Starting phenix.real_space_refine
on Wed Feb 12 02:59:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w88_32353/02_2025/7w88_32353.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w88_32353/02_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_32353/02_2025/7w88_32353.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w88_32353/02_2025/7w88_32353.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w88_32353/02_2025/7w88_32353.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w88_32353/02_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-5592/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: 4.55, per 1000 atoms: 0.64
  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: 1.59
  Conformation dependent library (CDL) restraints added in 982.2 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      31.4% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  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: 2.19

  Time building geometry restraints manager: 1.85 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:             1.140
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.910
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.280
-------------------------------------------------------------------------------
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   7293  Z= 0.199
  Angle     :  0.705   8.829   9850  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 

*********************** 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  : 0.798 
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: 0.2438
  time to fit residues: 53.0691
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  : 0.950 
-------------------------------------------------------------------------------
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 = 0.4226 r_free = 0.4226 target = 0.173746 restraints weight = 9471.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.174519 restraints weight = 6259.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.176676 restraints weight = 5339.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7043
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   7293  Z= 0.478
  Angle     :  0.834   9.287   9850  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 

*********************** 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  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 HIS cc_start: 0.6333 (OUTLIER) cc_final: 0.5660 (m-70)
REVERT: A  329 ARG cc_start: 0.7430 (mpp80) cc_final: 0.7174 (mpp80)
REVERT: A  606 PHE cc_start: 0.8131 (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: 0.7848 (OUTLIER) cc_final: 0.7268 (mt)
REVERT: A  721 LYS cc_start: 0.7650 (mmtt) cc_final: 0.7401 (mttp)
REVERT: A  942 ARG cc_start: 0.1872 (OUTLIER) cc_final: -0.1190 (ptt-90)
  outliers start: 84
  outliers final: 57
  residues processed: 161
  average time/residue: 0.1943
  time to fit residues: 41.7631
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  : 0.760 
-------------------------------------------------------------------------------
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:    0.0970
   chunk 41 optimal weight:    0.8980
   chunk 72 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   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:    0.7382

-------------------------------------------------------------------------------
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 = 0.4642 r_free = 0.4642 target = 0.216077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.183344 restraints weight = 9417.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.184176 restraints weight = 6418.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4336 r_free = 0.4336 target = 0.186425 restraints weight = 5313.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.4350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.1710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7293  Z= 0.191
  Angle     :  0.664   8.504   9850  Z= 0.338
  Chirality :  0.045   0.181   1084
  Planarity :  0.005   0.056   1260
  Dihedral  :  8.871  58.631   1040
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.77 %
    Favored  : 85.23 %
  Rotamer:
    Outliers :  7.97 %
    Allowed  : 26.22 %
    Favored  : 65.81 %
  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: -4.01 (0.26), residues: 880
  helix: -0.57 (0.33), residues: 244
  sheet: -4.06 (0.34), residues: 144
  loop : -3.47 (0.26), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 618 
 HIS   0.005   0.001   HIS A 869 
 PHE   0.011   0.001   PHE A 759 
 TYR   0.024   0.001   TYR A1001 
 ARG   0.006   0.000   ARG A 579 

*********************** 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
  156 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 94
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7521 (ptmt) cc_final: 0.7007 (mptt)
REVERT: A  329 ARG cc_start: 0.7469 (mpp80) cc_final: 0.6886 (mpp80)
REVERT: A  617 ASN cc_start: 0.7354 (t0) cc_final: 0.7071 (m-40)
REVERT: A  630 ILE cc_start: 0.6868 (mp) cc_final: 0.6458 (mp)
REVERT: A  708 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7060 (mt)
REVERT: A  924 MET cc_start: 0.7912 (mpp) cc_final: 0.7358 (mpp)
REVERT: A  942 ARG cc_start: 0.1461 (OUTLIER) cc_final: -0.0186 (ptt-90)
  outliers start: 62
  outliers final: 33
  residues processed: 150
  average time/residue: 0.2247
  time to fit residues: 44.0619
Evaluate side-chains
  120 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 85
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
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  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  406 SER
Chi-restraints excluded: chain A residue  437 LYS
Chi-restraints excluded: chain A residue  529 VAL
Chi-restraints excluded: chain A residue  536 GLU
Chi-restraints excluded: chain A residue  537 VAL
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  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:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 1 optimal weight:    4.9990
   chunk 61 optimal weight:    0.3980
   chunk 63 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.2582

-------------------------------------------------------------------------------
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 = 0.4626 r_free = 0.4626 target = 0.214564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.181530 restraints weight = 9533.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.181281 restraints weight = 6376.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.183472 restraints weight = 5974.475|
|-----------------------------------------------------------------------------|
r_work (final): 0.4315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7293  Z= 0.222
  Angle     :  0.658   7.589   9850  Z= 0.337
  Chirality :  0.045   0.162   1084
  Planarity :  0.005   0.053   1260
  Dihedral  :  8.347  59.504   1022
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.27 %
    Favored  : 82.73 %
  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: -3.82 (0.27), residues: 880
  helix: -0.45 (0.32), residues: 245
  sheet: -3.95 (0.34), residues: 142
  loop : -3.34 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 618 
 HIS   0.004   0.001   HIS A 718 
 PHE   0.016   0.002   PHE A 464 
 TYR   0.017   0.001   TYR A 695 
 ARG   0.005   0.000   ARG A 142 

*********************** 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
  157 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 91
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7479 (ptmt) cc_final: 0.7008 (mptt)
REVERT: A  173 HIS cc_start: 0.6192 (OUTLIER) cc_final: 0.5590 (m-70)
REVERT: A  329 ARG cc_start: 0.7507 (mpp80) cc_final: 0.7152 (mpp80)
REVERT: A  630 ILE cc_start: 0.6980 (OUTLIER) cc_final: 0.6608 (mp)
REVERT: A  708 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7156 (mt)
REVERT: A  924 MET cc_start: 0.7865 (mpp) cc_final: 0.7568 (mpp)
REVERT: A  942 ARG cc_start: 0.1475 (OUTLIER) cc_final: -0.0176 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4252 (OUTLIER) cc_final: 0.3479 (m-80)
  outliers start: 66
  outliers final: 44
  residues processed: 142
  average time/residue: 0.2098
  time to fit residues: 39.1116
Evaluate side-chains
  139 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 90
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
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  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  547 SER
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:    1.9990
   chunk 12 optimal weight:    9.9990
   chunk 39 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 13 optimal weight:    0.2980
   chunk 48 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 87 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.4628 r_free = 0.4628 target = 0.214952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.181569 restraints weight = 9373.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.181929 restraints weight = 6540.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.184376 restraints weight = 5285.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6876
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7293  Z= 0.196
  Angle     :  0.652   9.772   9850  Z= 0.332
  Chirality :  0.044   0.162   1084
  Planarity :  0.005   0.054   1260
  Dihedral  :  8.166  59.401   1021
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.25 %
    Favored  : 83.75 %
  Rotamer:
    Outliers :  8.48 %
    Allowed  : 25.96 %
    Favored  : 65.55 %
  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: -3.61 (0.27), residues: 880
  helix: -0.18 (0.33), residues: 245
  sheet: -3.76 (0.35), residues: 140
  loop : -3.29 (0.26), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 618 
 HIS   0.003   0.001   HIS A 703 
 PHE   0.017   0.001   PHE A1040 
 TYR   0.016   0.001   TYR A 695 
 ARG   0.008   0.000   ARG A 892 

*********************** 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
  160 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 94
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7472 (ptmt) cc_final: 0.6998 (mptt)
REVERT: A  173 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5640 (m-70)
REVERT: A  329 ARG cc_start: 0.7471 (mpp80) cc_final: 0.7033 (mpp80)
REVERT: A  617 ASN cc_start: 0.7342 (t0) cc_final: 0.7106 (m-40)
REVERT: A  630 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6530 (mp)
REVERT: A  708 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7081 (mt)
REVERT: A  924 MET cc_start: 0.7797 (mpp) cc_final: 0.7555 (mpt)
REVERT: A  935 ASP cc_start: 0.0168 (OUTLIER) cc_final: -0.0091 (m-30)
REVERT: A  942 ARG cc_start: 0.1349 (OUTLIER) cc_final: -0.0373 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4051 (OUTLIER) cc_final: 0.3343 (m-80)
  outliers start: 66
  outliers final: 44
  residues processed: 149
  average time/residue: 0.2190
  time to fit residues: 42.9694
Evaluate side-chains
  139 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 89
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
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  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  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  547 SER
Chi-restraints excluded: chain A residue  553 ILE
Chi-restraints excluded: chain A residue  555 THR
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  590 ASP
Chi-restraints excluded: chain A residue  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  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 1042 MET
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:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 31 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 83 optimal weight:    7.9990
   chunk 37 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4649 r_free = 0.4649 target = 0.217251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.184304 restraints weight = 9405.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.184859 restraints weight = 6397.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.186962 restraints weight = 5819.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6843
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7293  Z= 0.188
  Angle     :  0.652   9.232   9850  Z= 0.331
  Chirality :  0.044   0.257   1084
  Planarity :  0.005   0.054   1260
  Dihedral  :  7.989  57.279   1018
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.14 %
    Favored  : 83.86 %
  Rotamer:
    Outliers :  8.48 %
    Allowed  : 26.22 %
    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: -3.47 (0.27), residues: 880
  helix: -0.16 (0.33), residues: 247
  sheet: -3.55 (0.36), residues: 136
  loop : -3.21 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 618 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.014   0.001   PHE A 464 
 TYR   0.015   0.001   TYR A 695 
 ARG   0.009   0.001   ARG A1086 

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

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

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

  1760 Ramachandran restraints generated.
    880 Oldfield, 0 Emsley, 880 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 92
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7442 (ptmt) cc_final: 0.7023 (mptt)
REVERT: A  173 HIS cc_start: 0.6195 (OUTLIER) cc_final: 0.5580 (m-70)
REVERT: A  240 LYS cc_start: 0.8535 (ttmm) cc_final: 0.8015 (tttm)
REVERT: A  241 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8400 (tt)
REVERT: A  329 ARG cc_start: 0.7463 (mpp80) cc_final: 0.7069 (mpp80)
REVERT: A  612 MET cc_start: 0.5914 (tmm) cc_final: 0.5382 (tmm)
REVERT: A  617 ASN cc_start: 0.7340 (t0) cc_final: 0.7073 (m-40)
REVERT: A  630 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6512 (mp)
REVERT: A  708 LEU cc_start: 0.7755 (OUTLIER) cc_final: 0.7070 (mt)
REVERT: A  924 MET cc_start: 0.7816 (mpp) cc_final: 0.7492 (mpp)
REVERT: A  935 ASP cc_start: 0.0395 (OUTLIER) cc_final: 0.0062 (m-30)
REVERT: A  941 GLU cc_start: 0.2445 (OUTLIER) cc_final: 0.1815 (pt0)
REVERT: A  942 ARG cc_start: 0.1290 (OUTLIER) cc_final: -0.0270 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4056 (OUTLIER) cc_final: 0.3404 (m-80)
  outliers start: 66
  outliers final: 49
  residues processed: 147
  average time/residue: 0.2131
  time to fit residues: 41.0444
Evaluate side-chains
  147 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 90
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 SER
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  165 ASP
Chi-restraints excluded: chain A residue  173 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  194 ILE
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  311 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  346 GLN
Chi-restraints excluded: chain A residue  384 ILE
Chi-restraints excluded: chain A residue  395 ASN
Chi-restraints excluded: chain A residue  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  553 ILE
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  706 ASN
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  765 LYS
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain A residue  843 VAL
Chi-restraints excluded: chain A residue  875 ILE
Chi-restraints excluded: chain A residue  878 THR
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  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 1042 MET
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:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 19 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.4622 r_free = 0.4622 target = 0.214527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.180731 restraints weight = 9350.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.181725 restraints weight = 6228.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.182921 restraints weight = 5472.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7293  Z= 0.230
  Angle     :  0.660   8.316   9850  Z= 0.336
  Chirality :  0.044   0.160   1084
  Planarity :  0.005   0.054   1260
  Dihedral  :  8.034  56.658   1018
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.05 %
    Favored  : 82.95 %
  Rotamer:
    Outliers :  8.74 %
    Allowed  : 26.99 %
    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: -3.49 (0.27), residues: 880
  helix: -0.14 (0.33), residues: 247
  sheet: -3.64 (0.35), residues: 140
  loop : -3.20 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 618 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.017   0.002   PHE A 464 
 TYR   0.016   0.001   TYR A 695 
 ARG   0.004   0.000   ARG A1086 

*********************** 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
  160 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 92
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7460 (ptmt) cc_final: 0.7047 (mptt)
REVERT: A  173 HIS cc_start: 0.6238 (OUTLIER) cc_final: 0.5612 (m-70)
REVERT: A  240 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8036 (tttm)
REVERT: A  241 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8384 (tt)
REVERT: A  329 ARG cc_start: 0.7435 (mpp80) cc_final: 0.7031 (mpp80)
REVERT: A  617 ASN cc_start: 0.7371 (t0) cc_final: 0.7078 (m-40)
REVERT: A  630 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6553 (mp)
REVERT: A  645 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5453 (tt0)
REVERT: A  708 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7010 (mt)
REVERT: A  909 HIS cc_start: 0.7006 (m-70) cc_final: 0.6708 (m-70)
REVERT: A  924 MET cc_start: 0.7798 (mpp) cc_final: 0.7469 (mpp)
REVERT: A  935 ASP cc_start: 0.0371 (OUTLIER) cc_final: -0.0013 (m-30)
REVERT: A  942 ARG cc_start: 0.1416 (OUTLIER) cc_final: -0.0342 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4080 (OUTLIER) cc_final: 0.3365 (m-80)
  outliers start: 68
  outliers final: 53
  residues processed: 148
  average time/residue: 0.2161
  time to fit residues: 42.3575
Evaluate side-chains
  146 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 85
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
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  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  553 ILE
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 1042 MET
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:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0070
   chunk 54 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 62 optimal weight:    0.2980
   chunk 84 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    0.5998

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4673 r_free = 0.4673 target = 0.219851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.186580 restraints weight = 9426.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.186789 restraints weight = 6457.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.189554 restraints weight = 5367.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.4361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6795
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7293  Z= 0.168
  Angle     :  0.637   8.325   9850  Z= 0.323
  Chirality :  0.043   0.167   1084
  Planarity :  0.004   0.056   1260
  Dihedral  :  7.791  59.211   1018
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.20 %
    Favored  : 85.80 %
  Rotamer:
    Outliers :  7.58 %
    Allowed  : 28.02 %
    Favored  : 64.40 %
  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: -3.20 (0.27), residues: 880
  helix:  0.06 (0.34), residues: 247
  sheet: -3.37 (0.37), residues: 136
  loop : -3.04 (0.26), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 618 
 HIS   0.004   0.001   HIS A 703 
 PHE   0.011   0.001   PHE A 464 
 TYR   0.014   0.001   TYR A 695 
 ARG   0.004   0.000   ARG A 142 

*********************** 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
  150 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 91
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7429 (ptmt) cc_final: 0.7006 (mptt)
REVERT: A  173 HIS cc_start: 0.6258 (OUTLIER) cc_final: 0.5661 (m-70)
REVERT: A  240 LYS cc_start: 0.8472 (ttmm) cc_final: 0.7963 (tttm)
REVERT: A  241 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8329 (tt)
REVERT: A  329 ARG cc_start: 0.7500 (mpp80) cc_final: 0.7053 (mpp80)
REVERT: A  630 ILE cc_start: 0.6713 (OUTLIER) cc_final: 0.6310 (mp)
REVERT: A  645 GLU cc_start: 0.5554 (OUTLIER) cc_final: 0.5256 (tt0)
REVERT: A  647 MET cc_start: 0.6673 (mpt) cc_final: 0.6427 (mpt)
REVERT: A  708 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.6922 (mt)
REVERT: A  888 ILE cc_start: 0.5421 (mp) cc_final: 0.5093 (mp)
REVERT: A  909 HIS cc_start: 0.6965 (m-70) cc_final: 0.6762 (m-70)
REVERT: A  924 MET cc_start: 0.7676 (mpp) cc_final: 0.7126 (mpp)
REVERT: A  935 ASP cc_start: 0.0381 (OUTLIER) cc_final: 0.0071 (m-30)
REVERT: A  941 GLU cc_start: 0.2254 (OUTLIER) cc_final: 0.1643 (pt0)
REVERT: A  942 ARG cc_start: 0.1186 (OUTLIER) cc_final: -0.0418 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4050 (OUTLIER) cc_final: 0.3400 (m-80)
  outliers start: 59
  outliers final: 44
  residues processed: 140
  average time/residue: 0.2228
  time to fit residues: 40.7558
Evaluate side-chains
  138 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 85
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
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  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  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  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 1042 MET
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:    0.9990
   chunk 85 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 8 optimal weight:    0.4980
   chunk 37 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0010
   chunk 1 optimal weight:    0.9980
   chunk 83 optimal weight:    0.1980
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 577 GLN
A1036 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4700 r_free = 0.4700 target = 0.222493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.192211 restraints weight = 9695.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.190009 restraints weight = 8422.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.193225 restraints weight = 6670.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.4418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6783
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7293  Z= 0.159
  Angle     :  0.631   8.009   9850  Z= 0.320
  Chirality :  0.043   0.163   1084
  Planarity :  0.005   0.078   1260
  Dihedral  :  7.516  56.938   1017
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.43 %
    Favored  : 85.57 %
  Rotamer:
    Outliers :  7.71 %
    Allowed  : 28.53 %
    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: -2.98 (0.28), residues: 880
  helix:  0.17 (0.33), residues: 249
  sheet: -3.13 (0.41), residues: 129
  loop : -2.93 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 618 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.036   0.001   PHE A 522 
 TYR   0.015   0.001   TYR A 695 
 ARG   0.007   0.000   ARG A 142 

*********************** 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
  164 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 104
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7490 (ptmt) cc_final: 0.7160 (mptt)
REVERT: A  173 HIS cc_start: 0.6197 (OUTLIER) cc_final: 0.5671 (m-70)
REVERT: A  240 LYS cc_start: 0.8402 (ttmm) cc_final: 0.7986 (tttm)
REVERT: A  241 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8279 (tt)
REVERT: A  329 ARG cc_start: 0.7293 (mpp80) cc_final: 0.6897 (mpp80)
REVERT: A  506 LYS cc_start: 0.7994 (mtpp) cc_final: 0.7039 (mmmt)
REVERT: A  630 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6533 (mp)
REVERT: A  888 ILE cc_start: 0.5488 (mp) cc_final: 0.5252 (mt)
REVERT: A  924 MET cc_start: 0.7709 (mpp) cc_final: 0.7236 (mpp)
REVERT: A  935 ASP cc_start: 0.0398 (OUTLIER) cc_final: 0.0089 (m-30)
REVERT: A  941 GLU cc_start: 0.2207 (OUTLIER) cc_final: 0.1612 (pt0)
REVERT: A  942 ARG cc_start: 0.1058 (OUTLIER) cc_final: -0.0380 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.3957 (OUTLIER) cc_final: 0.3379 (m-80)
  outliers start: 60
  outliers final: 40
  residues processed: 154
  average time/residue: 0.2141
  time to fit residues: 43.4373
Evaluate side-chains
  144 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 97
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
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  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  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  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  630 ILE
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  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 1042 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 81 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:   10.0000
   chunk 71 optimal weight:    0.8980
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 276 ASN
A 520 GLN
A 560 GLN
** A 617 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 909 HIS
A1036 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4687 r_free = 0.4687 target = 0.220600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.188849 restraints weight = 9509.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.189353 restraints weight = 7371.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4397 r_free = 0.4397 target = 0.192011 restraints weight = 6051.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6795
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7293  Z= 0.188
  Angle     :  0.666   7.847   9850  Z= 0.335
  Chirality :  0.043   0.161   1084
  Planarity :  0.005   0.077   1260
  Dihedral  :  7.309  54.040   1015
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.11 %
    Favored  : 84.89 %
  Rotamer:
    Outliers :  6.81 %
    Allowed  : 29.69 %
    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: -2.99 (0.27), residues: 880
  helix:  0.07 (0.33), residues: 249
  sheet: -3.06 (0.43), residues: 113
  loop : -2.93 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 618 
 HIS   0.008   0.001   HIS A 909 
 PHE   0.031   0.001   PHE A 522 
 TYR   0.015   0.001   TYR A 695 
 ARG   0.008   0.000   ARG A 142 

********************** 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
  154 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 101
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 LYS cc_start: 0.7486 (ptmt) cc_final: 0.7163 (mptt)
REVERT: A  173 HIS cc_start: 0.6170 (OUTLIER) cc_final: 0.5654 (m-70)
REVERT: A  240 LYS cc_start: 0.8371 (ttmm) cc_final: 0.7995 (tttm)
REVERT: A  241 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8280 (tt)
REVERT: A  329 ARG cc_start: 0.7261 (mpp80) cc_final: 0.6885 (mpp80)
REVERT: A  506 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7048 (mmmt)
REVERT: A  630 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6545 (mp)
REVERT: A  888 ILE cc_start: 0.5500 (mp) cc_final: 0.5289 (mt)
REVERT: A  924 MET cc_start: 0.7704 (mpp) cc_final: 0.7266 (mpp)
REVERT: A  935 ASP cc_start: 0.0510 (OUTLIER) cc_final: 0.0153 (m-30)
REVERT: A  941 GLU cc_start: 0.2289 (OUTLIER) cc_final: 0.1671 (pt0)
REVERT: A  942 ARG cc_start: 0.1162 (OUTLIER) cc_final: -0.0343 (ptt-90)
REVERT: A 1081 TYR cc_start: 0.4008 (OUTLIER) cc_final: 0.3410 (m-80)
  outliers start: 53
  outliers final: 40
  residues processed: 144
  average time/residue: 0.2266
  time to fit residues: 42.7126
Evaluate side-chains
  143 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 96
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
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  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  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  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  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  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 1042 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0670
   chunk 8 optimal weight:    7.9990
   chunk 72 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0020
   chunk 10 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.8128

-------------------------------------------------------------------------------
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 859 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4672 r_free = 0.4672 target = 0.220012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.186123 restraints weight = 9354.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.186817 restraints weight = 6267.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.188966 restraints weight = 5121.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.4368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7293  Z= 0.184
  Angle     :  0.666  10.561   9850  Z= 0.335
  Chirality :  0.044   0.205   1084
  Planarity :  0.005   0.084   1260
  Dihedral  :  7.294  52.134   1015
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.11 %
    Favored  : 84.89 %
  Rotamer:
    Outliers :  6.94 %
    Allowed  : 30.08 %
    Favored  : 62.98 %
  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: -2.99 (0.27), residues: 880
  helix:  0.03 (0.33), residues: 255
  sheet: -3.05 (0.43), residues: 113
  loop : -2.94 (0.26), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 618 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.012   0.001   PHE A 464 
 TYR   0.015   0.001   TYR A 695 
 ARG   0.010   0.001   ARG A 142 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2425.54 seconds
wall clock time: 44 minutes 14.23 seconds (2654.23 seconds total)