Starting phenix.real_space_refine
on Tue Feb 11 19:20:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n8x_24248/02_2025/7n8x_24248.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n8x_24248/02_2025/7n8x_24248.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n8x_24248/02_2025/7n8x_24248.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n8x_24248/02_2025/7n8x_24248.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n8x_24248/02_2025/7n8x_24248.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n8x_24248/02_2025/7n8x_24248.cif"
  }
  resolution = 3.4
  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=   0.023 sd=   0.773
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      23      5.16       5
     C    4202      2.51       5
     N    1073      2.21       5
     O    1319      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 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: 6617
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 1093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1093
          Classifications: {'peptide': 140}
          Link IDs: {'PTRANS': 13, 'TRANS': 126}
    Chain: "A"
      Number of atoms: 5524
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 691, 5524
          Classifications: {'peptide': 691}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 669}
          Chain breaks: 1
  Time building chain proxies: 4.12, per 1000 atoms: 0.62
  Number of scatterers: 6617
  At special positions: 0
  Unit cell: (109.61, 84.75, 91.53, 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      23     16.00
     O    1319      8.00
     N    1073      7.00
     C    4202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B   6 " - pdb=" SG  CYS B 124 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.74
  Conformation dependent library (CDL) restraints added in 903.2 milliseconds
  

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1580

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 8 sheets defined
      29.0% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'B' and resid 13 through 17
    Processing helix  chain 'B' and resid 48 through 53
    Processing helix  chain 'B' and resid 87 through 92
    Processing helix  chain 'B' and resid 123 through 127
    Processing helix  chain 'A' and resid 398 through 415
    Processing helix  chain 'A' and resid 416 through 420
      removed outlier: 3.708A  pdb=" N   GLU A 420 " --> pdb=" O   ALA A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 438
      removed outlier: 3.657A  pdb=" N   GLU A 438 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 450
      removed outlier: 4.326A  pdb=" N   GLU A 449 " --> pdb=" O   ARG A 445 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   LEU A 450 " --> pdb=" O   PHE A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 456
      removed outlier: 4.616A  pdb=" N   LEU A 454 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL A 456 " --> pdb=" O   TYR A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 470
      removed outlier: 3.513A  pdb=" N   ASN A 467 " --> pdb=" O   LYS A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 4.334A  pdb=" N   ALA A 476 " --> pdb=" O   GLU A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 510
    Processing helix  chain 'A' and resid 511 through 516
    Processing helix  chain 'A' and resid 523 through 539
      removed outlier: 4.483A  pdb=" N   ALA A 529 " --> pdb=" O   ALA A 525 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   GLU A 532 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 569
    Processing helix  chain 'A' and resid 588 through 601
      removed outlier: 4.026A  pdb=" N   THR A 601 " --> pdb=" O   LEU A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 667 through 682
    Processing helix  chain 'A' and resid 710 through 727
      removed outlier: 4.533A  pdb=" N   ASP A 721 " --> pdb=" O   LEU A 717 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   LYS A 722 " --> pdb=" O   LYS A 718 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   GLU A 725 " --> pdb=" O   ASP A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 764 through 775
      removed outlier: 3.741A  pdb=" N   ILE A 768 " --> pdb=" O   LYS A 764 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 793 through 809
    Processing helix  chain 'A' and resid 814 through 836
    Processing helix  chain 'A' and resid 1773 through 1778
      removed outlier: 3.690A  pdb=" N   ASN A1778 " --> pdb=" O   LYS A1774 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1792 through 1796
    Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 31
      removed outlier: 6.870A  pdb=" N   VAL B  30 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE B 135 " --> pdb=" O   ASP B 107 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL B 110 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ARG B  65 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 31
      removed outlier: 6.870A  pdb=" N   VAL B  30 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE B 135 " --> pdb=" O   ASP B 107 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   VAL B 110 " --> pdb=" O   ARG B  65 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ARG B  65 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 37
    Processing sheet with id=AA4, first strand: chain 'A' and resid 628 through 629
      removed outlier: 4.517A  pdb=" N   TYR A 621 " --> pdb=" O   SER A 605 " (cutoff:3.500A)
      removed outlier: 7.326A  pdb=" N   SER A 605 " --> pdb=" O   TYR A 621 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   THR A 649 " --> pdb=" O   TYR A 580 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   ILE A 646 " --> pdb=" O   GLU A 692 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   ASN A 694 " --> pdb=" O   ILE A 646 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   LEU A 648 " --> pdb=" O   ASN A 694 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   LEU A 696 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   PHE A 650 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 744 through 746
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1654 through 1657
      removed outlier: 5.879A  pdb=" N   MET A1655 " --> pdb=" O   VAL A1692 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   VAL A1691 " --> pdb=" O   ILE A1718 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ILE A1765 " --> pdb=" O   LEU A1751 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1701 through 1704
      removed outlier: 6.043A  pdb=" N   ILE A1702 " --> pdb=" O   ASN A1732 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   VAL A1731 " --> pdb=" O   ASN A1783 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1844 through 1845
      removed outlier: 4.631A  pdb=" N   TYR A1844 " --> pdb=" O   ILE A1853 " (cutoff:3.500A)

    190 hydrogen bonds defined for protein.
    504 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.93

  Time building geometry restraints manager: 2.01 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: 2171
        1.34 -     1.46: 927
        1.46 -     1.57: 3604
        1.57 -     1.69: 0
        1.69 -     1.81: 39
  Bond restraints: 6741
  Sorted by residual:
  bond pdb=" C   VAL B  43 "
       pdb=" O   VAL B  43 "
    ideal  model  delta    sigma   weight residual
    1.236  1.220  0.016 1.19e-02 7.06e+03 1.84e+00
  bond pdb=" N   ASP A 614 "
       pdb=" CA  ASP A 614 "
    ideal  model  delta    sigma   weight residual
    1.457  1.474 -0.017 1.29e-02 6.01e+03 1.70e+00
  bond pdb=" CB  PRO A 644 "
       pdb=" CG  PRO A 644 "
    ideal  model  delta    sigma   weight residual
    1.492  1.552 -0.060 5.00e-02 4.00e+02 1.45e+00
  bond pdb=" C   PRO A1847 "
       pdb=" N   PRO A1848 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.33e+00
  bond pdb=" CG1 ILE A 578 "
       pdb=" CD1 ILE A 578 "
    ideal  model  delta    sigma   weight residual
    1.513  1.472  0.041 3.90e-02 6.57e+02 1.09e+00
  ... (remaining 6736 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.74: 9026
        2.74 -     5.47: 100
        5.47 -     8.21: 9
        8.21 -    10.94: 1
       10.94 -    13.68: 2
  Bond angle restraints: 9138
  Sorted by residual:
  angle pdb=" C   LEU A 519 "
        pdb=" CA  LEU A 519 "
        pdb=" CB  LEU A 519 "
      ideal   model   delta    sigma   weight residual
     116.63  111.22    5.41 1.16e+00 7.43e-01 2.18e+01
  angle pdb=" CA  LEU B  72 "
        pdb=" CB  LEU B  72 "
        pdb=" CG  LEU B  72 "
      ideal   model   delta    sigma   weight residual
     116.30  129.98  -13.68 3.50e+00 8.16e-02 1.53e+01
  angle pdb=" CG1 ILE A 640 "
        pdb=" CB  ILE A 640 "
        pdb=" CG2 ILE A 640 "
      ideal   model   delta    sigma   weight residual
     110.70   99.57   11.13 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" CA  PRO A 644 "
        pdb=" N   PRO A 644 "
        pdb=" CD  PRO A 644 "
      ideal   model   delta    sigma   weight residual
     112.00  107.10    4.90 1.40e+00 5.10e-01 1.23e+01
  angle pdb=" C   GLU A 613 "
        pdb=" N   ASP A 614 "
        pdb=" CA  ASP A 614 "
      ideal   model   delta    sigma   weight residual
     121.54  127.62   -6.08 1.91e+00 2.74e-01 1.01e+01
  ... (remaining 9133 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 3728
       17.27 -    34.54: 316
       34.54 -    51.80: 47
       51.80 -    69.07: 6
       69.07 -    86.34: 8
  Dihedral angle restraints: 4105
    sinusoidal: 1658
      harmonic: 2447
  Sorted by residual:
  dihedral pdb=" CA  ARG A 643 "
           pdb=" C   ARG A 643 "
           pdb=" N   PRO A 644 "
           pdb=" CA  PRO A 644 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -147.82  -32.18     0      5.00e+00 4.00e-02 4.14e+01
  dihedral pdb=" CA  LYS A1764 "
           pdb=" C   LYS A1764 "
           pdb=" N   ILE A1765 "
           pdb=" CA  ILE A1765 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.92  -27.08     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  ASP B 104 "
           pdb=" C   ASP B 104 "
           pdb=" N   THR B 105 "
           pdb=" CA  THR B 105 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.24   25.76     0      5.00e+00 4.00e-02 2.65e+01
  ... (remaining 4102 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 734
       0.047 -    0.095: 220
       0.095 -    0.142: 72
       0.142 -    0.189: 2
       0.189 -    0.237: 3
  Chirality restraints: 1031
  Sorted by residual:
  chirality pdb=" CB  ILE A 640 "
            pdb=" CA  ILE A 640 "
            pdb=" CG1 ILE A 640 "
            pdb=" CG2 ILE A 640 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.88   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CB  THR A 430 "
            pdb=" CA  THR A 430 "
            pdb=" OG1 THR A 430 "
            pdb=" CG2 THR A 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality pdb=" CA  PRO A 644 "
            pdb=" N   PRO A 644 "
            pdb=" C   PRO A 644 "
            pdb=" CB  PRO A 644 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 9.88e-01
  ... (remaining 1028 not shown)

  Planarity restraints: 1193
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 643 "   -0.092 5.00e-02 4.00e+02   1.39e-01 3.08e+01
        pdb=" N   PRO A 644 "    0.240 5.00e-02 4.00e+02
        pdb=" CA  PRO A 644 "   -0.075 5.00e-02 4.00e+02
        pdb=" CD  PRO A 644 "   -0.073 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 699 "   -0.009 2.00e-02 2.50e+03   1.88e-02 3.55e+00
        pdb=" C   ASN A 699 "    0.033 2.00e-02 2.50e+03
        pdb=" O   ASN A 699 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   MET A 700 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 462 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.41e+00
        pdb=" C   VAL A 462 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   VAL A 462 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LYS A 463 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1190 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 188
        2.70 -     3.25: 6969
        3.25 -     3.80: 9773
        3.80 -     4.35: 12870
        4.35 -     4.90: 21155
  Nonbonded interactions: 50955
  Sorted by model distance:
  nonbonded pdb=" O   ARG A1739 "
            pdb=" NZ  LYS A1764 "
     model   vdw
     2.153 3.120
  nonbonded pdb=" N   GLY A1814 "
            pdb=" O   TYR A1824 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OD2 ASP B  89 "
            pdb=" OH  TYR A1819 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD1 ASP A 423 "
            pdb=" OG1 THR A 426 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" O   ASN A 699 "
            pdb=" ND2 ASN A 699 "
     model   vdw
     2.269 3.120
  ... (remaining 50950 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.240
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.970
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6571
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   0.060   6741  Z= 0.226
  Angle     :  0.735  13.681   9138  Z= 0.390
  Chirality :  0.049   0.237   1031
  Planarity :  0.006   0.139   1193
  Dihedral  : 13.271  86.339   2522
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 9.30
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 10.06 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -1.42 (0.30), residues: 825
  helix:  0.74 (0.38), residues: 209
  sheet: -1.64 (0.44), residues: 141
  loop : -1.52 (0.29), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  40 
 HIS   0.009   0.002   HIS B  69 
 PHE   0.030   0.002   PHE A1676 
 TYR   0.014   0.001   TYR A1661 
 ARG   0.002   0.000   ARG A 643 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.773 
Fit side-chains
REVERT: B  108 GLN cc_start: 0.7970 (pm20) cc_final: 0.7311 (pp30)
REVERT: A  375 ILE cc_start: 0.6364 (tp) cc_final: 0.5961 (tp)
REVERT: A  384 ASN cc_start: 0.5695 (t0) cc_final: 0.5350 (t0)
REVERT: A  466 ILE cc_start: 0.8196 (tp) cc_final: 0.7912 (tp)
REVERT: A  705 ILE cc_start: 0.7805 (tp) cc_final: 0.7566 (tp)
REVERT: A  742 TYR cc_start: 0.7319 (m-80) cc_final: 0.7054 (m-10)
REVERT: A 1705 THR cc_start: 0.7932 (m) cc_final: 0.7684 (m)
REVERT: A 1727 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6572 (pt0)
REVERT: A 1752 MET cc_start: 0.5166 (ttp) cc_final: 0.4879 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.2050
  time to fit residues: 39.1517
Evaluate side-chains
  128 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 62 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 48 optimal weight:    5.9990
   chunk 75 optimal weight:    0.8980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 706 ASN
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.205845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.192910 restraints weight = 8705.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.4349 rms_B_bonded: 1.82
r_work: 0.4266 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.4146 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.4146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   6741  Z= 0.214
  Angle     :  0.691  12.679   9138  Z= 0.350
  Chirality :  0.049   0.216   1031
  Planarity :  0.005   0.134   1193
  Dihedral  :  6.168  34.514    894
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.12 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  :  7.70 %
    Favored  : 91.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -1.50 (0.30), residues: 825
  helix:  0.74 (0.37), residues: 213
  sheet: -1.88 (0.43), residues: 140
  loop : -1.56 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 520 
 HIS   0.003   0.001   HIS B  69 
 PHE   0.021   0.002   PHE A 780 
 TYR   0.021   0.002   TYR A1819 
 ARG   0.002   0.000   ARG B 118 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 144
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A  375 ILE cc_start: 0.6704 (tp) cc_final: 0.6261 (tp)
REVERT: A  384 ASN cc_start: 0.6046 (t0) cc_final: 0.5524 (t0)
REVERT: A  394 TYR cc_start: 0.5890 (m-80) cc_final: 0.4009 (m-10)
REVERT: A  410 LEU cc_start: 0.7981 (tp) cc_final: 0.7390 (mp)
REVERT: A  466 ILE cc_start: 0.8069 (tp) cc_final: 0.7806 (tp)
REVERT: A  569 LEU cc_start: 0.6474 (tp) cc_final: 0.6157 (pp)
REVERT: A  705 ILE cc_start: 0.8079 (tp) cc_final: 0.7750 (tp)
REVERT: A  709 GLU cc_start: 0.7464 (mp0) cc_final: 0.7227 (tm-30)
REVERT: A  766 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7654 (tt0)
REVERT: A  818 LYS cc_start: 0.8390 (tptt) cc_final: 0.7845 (tptt)
REVERT: A 1681 LEU cc_start: 0.7413 (tt) cc_final: 0.7203 (tt)
REVERT: A 1705 THR cc_start: 0.7729 (m) cc_final: 0.7519 (m)
REVERT: A 1727 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6467 (tp30)
REVERT: A 1734 ASN cc_start: 0.7972 (m110) cc_final: 0.7469 (p0)
REVERT: A 1735 ASP cc_start: 0.7377 (m-30) cc_final: 0.7071 (m-30)
REVERT: A 1752 MET cc_start: 0.5284 (ttp) cc_final: 0.5017 (ttp)
  outliers start: 5
  outliers final: 3
  residues processed: 146
  average time/residue: 0.1921
  time to fit residues: 37.2409
Evaluate side-chains
  134 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 131
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain A residue 1679 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 8 optimal weight:    0.4980
   chunk 80 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 81 optimal weight:    5.9990
   chunk 69 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.202067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.189118 restraints weight = 8695.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.4308 rms_B_bonded: 1.83
r_work: 0.4222 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4096 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6741  Z= 0.270
  Angle     :  0.704  12.394   9138  Z= 0.359
  Chirality :  0.050   0.198   1031
  Planarity :  0.006   0.133   1193
  Dihedral  :  6.342  35.300    894
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.94 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.48 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.66 (0.29), residues: 825
  helix:  0.51 (0.37), residues: 214
  sheet: -2.08 (0.42), residues: 140
  loop : -1.58 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 520 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.017   0.002   PHE A 459 
 TYR   0.019   0.002   TYR A1819 
 ARG   0.002   0.000   ARG A 499 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   54 LEU cc_start: 0.8419 (mt) cc_final: 0.8015 (tp)
REVERT: A  375 ILE cc_start: 0.6918 (tp) cc_final: 0.6517 (tp)
REVERT: A  384 ASN cc_start: 0.6002 (t0) cc_final: 0.5580 (t0)
REVERT: A  394 TYR cc_start: 0.6322 (m-80) cc_final: 0.3640 (m-80)
REVERT: A  401 LYS cc_start: 0.6930 (mtmt) cc_final: 0.6517 (mtmt)
REVERT: A  410 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7427 (mp)
REVERT: A  436 MET cc_start: 0.5838 (ptp) cc_final: 0.5563 (ptm)
REVERT: A  466 ILE cc_start: 0.8126 (tp) cc_final: 0.7862 (tp)
REVERT: A  569 LEU cc_start: 0.6622 (tp) cc_final: 0.6170 (pp)
REVERT: A  705 ILE cc_start: 0.8079 (tp) cc_final: 0.7749 (tp)
REVERT: A  709 GLU cc_start: 0.7589 (mp0) cc_final: 0.7314 (tm-30)
REVERT: A  781 ASN cc_start: 0.8002 (t0) cc_final: 0.7703 (t0)
REVERT: A 1681 LEU cc_start: 0.7726 (tt) cc_final: 0.7347 (tt)
REVERT: A 1705 THR cc_start: 0.7789 (m) cc_final: 0.7562 (m)
REVERT: A 1727 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6975 (pt0)
REVERT: A 1752 MET cc_start: 0.5325 (ttp) cc_final: 0.5096 (ttp)
  outliers start: 11
  outliers final: 9
  residues processed: 143
  average time/residue: 0.2047
  time to fit residues: 38.1468
Evaluate side-chains
  142 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue 1849 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 63 optimal weight:    0.1980
   chunk 71 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A 402 GLN
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4453 r_free = 0.4453 target = 0.203812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.191259 restraints weight = 8710.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.4323 rms_B_bonded: 1.78
r_work: 0.4239 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.4119 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7003
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6741  Z= 0.277
  Angle     :  0.706  11.886   9138  Z= 0.360
  Chirality :  0.050   0.186   1031
  Planarity :  0.006   0.132   1193
  Dihedral  :  6.413  35.103    894
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 10.18 %
    Favored  : 89.33 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.21 %
    Favored  : 82.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.29), residues: 825
  helix:  0.64 (0.37), residues: 202
  sheet: -2.27 (0.42), residues: 140
  loop : -1.56 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 520 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.020   0.002   PHE A 780 
 TYR   0.019   0.002   TYR A1819 
 ARG   0.002   0.000   ARG A 499 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: B   54 LEU cc_start: 0.8428 (mt) cc_final: 0.8018 (tp)
REVERT: A  375 ILE cc_start: 0.6974 (tp) cc_final: 0.6559 (tp)
REVERT: A  384 ASN cc_start: 0.5968 (t0) cc_final: 0.5577 (t0)
REVERT: A  394 TYR cc_start: 0.6468 (OUTLIER) cc_final: 0.3324 (m-80)
REVERT: A  401 LYS cc_start: 0.6965 (mtmt) cc_final: 0.6677 (mtmt)
REVERT: A  410 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7446 (mp)
REVERT: A  436 MET cc_start: 0.5553 (ptp) cc_final: 0.5265 (ptm)
REVERT: A  446 PHE cc_start: 0.8542 (t80) cc_final: 0.8339 (t80)
REVERT: A  466 ILE cc_start: 0.8134 (tp) cc_final: 0.7830 (tp)
REVERT: A  569 LEU cc_start: 0.6903 (tp) cc_final: 0.6403 (pp)
REVERT: A  709 GLU cc_start: 0.7530 (mp0) cc_final: 0.7292 (tm-30)
REVERT: A  776 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7017 (tt0)
REVERT: A  781 ASN cc_start: 0.7948 (t0) cc_final: 0.7714 (t0)
REVERT: A  818 LYS cc_start: 0.8447 (tptt) cc_final: 0.7875 (tptt)
REVERT: A 1681 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7291 (tt)
REVERT: A 1727 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7041 (pt0)
REVERT: A 1735 ASP cc_start: 0.7543 (m-30) cc_final: 0.7302 (m-30)
REVERT: A 1752 MET cc_start: 0.5137 (ttp) cc_final: 0.4881 (ttp)
  outliers start: 22
  outliers final: 13
  residues processed: 152
  average time/residue: 0.2158
  time to fit residues: 43.6193
Evaluate side-chains
  151 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  656 ASP
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  786 LYS
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1681 LEU
Chi-restraints excluded: chain A residue 1736 LEU
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1867 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 55 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0570
   chunk 64 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    0.9902

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

Flipped N/Q/H residues before XYZ refinement:
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1734 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.204050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.191116 restraints weight = 8666.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.4333 rms_B_bonded: 1.82
r_work: 0.4250 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.4127 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6953
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6741  Z= 0.197
  Angle     :  0.661  10.884   9138  Z= 0.333
  Chirality :  0.048   0.199   1031
  Planarity :  0.005   0.130   1193
  Dihedral  :  6.043  34.579    894
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.73 %
    Favored  : 90.79 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.47 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -1.66 (0.30), residues: 825
  helix:  0.54 (0.38), residues: 214
  sheet: -2.23 (0.42), residues: 140
  loop : -1.53 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  37 
 HIS   0.002   0.001   HIS A 579 
 PHE   0.009   0.001   PHE A 459 
 TYR   0.015   0.001   TYR A1819 
 ARG   0.001   0.000   ARG B  93 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 142
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
REVERT: B   54 LEU cc_start: 0.8361 (mt) cc_final: 0.7886 (tp)
REVERT: A  375 ILE cc_start: 0.6963 (tp) cc_final: 0.6546 (tp)
REVERT: A  384 ASN cc_start: 0.6185 (t0) cc_final: 0.5790 (t0)
REVERT: A  394 TYR cc_start: 0.6138 (OUTLIER) cc_final: 0.3046 (m-80)
REVERT: A  410 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7414 (mp)
REVERT: A  436 MET cc_start: 0.5531 (ptp) cc_final: 0.5221 (ptm)
REVERT: A  461 ASP cc_start: 0.7058 (p0) cc_final: 0.6770 (p0)
REVERT: A  466 ILE cc_start: 0.8081 (tp) cc_final: 0.7779 (tp)
REVERT: A  569 LEU cc_start: 0.6853 (tp) cc_final: 0.6388 (pp)
REVERT: A  709 GLU cc_start: 0.7538 (mp0) cc_final: 0.7312 (tm-30)
REVERT: A  766 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7667 (tt0)
REVERT: A  776 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6909 (tt0)
REVERT: A  818 LYS cc_start: 0.8412 (tptt) cc_final: 0.7793 (tptt)
REVERT: A 1727 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6425 (tp30)
REVERT: A 1752 MET cc_start: 0.5189 (ttp) cc_final: 0.4911 (ttp)
  outliers start: 21
  outliers final: 13
  residues processed: 153
  average time/residue: 0.1833
  time to fit residues: 37.3353
Evaluate side-chains
  149 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1770 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 15 optimal weight:    0.0000
   chunk 19 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 75 optimal weight:    0.2980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1744 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4462 r_free = 0.4462 target = 0.206314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.193555 restraints weight = 8752.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.4343 rms_B_bonded: 1.82
r_work: 0.4261 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.4137 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.4137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6741  Z= 0.175
  Angle     :  0.649  10.661   9138  Z= 0.328
  Chirality :  0.047   0.210   1031
  Planarity :  0.005   0.128   1193
  Dihedral  :  5.768  34.085    894
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.36 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.53 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -1.51 (0.30), residues: 825
  helix:  0.63 (0.38), residues: 214
  sheet: -2.12 (0.41), residues: 142
  loop : -1.42 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 520 
 HIS   0.002   0.001   HIS A 579 
 PHE   0.022   0.001   PHE A 780 
 TYR   0.013   0.001   TYR A1819 
 ARG   0.002   0.000   ARG B 127 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.713 
Fit side-chains
REVERT: B   53 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7169 (mt-10)
REVERT: B   54 LEU cc_start: 0.8290 (mt) cc_final: 0.7802 (tp)
REVERT: A  375 ILE cc_start: 0.6923 (tp) cc_final: 0.6329 (mm)
REVERT: A  384 ASN cc_start: 0.6144 (t0) cc_final: 0.5727 (t0)
REVERT: A  394 TYR cc_start: 0.6047 (OUTLIER) cc_final: 0.3397 (m-80)
REVERT: A  401 LYS cc_start: 0.6965 (mtmt) cc_final: 0.6680 (mtmt)
REVERT: A  410 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7401 (mp)
REVERT: A  436 MET cc_start: 0.5658 (ptp) cc_final: 0.5345 (ptm)
REVERT: A  448 MET cc_start: 0.6988 (mtm) cc_final: 0.6214 (ttp)
REVERT: A  461 ASP cc_start: 0.7050 (p0) cc_final: 0.6739 (p0)
REVERT: A  466 ILE cc_start: 0.8068 (tp) cc_final: 0.7776 (tp)
REVERT: A  709 GLU cc_start: 0.7565 (mp0) cc_final: 0.7325 (tm-30)
REVERT: A  766 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7616 (tt0)
REVERT: A  776 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6718 (tt0)
REVERT: A  818 LYS cc_start: 0.8506 (tptt) cc_final: 0.7874 (tptt)
REVERT: A 1681 LEU cc_start: 0.7823 (mt) cc_final: 0.7349 (tp)
REVERT: A 1727 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6347 (tp30)
REVERT: A 1752 MET cc_start: 0.5326 (ttp) cc_final: 0.5079 (ttp)
REVERT: A 1850 ASN cc_start: 0.7722 (m110) cc_final: 0.7449 (m-40)
  outliers start: 19
  outliers final: 12
  residues processed: 144
  average time/residue: 0.1850
  time to fit residues: 35.4306
Evaluate side-chains
  147 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  746 ILE
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1744 ASN
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1770 VAL
Chi-restraints excluded: chain A residue 1831 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 27 optimal weight:    0.0010
   chunk 54 optimal weight:    0.0980
   chunk 79 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0870
   chunk 57 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0030
   chunk 53 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.2374

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

Flipped N/Q/H residues before XYZ refinement:
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1744 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.211816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.198970 restraints weight = 8785.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.4388 rms_B_bonded: 1.82
r_work: 0.4308 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.4186 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.4186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6825
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060   6741  Z= 0.157
  Angle     :  0.629  10.469   9138  Z= 0.317
  Chirality :  0.047   0.218   1031
  Planarity :  0.005   0.126   1193
  Dihedral  :  5.495  33.609    894
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  7.03 %
    Favored  : 92.48 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.73 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -1.37 (0.30), residues: 825
  helix:  0.68 (0.38), residues: 214
  sheet: -2.04 (0.42), residues: 142
  loop : -1.29 (0.30), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 520 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.007   0.001   PHE A 701 
 TYR   0.010   0.001   TYR A1819 
 ARG   0.003   0.000   ARG A1739 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.687 
Fit side-chains
REVERT: B   53 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7169 (mt-10)
REVERT: B   54 LEU cc_start: 0.8176 (mt) cc_final: 0.7697 (tp)
REVERT: B  108 GLN cc_start: 0.8250 (pm20) cc_final: 0.7709 (pp30)
REVERT: A  375 ILE cc_start: 0.6769 (tp) cc_final: 0.6083 (mm)
REVERT: A  384 ASN cc_start: 0.5929 (t0) cc_final: 0.5558 (t0)
REVERT: A  394 TYR cc_start: 0.5578 (m-80) cc_final: 0.2906 (m-80)
REVERT: A  401 LYS cc_start: 0.6872 (mtmt) cc_final: 0.5925 (mtmt)
REVERT: A  410 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7360 (mp)
REVERT: A  411 ASN cc_start: 0.5683 (t0) cc_final: 0.5480 (t0)
REVERT: A  436 MET cc_start: 0.5594 (ptp) cc_final: 0.5306 (ptm)
REVERT: A  448 MET cc_start: 0.6962 (mtm) cc_final: 0.6090 (mpp)
REVERT: A  461 ASP cc_start: 0.6964 (p0) cc_final: 0.6721 (p0)
REVERT: A  466 ILE cc_start: 0.7981 (tp) cc_final: 0.7722 (tp)
REVERT: A  583 GLN cc_start: 0.8189 (tt0) cc_final: 0.7916 (tt0)
REVERT: A  766 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7560 (tt0)
REVERT: A  776 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6724 (tt0)
REVERT: A  818 LYS cc_start: 0.8486 (tptt) cc_final: 0.7859 (tptt)
REVERT: A 1681 LEU cc_start: 0.7490 (mt) cc_final: 0.7089 (tt)
  outliers start: 16
  outliers final: 8
  residues processed: 149
  average time/residue: 0.1744
  time to fit residues: 35.1313
Evaluate side-chains
  141 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1744 ASN
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1811 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 11 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 60 optimal weight:    7.9990
   chunk 56 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
B  18 ASN
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1744 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.204963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.192069 restraints weight = 8714.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.4323 rms_B_bonded: 1.85
r_work: 0.4239 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.4113 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.4113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6741  Z= 0.210
  Angle     :  0.664  10.751   9138  Z= 0.338
  Chirality :  0.048   0.212   1031
  Planarity :  0.006   0.126   1193
  Dihedral  :  5.735  33.627    894
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  8.24 %
    Favored  : 91.27 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 18.59 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -1.44 (0.30), residues: 825
  helix:  0.61 (0.38), residues: 215
  sheet: -2.23 (0.42), residues: 142
  loop : -1.28 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1742 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.022   0.002   PHE A 780 
 TYR   0.023   0.002   TYR A 742 
 ARG   0.002   0.000   ARG A1739 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.730 
Fit side-chains
REVERT: B   54 LEU cc_start: 0.8365 (mt) cc_final: 0.7882 (tp)
REVERT: B  108 GLN cc_start: 0.8405 (pm20) cc_final: 0.7839 (pp30)
REVERT: A  375 ILE cc_start: 0.7073 (tp) cc_final: 0.6676 (tp)
REVERT: A  384 ASN cc_start: 0.6010 (t0) cc_final: 0.5670 (t0)
REVERT: A  394 TYR cc_start: 0.5986 (m-80) cc_final: 0.3301 (m-80)
REVERT: A  401 LYS cc_start: 0.6955 (mtmt) cc_final: 0.6743 (mtmt)
REVERT: A  410 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7439 (mp)
REVERT: A  411 ASN cc_start: 0.5765 (t0) cc_final: 0.5553 (t0)
REVERT: A  436 MET cc_start: 0.5770 (ptp) cc_final: 0.5458 (ptm)
REVERT: A  448 MET cc_start: 0.7051 (mtm) cc_final: 0.6276 (ttp)
REVERT: A  461 ASP cc_start: 0.7095 (p0) cc_final: 0.6858 (p0)
REVERT: A  466 ILE cc_start: 0.8106 (tp) cc_final: 0.7813 (tp)
REVERT: A  601 THR cc_start: 0.8181 (p) cc_final: 0.7818 (p)
REVERT: A  766 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7593 (tt0)
REVERT: A  776 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6858 (tt0)
REVERT: A  818 LYS cc_start: 0.8507 (tptt) cc_final: 0.8179 (tptt)
REVERT: A 1681 LEU cc_start: 0.7640 (mt) cc_final: 0.7129 (tp)
  outliers start: 17
  outliers final: 13
  residues processed: 147
  average time/residue: 0.1806
  time to fit residues: 35.4728
Evaluate side-chains
  150 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  706 ASN
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1684 ILE
Chi-restraints excluded: chain A residue 1744 ASN
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1770 VAL
Chi-restraints excluded: chain A residue 1811 TYR
Chi-restraints excluded: chain A residue 1867 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0870
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** A 694 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1744 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.208424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.195606 restraints weight = 8838.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.4348 rms_B_bonded: 1.85
r_work: 0.4268 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.4143 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6885
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6741  Z= 0.167
  Angle     :  0.643  10.593   9138  Z= 0.326
  Chirality :  0.047   0.197   1031
  Planarity :  0.005   0.124   1193
  Dihedral  :  5.567  32.892    894
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  7.88 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 18.73 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -1.33 (0.31), residues: 825
  helix:  0.70 (0.38), residues: 214
  sheet: -2.15 (0.42), residues: 142
  loop : -1.21 (0.31), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 520 
 HIS   0.002   0.001   HIS B  69 
 PHE   0.007   0.001   PHE B  16 
 TYR   0.016   0.001   TYR A 580 
 ARG   0.003   0.000   ARG A1739 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.750 
Fit side-chains
REVERT: B   54 LEU cc_start: 0.8299 (mt) cc_final: 0.7823 (tp)
REVERT: B  108 GLN cc_start: 0.8344 (pm20) cc_final: 0.7821 (pp30)
REVERT: A  375 ILE cc_start: 0.6800 (tp) cc_final: 0.6113 (mm)
REVERT: A  384 ASN cc_start: 0.5903 (t0) cc_final: 0.5526 (t0)
REVERT: A  394 TYR cc_start: 0.5820 (OUTLIER) cc_final: 0.2821 (m-80)
REVERT: A  410 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7361 (mp)
REVERT: A  411 ASN cc_start: 0.5642 (t0) cc_final: 0.5435 (t0)
REVERT: A  436 MET cc_start: 0.5668 (ptp) cc_final: 0.5372 (ptm)
REVERT: A  448 MET cc_start: 0.7081 (mtm) cc_final: 0.6332 (ttm)
REVERT: A  461 ASP cc_start: 0.6978 (p0) cc_final: 0.6776 (p0)
REVERT: A  466 ILE cc_start: 0.8038 (tp) cc_final: 0.7775 (tp)
REVERT: A  601 THR cc_start: 0.7874 (p) cc_final: 0.7490 (p)
REVERT: A  709 GLU cc_start: 0.7305 (tt0) cc_final: 0.6810 (tm-30)
REVERT: A  766 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7602 (tt0)
REVERT: A  776 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6768 (tt0)
REVERT: A  818 LYS cc_start: 0.8486 (tptt) cc_final: 0.7846 (tptt)
  outliers start: 16
  outliers final: 11
  residues processed: 141
  average time/residue: 0.1765
  time to fit residues: 33.6139
Evaluate side-chains
  142 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1684 ILE
Chi-restraints excluded: chain A residue 1744 ASN
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1770 VAL
Chi-restraints excluded: chain A residue 1811 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   chunk 78 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 694 ASN
A 740 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.200132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.187515 restraints weight = 8866.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.4273 rms_B_bonded: 1.85
r_work: 0.4188 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.4060 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.2756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   6741  Z= 0.300
  Angle     :  0.736  10.988   9138  Z= 0.379
  Chirality :  0.050   0.185   1031
  Planarity :  0.006   0.125   1193
  Dihedral  :  6.205  33.533    894
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.33 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 19.12 %
    Favored  : 79.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -1.60 (0.30), residues: 825
  helix:  0.54 (0.38), residues: 209
  sheet: -2.36 (0.41), residues: 142
  loop : -1.38 (0.29), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A1742 
 HIS   0.003   0.001   HIS B  69 
 PHE   0.023   0.002   PHE A 780 
 TYR   0.026   0.002   TYR A 742 
 ARG   0.002   0.000   ARG A 643 

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
REVERT: B   54 LEU cc_start: 0.8556 (mt) cc_final: 0.8094 (tp)
REVERT: A  375 ILE cc_start: 0.7058 (tp) cc_final: 0.6593 (tp)
REVERT: A  384 ASN cc_start: 0.5843 (t0) cc_final: 0.5496 (t0)
REVERT: A  410 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7554 (mp)
REVERT: A  411 ASN cc_start: 0.5777 (t0) cc_final: 0.5573 (t0)
REVERT: A  436 MET cc_start: 0.5615 (ptp) cc_final: 0.5297 (ptm)
REVERT: A  448 MET cc_start: 0.7209 (mtm) cc_final: 0.6453 (ttp)
REVERT: A  461 ASP cc_start: 0.7079 (p0) cc_final: 0.6863 (p0)
REVERT: A  466 ILE cc_start: 0.8152 (tp) cc_final: 0.7859 (tp)
REVERT: A  569 LEU cc_start: 0.7307 (tp) cc_final: 0.6649 (pp)
REVERT: A  601 THR cc_start: 0.8312 (p) cc_final: 0.7998 (p)
REVERT: A  709 GLU cc_start: 0.7318 (tt0) cc_final: 0.6899 (tm-30)
REVERT: A  766 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7642 (tt0)
REVERT: A  776 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7093 (tt0)
REVERT: A  818 LYS cc_start: 0.8587 (tptt) cc_final: 0.8232 (tptt)
  outliers start: 14
  outliers final: 11
  residues processed: 140
  average time/residue: 0.1942
  time to fit residues: 36.1780
Evaluate side-chains
  147 residues out of total 753 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 134
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   60 LEU
Chi-restraints excluded: chain A residue  394 TYR
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  776 GLU
Chi-restraints excluded: chain A residue  837 VAL
Chi-restraints excluded: chain A residue 1676 PHE
Chi-restraints excluded: chain A residue 1684 ILE
Chi-restraints excluded: chain A residue 1763 VAL
Chi-restraints excluded: chain A residue 1770 VAL
Chi-restraints excluded: chain A residue 1811 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 66 optimal weight:    7.9990
   chunk 79 optimal weight:    0.0870
   chunk 53 optimal weight:    3.9990
   chunk 26 optimal weight:    0.3980
   chunk 21 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0010
   chunk 14 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.4964

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

Flipped N/Q/H residues before XYZ refinement:
A1744 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.209665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.196469 restraints weight = 8891.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.4336 rms_B_bonded: 1.98
r_work: 0.4248 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.4117 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.2878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6741  Z= 0.173
  Angle     :  0.675  10.713   9138  Z= 0.345
  Chirality :  0.047   0.161   1031
  Planarity :  0.005   0.123   1193
  Dihedral  :  5.749  32.409    894
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  :  7.27 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 19.79 %
    Favored  : 78.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    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: -1.37 (0.31), residues: 825
  helix:  0.75 (0.39), residues: 208
  sheet: -2.27 (0.41), residues: 142
  loop : -1.23 (0.30), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 520 
 HIS   0.003   0.001   HIS A 757 
 PHE   0.020   0.001   PHE A 431 
 TYR   0.022   0.001   TYR A 742 
 ARG   0.002   0.000   ARG B 126 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3260.10 seconds
wall clock time: 58 minutes 38.11 seconds (3518.11 seconds total)