  0.043   0.167   1084
  Planarity :  0.005   0.078   1260
  Dihedral  :  6.803  52.097   1009
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.32 %
    Favored  : 85.68 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 27.63 %
    Favored  : 65.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -3.12 (0.27), residues: 880
  helix:  0.04 (0.33), residues: 254
  sheet: -3.32 (0.38), residues: 135
  loop : -2.99 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 142 
 TYR   0.019   0.001   TYR A 695 
 PHE   0.012   0.001   PHE A 464 
 TRP   0.023   0.001   TRP A 618 
 HIS   0.004   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7293)
  covalent geometry    : angle       0.66894 ( 9850)
  SS BOND              : bond        0.00397 (    1)
  SS BOND              : angle       0.01995 (    2)
  hydrogen bonds       : bond        0.03173 (  195)
  hydrogen bonds       : angle       5.17017 (  540)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1339.73 seconds
wall clock time: 23 minutes 47.69 seconds (1427.69 seconds total)