Starting phenix.real_space_refine
on Fri Jun  6 03:13:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w88_32353/06_2025/7w88_32353.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w88_32353/06_2025/7w88_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_32353/06_2025/7w88_32353.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w88_32353/06_2025/7w88_32353.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w88_32353/06_2025/7w88_32353.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w88_32353/06_2025/7w88_32353.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 4.94, per 1000 atoms: 0.69
  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: 1.83
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.82
  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: 2.08

  Time building geometry restraints manager: 2.18 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:             1.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     21.120
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:3.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6865
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 : 15.29
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.008   0.001   TRP A1096 
 HIS   0.005   0.001   HIS A 718 
 PHE   0.012   0.001   PHE A 464 
 TYR   0.012   0.001   TYR A 695 
 ARG   0.003   0.000   ARG A 929 

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

*********************** 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  : 0.857 
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: 0.1645 (OUTLIER) cc_final: -0.0978 (ptt-90)
  outliers start: 64
  outliers final: 35
  residues processed: 166
  average time/residue: 0.2216
  time to fit residues: 47.6770
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  : 0.773 
-------------------------------------------------------------------------------
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 75 optimal weight:    9.9990
   chunk 67 optimal weight:    4.9990
   chunk 37 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0050
   chunk 80 optimal weight:    7.9990
   overall best weight:    3.4002

-------------------------------------------------------------------------------
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 661 ASN
A 686 GLN
A 706 ASN
A 739 GLN
A 748 HIS
A 756 GLN
A 778 ASN
A 869 HIS
A 948 ASN
A1024 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4555 r_free = 0.4555 target = 0.206777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.173754 restraints weight = 9471.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.174556 restraints weight = 6258.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.176732 restraints weight = 5317.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073   7294  Z= 0.312
  Angle     :  0.834   9.287   9852  Z= 0.435
  Chirality :  0.051   0.207   1084
  Planarity :  0.006   0.062   1260
  Dihedral  : 10.194  59.408   1063
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 17.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.91 %
    Favored  : 79.09 %
  Rotamer:
    Outliers : 10.80 %
    Allowed  : 23.01 %
    Favored  : 66.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.79 (0.25), residues: 880
  helix: -1.57 (0.29), residues: 246
  sheet: -4.42 (0.31), residues: 147
  loop : -3.77 (0.26), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 940 
 HIS   0.007   0.001   HIS A 718 
 PHE   0.023   0.003   PHE A 480 
 TYR   0.023   0.002   TYR A 695 
 ARG   0.007   0.001   ARG A 579 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05746 (  195)
  hydrogen bonds       : angle       6.33355 (  540)
  SS BOND              : bond        0.01069 (    1)
  SS BOND              : angle       0.59674 (    2)
  covalent geometry    : bond        0.00723 ( 7293)
  covalent geometry    : angle       0.83427 ( 9850)

*********************** 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
  175 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 91
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 HIS cc_start: 0.6330 (OUTLIER) cc_final: 0.5659 (m-70)
REVERT: A  329 ARG cc_start: 0.7430 (mpp80) cc_final: 0.7174 (mpp80)
REVERT: A  606 PHE cc_start: 0.8130 (OUTLIER) cc_final: 0.7882 (p90)
REVERT: A  630 ILE cc_start: 0.7201 (OUTLIER) cc_final: 0.6794 (mp)
REVERT: A  708 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7267 (mt)
REVERT: A  721 LYS cc_start: 0.7649 (mmtt) cc_final: 0.7401 (mttp)
REVERT: A  942 ARG cc_start: 0.1871 (OUTLIER) cc_final: -0.1190 (ptt-90)
  outliers start: 84
  outliers final: 57
  residues processed: 161
  average time/residue: 0.2191
  time to fit residues: 48.2716
Evaluate side-chains
  149 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 87
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
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  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  281 VAL
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  323 SER
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  397 VAL
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  487 THR
Chi-restraints excluded: chain A residue  504 VAL
Chi-restraints excluded: chain A residue  505 SER
Chi-restraints excluded: chain A residue  518 SER
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  528 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  553 ILE
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  587 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  592 THR
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  660 THR
Chi-restraints excluded: chain A residue  666 LEU
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  745 THR
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  773 VAL
Chi-restraints excluded: chain A residue  803 ILE
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 1053 LEU
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 1099 CYS
Chi-restraints excluded: chain A residue 1100 ASP
Chi-restraints excluded: chain A residue 1101 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 33 optimal weight:    0.3980
   chunk 41 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 1 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 756 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.215451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.182628 restraints weight = 9411.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.183476 restraints weight = 6415.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.185751 restraints weight = 5312.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7294  Z= 0.132
  Angle     :  0.668   8.459   9852  Z= 0.340
  Chirality :  0.044   0.176   1084
  Planarity :  0.005   0.055   1260
  Dihedral  :  8.903  58.860   1040
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.23 %
    Favored  : 84.77 %
  Rotamer:
    Outliers :  8.48 %
    Allowed  : 25.58 %
    Favored  : 65.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.26), residues: 880
  helix: -0.61 (0.32), residues: 244
  sheet: -4.09 (0.34), residues: 144
  loop : -3.49 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1076 
 HIS   0.005   0.001   HIS A 718 
 PHE   0.011   0.001   PHE A 464 
 TYR   0.022   0.001   TYR A1001 
 ARG   0.005   0.000   ARG A 579 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03940 (  195)
  hydrogen bonds       : angle       5.70439 (  540)
  SS BOND              : bond        0.00396 (    1)
  SS BOND              : angle       0.09045 (    2)
  covalent geometry    : bond        0.00294 ( 7293)
  covalent geometry    : angle       0.66796 ( 9850)

*********************** 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
  162 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 96
  time to evaluate  : 0.805 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7522 (ptmt) cc_final: 0.6985 (mptt)
REVERT: A  173 HIS cc_start: 0.6162 (OUTLIER) cc_final: 0.5552 (m-70)
REVERT: A  329 ARG cc_start: 0.7489 (mpp80) cc_final: 0.6911 (mpp80)
REVERT: A  617 ASN cc_start: 0.7408 (t0) cc_final: 0.7097 (m-40)
REVERT: A  630 ILE cc_start: 0.6862 (mp) cc_final: 0.6445 (mp)
REVERT: A  708 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7044 (mt)
REVERT: A  924 MET cc_start: 0.7853 (mpp) cc_final: 0.7275 (mpp)
REVERT: A  942 ARG cc_start: 0.1470 (OUTLIER) cc_final: -0.0176 (ptt-90)
  outliers start: 66
  outliers final: 36
  residues processed: 153
  average time/residue: 0.2039
  time to fit residues: 40.7895
Evaluate side-chains
  125 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 86
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
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  311 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  323 SER
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  542 THR
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  660 THR
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  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 1084 ASP
Chi-restraints excluded: chain A residue 1091 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0980
   chunk 46 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 61 optimal weight:    0.5980
   chunk 63 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.4613 r_free = 0.4613 target = 0.213107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.179837 restraints weight = 9512.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.180254 restraints weight = 6460.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.182498 restraints weight = 5562.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.4318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.1913

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= 0.151
  Angle     :  0.664   7.451   9852  Z= 0.341
  Chirality :  0.045   0.162   1084
  Planarity :  0.005   0.055   1260
  Dihedral  :  8.404  59.108   1025
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.27 %
    Favored  : 82.73 %
  Rotamer:
    Outliers :  8.61 %
    Allowed  : 25.45 %
    Favored  : 65.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.85 (0.27), residues: 880
  helix: -0.48 (0.32), residues: 245
  sheet: -3.97 (0.34), residues: 142
  loop : -3.35 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 618 
 HIS   0.004   0.001   HIS A 718 
 PHE   0.017   0.002   PHE A 464 
 TYR   0.017   0.001   TYR A 695 
 ARG   0.005   0.001   ARG A 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03883 (  195)
  hydrogen bonds       : angle       5.55841 (  540)
  SS BOND              : bond        0.00587 (    1)
  SS BOND              : angle       0.11264 (    2)
  covalent geometry    : bond        0.00343 ( 7293)
  covalent geometry    : angle       0.66368 ( 9850)

*********************** 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
  160 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 93
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7466 (ptmt) cc_final: 0.7003 (mptt)
REVERT: A  173 HIS cc_start: 0.6195 (OUTLIER) cc_final: 0.5592 (m-70)
REVERT: A  329 ARG cc_start: 0.7500 (mpp80) cc_final: 0.7150 (mpp80)
REVERT: A  630 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6618 (mp)
REVERT: A  708 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7144 (mt)
REVERT: A  924 MET cc_start: 0.7842 (mpp) cc_final: 0.7543 (mpp)
REVERT: A  942 ARG cc_start: 0.1490 (OUTLIER) cc_final: -0.0173 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4254 (OUTLIER) cc_final: 0.3473 (m-80)
  outliers start: 67
  outliers final: 42
  residues processed: 145
  average time/residue: 0.2176
  time to fit residues: 41.6126
Evaluate side-chains
  139 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 92
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
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  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  397 VAL
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  518 SER
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  553 ILE
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  564 LEU
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  660 THR
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 12 optimal weight:    9.9990
   chunk 39 optimal weight:    0.6980
   chunk 45 optimal weight:    0.3980
   chunk 15 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 87 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4645 r_free = 0.4645 target = 0.216761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.183698 restraints weight = 9402.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.184075 restraints weight = 6374.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.186553 restraints weight = 5185.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.4339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6858
moved from start:          0.2049

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     :  0.646   9.552   9852  Z= 0.329
  Chirality :  0.044   0.164   1084
  Planarity :  0.005   0.055   1260
  Dihedral  :  8.154  59.543   1023
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.91 %
    Favored  : 84.09 %
  Rotamer:
    Outliers :  8.23 %
    Allowed  : 26.48 %
    Favored  : 65.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.58 (0.27), residues: 880
  helix: -0.15 (0.33), residues: 245
  sheet: -3.76 (0.35), residues: 140
  loop : -3.27 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 618 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.017   0.001   PHE A1040 
 TYR   0.015   0.001   TYR A 695 
 ARG   0.007   0.000   ARG A 892 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03514 (  195)
  hydrogen bonds       : angle       5.39019 (  540)
  SS BOND              : bond        0.00440 (    1)
  SS BOND              : angle       0.18036 (    2)
  covalent geometry    : bond        0.00280 ( 7293)
  covalent geometry    : angle       0.64616 ( 9850)

*********************** 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
  163 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 99
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7439 (ptmt) cc_final: 0.6992 (mptt)
REVERT: A  173 HIS cc_start: 0.6215 (OUTLIER) cc_final: 0.5628 (m-70)
REVERT: A  329 ARG cc_start: 0.7484 (mpp80) cc_final: 0.7094 (mpp80)
REVERT: A  617 ASN cc_start: 0.7340 (t0) cc_final: 0.7106 (m-40)
REVERT: A  630 ILE cc_start: 0.6897 (OUTLIER) cc_final: 0.6493 (mp)
REVERT: A  708 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7072 (mt)
REVERT: A  924 MET cc_start: 0.7774 (mpp) cc_final: 0.7534 (mpt)
REVERT: A  935 ASP cc_start: 0.0150 (OUTLIER) cc_final: -0.0100 (m-30)
REVERT: A  942 ARG cc_start: 0.1319 (OUTLIER) cc_final: -0.0398 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4043 (OUTLIER) cc_final: 0.3336 (m-80)
  outliers start: 64
  outliers final: 42
  residues processed: 152
  average time/residue: 0.2096
  time to fit residues: 41.8962
Evaluate side-chains
  142 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 94
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
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  311 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  323 SER
Chi-restraints excluded: chain A residue  332 GLU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  346 GLN
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  437 LYS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  518 SER
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  590 ASP
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  642 GLU
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  908 LEU
Chi-restraints excluded: chain A residue  935 ASP
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 31 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 83 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 77 optimal weight:    0.2980
   chunk 46 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 560 GLN
** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1036 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4661 r_free = 0.4661 target = 0.218699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.185428 restraints weight = 9406.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.185906 restraints weight = 6403.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.188393 restraints weight = 5168.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.4360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6828
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7294  Z= 0.118
  Angle     :  0.641   8.942   9852  Z= 0.325
  Chirality :  0.044   0.218   1084
  Planarity :  0.005   0.055   1260
  Dihedral  :  7.893  57.587   1018
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.23 %
    Favored  : 84.77 %
  Rotamer:
    Outliers :  8.48 %
    Allowed  : 26.86 %
    Favored  : 64.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.40 (0.27), residues: 880
  helix: -0.09 (0.33), residues: 253
  sheet: -3.49 (0.36), residues: 136
  loop : -3.21 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 618 
 HIS   0.003   0.001   HIS A 718 
 PHE   0.012   0.001   PHE A 464 
 TYR   0.015   0.001   TYR A 695 
 ARG   0.009   0.001   ARG A1086 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03289 (  195)
  hydrogen bonds       : angle       5.27386 (  540)
  SS BOND              : bond        0.00373 (    1)
  SS BOND              : angle       0.12513 (    2)
  covalent geometry    : bond        0.00262 ( 7293)
  covalent geometry    : angle       0.64083 ( 9850)

*********************** 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
  163 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 97
  time to evaluate  : 0.886 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7444 (ptmt) cc_final: 0.7030 (mptt)
REVERT: A  173 HIS cc_start: 0.6232 (OUTLIER) cc_final: 0.5609 (m-70)
REVERT: A  240 LYS cc_start: 0.8522 (ttmm) cc_final: 0.7994 (tttm)
REVERT: A  241 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8329 (tt)
REVERT: A  329 ARG cc_start: 0.7457 (mpp80) cc_final: 0.6968 (mpp80)
REVERT: A  355 MET cc_start: 0.6930 (mtm) cc_final: 0.6726 (mtm)
REVERT: A  612 MET cc_start: 0.5923 (tmm) cc_final: 0.5419 (tmm)
REVERT: A  630 ILE cc_start: 0.6822 (OUTLIER) cc_final: 0.6405 (mp)
REVERT: A  647 MET cc_start: 0.6744 (mpt) cc_final: 0.6493 (mpt)
REVERT: A  708 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7004 (mt)
REVERT: A  924 MET cc_start: 0.7743 (mpp) cc_final: 0.7209 (mpp)
REVERT: A  935 ASP cc_start: 0.0222 (OUTLIER) cc_final: -0.0050 (m-30)
REVERT: A  941 GLU cc_start: 0.2390 (OUTLIER) cc_final: 0.1780 (pt0)
REVERT: A  942 ARG cc_start: 0.1241 (OUTLIER) cc_final: -0.0335 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4003 (OUTLIER) cc_final: 0.3380 (m-80)
  outliers start: 66
  outliers final: 47
  residues processed: 154
  average time/residue: 0.2019
  time to fit residues: 41.8242
Evaluate side-chains
  144 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 89
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
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  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  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  518 SER
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  587 ILE
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  642 GLU
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  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  935 ASP
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 1 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 6 optimal weight:   20.0000
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
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 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 739 GLN
A1036 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.215302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.181757 restraints weight = 9364.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.181526 restraints weight = 6342.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.183828 restraints weight = 5409.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7294  Z= 0.171
  Angle     :  0.678   8.119   9852  Z= 0.348
  Chirality :  0.045   0.163   1084
  Planarity :  0.005   0.055   1260
  Dihedral  :  8.083  58.640   1018
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 13.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.50 %
    Favored  : 82.50 %
  Rotamer:
    Outliers :  8.48 %
    Allowed  : 26.99 %
    Favored  : 64.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.27), residues: 880
  helix: -0.28 (0.33), residues: 247
  sheet: -3.67 (0.36), residues: 140
  loop : -3.21 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 618 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.018   0.002   PHE A 464 
 TYR   0.017   0.001   TYR A 695 
 ARG   0.005   0.001   ARG A1086 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03752 (  195)
  hydrogen bonds       : angle       5.53093 (  540)
  SS BOND              : bond        0.00736 (    1)
  SS BOND              : angle       0.40790 (    2)
  covalent geometry    : bond        0.00393 ( 7293)
  covalent geometry    : angle       0.67815 ( 9850)

*********************** 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
  158 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 92
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7451 (ptmt) cc_final: 0.7040 (mptt)
REVERT: A  173 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.5696 (m-70)
REVERT: A  240 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8023 (tttm)
REVERT: A  241 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8379 (tt)
REVERT: A  329 ARG cc_start: 0.7477 (mpp80) cc_final: 0.7061 (mpp80)
REVERT: A  630 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6575 (mp)
REVERT: A  645 GLU cc_start: 0.5763 (OUTLIER) cc_final: 0.5419 (tt0)
REVERT: A  708 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7060 (mt)
REVERT: A  909 HIS cc_start: 0.7085 (m-70) cc_final: 0.6827 (m-70)
REVERT: A  924 MET cc_start: 0.7781 (mpp) cc_final: 0.7207 (mpp)
REVERT: A  935 ASP cc_start: 0.0402 (OUTLIER) cc_final: 0.0005 (m-30)
REVERT: A  942 ARG cc_start: 0.1441 (OUTLIER) cc_final: -0.0342 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4070 (OUTLIER) cc_final: 0.3361 (m-80)
  outliers start: 66
  outliers final: 52
  residues processed: 147
  average time/residue: 0.2085
  time to fit residues: 40.6170
Evaluate side-chains
  148 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 88
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
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  323 SER
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  437 LYS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  518 SER
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  597 LEU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  642 GLU
Chi-restraints excluded: chain A residue  645 GLU
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  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  935 ASP
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 27 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 54 optimal weight:    4.9990
   chunk 70 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 73 optimal weight:    0.4980
   chunk 62 optimal weight:    0.8980
   chunk 84 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 739 GLN
A1036 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.218905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.185250 restraints weight = 9468.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.186323 restraints weight = 6290.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.187676 restraints weight = 5626.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.4344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7294  Z= 0.123
  Angle     :  0.651   7.891   9852  Z= 0.330
  Chirality :  0.044   0.164   1084
  Planarity :  0.004   0.056   1260
  Dihedral  :  7.878  59.459   1018
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 11.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.55 %
    Favored  : 85.45 %
  Rotamer:
    Outliers :  8.23 %
    Allowed  : 27.51 %
    Favored  : 64.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.29 (0.27), residues: 880
  helix: -0.06 (0.33), residues: 248
  sheet: -3.43 (0.37), residues: 136
  loop : -3.07 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 618 
 HIS   0.004   0.001   HIS A 703 
 PHE   0.033   0.001   PHE A 522 
 TYR   0.015   0.001   TYR A 695 
 ARG   0.004   0.000   ARG A 579 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03286 (  195)
  hydrogen bonds       : angle       5.33716 (  540)
  SS BOND              : bond        0.00348 (    1)
  SS BOND              : angle       0.11952 (    2)
  covalent geometry    : bond        0.00279 ( 7293)
  covalent geometry    : angle       0.65076 ( 9850)

*********************** 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
  159 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 95
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7441 (ptmt) cc_final: 0.7034 (mptt)
REVERT: A  173 HIS cc_start: 0.6251 (OUTLIER) cc_final: 0.5657 (m-70)
REVERT: A  240 LYS cc_start: 0.8485 (ttmm) cc_final: 0.8005 (tttm)
REVERT: A  241 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8328 (tt)
REVERT: A  329 ARG cc_start: 0.7472 (mpp80) cc_final: 0.7047 (mpp80)
REVERT: A  630 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6447 (mp)
REVERT: A  645 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5381 (tt0)
REVERT: A  708 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.6966 (mt)
REVERT: A  888 ILE cc_start: 0.5444 (mp) cc_final: 0.5113 (mp)
REVERT: A  909 HIS cc_start: 0.6931 (m-70) cc_final: 0.6721 (m-70)
REVERT: A  924 MET cc_start: 0.7715 (mpp) cc_final: 0.7199 (mpp)
REVERT: A  935 ASP cc_start: 0.0497 (OUTLIER) cc_final: 0.0152 (m-30)
REVERT: A  941 GLU cc_start: 0.2337 (OUTLIER) cc_final: 0.1738 (pt0)
REVERT: A  942 ARG cc_start: 0.1277 (OUTLIER) cc_final: -0.0363 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4093 (OUTLIER) cc_final: 0.3415 (m-80)
  outliers start: 64
  outliers final: 49
  residues processed: 147
  average time/residue: 0.2079
  time to fit residues: 40.3611
Evaluate side-chains
  145 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 87
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
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  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  323 SER
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  518 SER
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  642 GLU
Chi-restraints excluded: chain A residue  645 GLU
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  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  935 ASP
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 1099 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 9 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 739 GLN
A1036 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.215198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.181490 restraints weight = 9412.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.181465 restraints weight = 6574.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.183746 restraints weight = 5423.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6882
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7294  Z= 0.148
  Angle     :  0.668   7.468   9852  Z= 0.341
  Chirality :  0.044   0.158   1084
  Planarity :  0.005   0.080   1260
  Dihedral  :  7.913  58.029   1018
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.70 %
    Favored  : 83.30 %
  Rotamer:
    Outliers :  9.13 %
    Allowed  : 27.38 %
    Favored  : 63.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (0.27), residues: 880
  helix: -0.13 (0.33), residues: 248
  sheet: -3.40 (0.39), residues: 124
  loop : -3.01 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 618 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.037   0.002   PHE A 522 
 TYR   0.016   0.001   TYR A 695 
 ARG   0.008   0.000   ARG A 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03494 (  195)
  hydrogen bonds       : angle       5.37906 (  540)
  SS BOND              : bond        0.01619 (    1)
  SS BOND              : angle       3.07653 (    2)
  covalent geometry    : bond        0.00340 ( 7293)
  covalent geometry    : angle       0.66651 ( 9850)

*********************** 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
  158 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 87
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7446 (ptmt) cc_final: 0.7033 (mptt)
REVERT: A  173 HIS cc_start: 0.6351 (OUTLIER) cc_final: 0.5724 (m-70)
REVERT: A  240 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8010 (tttm)
REVERT: A  241 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8327 (tt)
REVERT: A  294 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7869 (mt)
REVERT: A  329 ARG cc_start: 0.7457 (mpp80) cc_final: 0.7032 (mpp80)
REVERT: A  630 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6464 (mp)
REVERT: A  645 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5496 (tt0)
REVERT: A  708 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7015 (mt)
REVERT: A  888 ILE cc_start: 0.5396 (mp) cc_final: 0.5064 (mp)
REVERT: A  909 HIS cc_start: 0.6989 (m-70) cc_final: 0.6771 (m-70)
REVERT: A  924 MET cc_start: 0.7715 (mpp) cc_final: 0.7191 (mpp)
REVERT: A  935 ASP cc_start: 0.0401 (OUTLIER) cc_final: -0.0002 (m-30)
REVERT: A  941 GLU cc_start: 0.2299 (OUTLIER) cc_final: 0.1567 (pt0)
REVERT: A  942 ARG cc_start: 0.1354 (OUTLIER) cc_final: -0.0220 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4061 (OUTLIER) cc_final: 0.3367 (m-80)
  outliers start: 71
  outliers final: 53
  residues processed: 146
  average time/residue: 0.2125
  time to fit residues: 41.1851
Evaluate side-chains
  150 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 87
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
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  294 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  323 SER
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  437 LYS
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  518 SER
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  597 LEU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  642 GLU
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  666 LEU
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  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  935 ASP
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 1099 CYS
Chi-restraints excluded: chain A residue 1100 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 65 optimal weight:    0.1980
   chunk 38 optimal weight:    0.8980
   chunk 81 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 29 optimal weight:    0.3980
   chunk 11 optimal weight:    0.0040
   chunk 71 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.4392

-------------------------------------------------------------------------------
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 = 0.4681 r_free = 0.4681 target = 0.220805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.186511 restraints weight = 9604.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.187783 restraints weight = 6107.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.189743 restraints weight = 4844.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.4374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.2739

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= 0.113
  Angle     :  0.656   8.396   9852  Z= 0.332
  Chirality :  0.043   0.164   1084
  Planarity :  0.005   0.075   1260
  Dihedral  :  7.572  54.788   1018
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.20 %
    Favored  : 85.80 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 28.92 %
    Favored  : 63.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.27), residues: 880
  helix:  0.03 (0.33), residues: 255
  sheet: -3.07 (0.43), residues: 113
  loop : -2.96 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 618 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.034   0.001   PHE A 522 
 TYR   0.014   0.001   TYR A 695 
 ARG   0.008   0.000   ARG A 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03121 (  195)
  hydrogen bonds       : angle       5.18416 (  540)
  SS BOND              : bond        0.00975 (    1)
  SS BOND              : angle       2.18633 (    2)
  covalent geometry    : bond        0.00251 ( 7293)
  covalent geometry    : angle       0.65511 ( 9850)

********************** 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
  155 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 99
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7474 (ptmt) cc_final: 0.7039 (mptt)
REVERT: A  165 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6440 (p0)
REVERT: A  240 LYS cc_start: 0.8495 (ttmm) cc_final: 0.7950 (tttm)
REVERT: A  241 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8254 (tt)
REVERT: A  329 ARG cc_start: 0.7461 (mpp80) cc_final: 0.7024 (mpp80)
REVERT: A  506 LYS cc_start: 0.7810 (mtpp) cc_final: 0.6913 (mmmt)
REVERT: A  630 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.6304 (mp)
REVERT: A  647 MET cc_start: 0.6625 (mpt) cc_final: 0.6361 (mpt)
REVERT: A  924 MET cc_start: 0.7599 (mpp) cc_final: 0.7075 (mpp)
REVERT: A  935 ASP cc_start: 0.0093 (OUTLIER) cc_final: -0.0184 (m-30)
REVERT: A  941 GLU cc_start: 0.2229 (OUTLIER) cc_final: 0.1584 (pt0)
REVERT: A  942 ARG cc_start: 0.1112 (OUTLIER) cc_final: -0.0388 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.3925 (OUTLIER) cc_final: 0.3334 (m-80)
  outliers start: 56
  outliers final: 40
  residues processed: 145
  average time/residue: 0.2353
  time to fit residues: 45.2159
Evaluate side-chains
  142 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 95
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
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  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  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  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  587 ILE
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  642 GLU
Chi-restraints excluded: chain A residue  666 LEU
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  715 CYS
Chi-restraints excluded: chain A residue  731 GLU
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  908 LEU
Chi-restraints excluded: chain A residue  935 ASP
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 1099 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   chunk 82 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 10 optimal weight:    0.4980
   chunk 54 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.219902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.186021 restraints weight = 9367.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.186568 restraints weight = 6261.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.188603 restraints weight = 5098.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.4367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6804
moved from start:          0.2825

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= 0.120
  Angle     :  0.654   7.830   9852  Z= 0.332
  Chirality :  0.043   0.163   1084
  Planarity :  0.005   0.077   1260
  Dihedral  :  7.321  52.285   1015
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.34 %
    Favored  : 84.66 %
  Rotamer:
    Outliers :  6.17 %
    Allowed  : 30.08 %
    Favored  : 63.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.97 (0.27), residues: 880
  helix:  0.05 (0.33), residues: 254
  sheet: -3.06 (0.44), residues: 113
  loop : -2.92 (0.26), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 618 
 HIS   0.005   0.001   HIS A 909 
 PHE   0.034   0.001   PHE A 522 
 TYR   0.015   0.001   TYR A 695 
 ARG   0.009   0.000   ARG A 142 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03158 (  195)
  hydrogen bonds       : angle       5.15933 (  540)
  SS BOND              : bond        0.00954 (    1)
  SS BOND              : angle       2.12534 (    2)
  covalent geometry    : bond        0.00271 ( 7293)
  covalent geometry    : angle       0.65380 ( 9850)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2674.27 seconds
wall clock time: 47 minutes 0.69 seconds (2820.69 seconds total)