Starting phenix.real_space_refine
on Wed Mar 12 04:24:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vjy_21220/03_2025/6vjy_21220.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vjy_21220/03_2025/6vjy_21220.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vjy_21220/03_2025/6vjy_21220.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vjy_21220/03_2025/6vjy_21220.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vjy_21220/03_2025/6vjy_21220.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vjy_21220/03_2025/6vjy_21220.cif"
  }
  resolution = 4.3
  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=   0.003
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      34      5.16       5
     C    4716      2.51       5
     N    1204      2.21       5
     O    1312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7266
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 2343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2343
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 275}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 4923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 603, 4923
          Classifications: {'peptide': 603}
          Link IDs: {'PTRANS': 20, 'TRANS': 582}
          Chain breaks: 4
  Time building chain proxies: 4.76, per 1000 atoms: 0.66
  Number of scatterers: 7266
  At special positions: 0
  Unit cell: (93.79, 124.3, 123.17, 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      34     16.00
     O    1312      8.00
     N    1204      7.00
     C    4716      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.90
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1702

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 0 sheets defined
      80.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 31
    Processing helix  chain 'B' and resid 34 through 43
    Processing helix  chain 'B' and resid 44 through 72
    Processing helix  chain 'B' and resid 75 through 99
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 105 through 135
      removed outlier: 3.537A  pdb=" N   ALA B 109 " --> pdb=" O   PHE B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 175
    Processing helix  chain 'B' and resid 179 through 220
      removed outlier: 3.516A  pdb=" N   THR B 183 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 294
      removed outlier: 4.071A  pdb=" N   TYR B 270 " --> pdb=" O   GLY B 266 " (cutoff:3.500A)
      Proline residue:  B 292  - end of helix
    Processing helix  chain 'B' and resid 296 through 324
      removed outlier: 4.214A  pdb=" N   LEU B 300 " --> pdb=" O   PRO B 296 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   TRP B 305 " --> pdb=" O   LYS B 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 35
    Processing helix  chain 'A' and resid 42 through 47
      removed outlier: 3.829A  pdb=" N   GLU A  46 " --> pdb=" O   ASP A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 81
    Processing helix  chain 'A' and resid 83 through 100
      removed outlier: 3.637A  pdb=" N   PHE A 100 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 116
      removed outlier: 3.645A  pdb=" N   THR A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 139
      removed outlier: 3.751A  pdb=" N   HIS A 128 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 156
      removed outlier: 3.518A  pdb=" N   ILE A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 184
      removed outlier: 3.630A  pdb=" N   ALA A 174 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 184 " --> pdb=" O   ARG A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 200
    Processing helix  chain 'A' and resid 207 through 225
      removed outlier: 3.604A  pdb=" N   TYR A 225 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 232
    Processing helix  chain 'A' and resid 315 through 331
      removed outlier: 3.668A  pdb=" N   ILE A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ILE A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 355
    Processing helix  chain 'A' and resid 357 through 361
      removed outlier: 3.751A  pdb=" N   ASN A 360 " --> pdb=" O   HIS A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 3.852A  pdb=" N   TYR A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 407
      removed outlier: 3.827A  pdb=" N   ARG A 407 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 426
      removed outlier: 3.549A  pdb=" N   TYR A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 441
    Processing helix  chain 'A' and resid 448 through 461
    Processing helix  chain 'A' and resid 462 through 465
    Processing helix  chain 'A' and resid 468 through 480
    Processing helix  chain 'A' and resid 481 through 495
      removed outlier: 3.670A  pdb=" N   TYR A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 517
      removed outlier: 4.202A  pdb=" N   GLU A 517 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
      removed outlier: 4.226A  pdb=" N   THR A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 549
      removed outlier: 3.951A  pdb=" N   ALA A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   GLU A 548 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   GLN A 549 " --> pdb=" O   GLN A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 563
    Processing helix  chain 'A' and resid 576 through 594
      removed outlier: 3.649A  pdb=" N   LYS A 580 " --> pdb=" O   THR A 576 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   SER A 585 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLY A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 609
      removed outlier: 3.651A  pdb=" N   VAL A 600 " --> pdb=" O   ILE A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 624
    Processing helix  chain 'A' and resid 627 through 640
    Processing helix  chain 'A' and resid 647 through 662
      removed outlier: 3.797A  pdb=" N   ASP A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 686
      removed outlier: 3.862A  pdb=" N   THR A 686 " --> pdb=" O   LEU A 682 " (cutoff:3.500A)

    508 hydrogen bonds defined for protein.
    1518 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: 1.98

  Time building geometry restraints manager: 2.25 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2272
        1.34 -     1.46: 1757
        1.46 -     1.58: 3355
        1.58 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 7445
  Sorted by residual:
  bond pdb=" N   ARG B 294 "
       pdb=" CA  ARG B 294 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.018 1.29e-02 6.01e+03 1.94e+00
  bond pdb=" C   ALA A 521 "
       pdb=" N   PRO A 522 "
    ideal  model  delta    sigma   weight residual
    1.337  1.320  0.017 1.24e-02 6.50e+03 1.84e+00
  bond pdb=" C   VAL B   2 "
       pdb=" O   VAL B   2 "
    ideal  model  delta    sigma   weight residual
    1.232  1.242 -0.011 1.01e-02 9.80e+03 1.12e+00
  bond pdb=" C   ASN B 153 "
       pdb=" O   ASN B 153 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.010 1.15e-02 7.56e+03 8.08e-01
  bond pdb=" CA  ILE A 596 "
       pdb=" CB  ILE A 596 "
    ideal  model  delta    sigma   weight residual
    1.545  1.537  0.008 9.10e-03 1.21e+04 8.03e-01
  ... (remaining 7440 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 9894
        1.97 -     3.94: 161
        3.94 -     5.92: 19
        5.92 -     7.89: 3
        7.89 -     9.86: 1
  Bond angle restraints: 10078
  Sorted by residual:
  angle pdb=" CA  ILE B 291 "
        pdb=" C   ILE B 291 "
        pdb=" N   PRO B 292 "
      ideal   model   delta    sigma   weight residual
     120.83  117.79    3.04 6.10e-01 2.69e+00 2.49e+01
  angle pdb=" O   ILE B 291 "
        pdb=" C   ILE B 291 "
        pdb=" N   PRO B 292 "
      ideal   model   delta    sigma   weight residual
     120.42  123.40   -2.98 6.40e-01 2.44e+00 2.17e+01
  angle pdb=" C   ASN A 533 "
        pdb=" N   ASP A 534 "
        pdb=" CA  ASP A 534 "
      ideal   model   delta    sigma   weight residual
     121.54  127.83   -6.29 1.91e+00 2.74e-01 1.09e+01
  angle pdb=" C   PHE B 214 "
        pdb=" N   TYR B 215 "
        pdb=" CA  TYR B 215 "
      ideal   model   delta    sigma   weight residual
     120.44  124.14   -3.70 1.30e+00 5.92e-01 8.10e+00
  angle pdb=" C   PHE A 201 "
        pdb=" N   ASN A 202 "
        pdb=" CA  ASN A 202 "
      ideal   model   delta    sigma   weight residual
     121.54  126.96   -5.42 1.91e+00 2.74e-01 8.05e+00
  ... (remaining 10073 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 3925
       17.78 -    35.55: 406
       35.55 -    53.33: 59
       53.33 -    71.11: 15
       71.11 -    88.89: 3
  Dihedral angle restraints: 4408
    sinusoidal: 1773
      harmonic: 2635
  Sorted by residual:
  dihedral pdb=" CA  ASN A 516 "
           pdb=" C   ASN A 516 "
           pdb=" N   GLU A 517 "
           pdb=" CA  GLU A 517 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.20   22.80     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASN A 645 "
           pdb=" C   ASN A 645 "
           pdb=" N   ARG A 646 "
           pdb=" CA  ARG A 646 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.37   20.63     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  ALA A  38 "
           pdb=" C   ALA A  38 "
           pdb=" N   LYS A  39 "
           pdb=" CA  LYS A  39 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.59  -18.41     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 4405 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 758
       0.036 -    0.072: 280
       0.072 -    0.109: 59
       0.109 -    0.145: 10
       0.145 -    0.181: 1
  Chirality restraints: 1108
  Sorted by residual:
  chirality pdb=" CA  ASP A 362 "
            pdb=" N   ASP A 362 "
            pdb=" C   ASP A 362 "
            pdb=" CB  ASP A 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.19e-01
  chirality pdb=" CA  VAL A 203 "
            pdb=" N   VAL A 203 "
            pdb=" C   VAL A 203 "
            pdb=" CB  VAL A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.82e-01
  chirality pdb=" CB  VAL B 303 "
            pdb=" CA  VAL B 303 "
            pdb=" CG1 VAL B 303 "
            pdb=" CG2 VAL B 303 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.61e-01
  ... (remaining 1105 not shown)

  Planarity restraints: 1259
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 295 "   -0.027 5.00e-02 4.00e+02   4.16e-02 2.77e+00
        pdb=" N   PRO B 296 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B 296 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 296 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 282 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   LYS B 282 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LYS B 282 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   THR B 283 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A  27 "   -0.023 5.00e-02 4.00e+02   3.48e-02 1.94e+00
        pdb=" N   PRO A  28 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A  28 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  28 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1256 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1297
        2.76 -     3.29: 7787
        3.29 -     3.83: 11944
        3.83 -     4.36: 12907
        4.36 -     4.90: 21608
  Nonbonded interactions: 55543
  Sorted by model distance:
  nonbonded pdb=" O   LEU B 118 "
            pdb=" ND1 HIS B 122 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" O   VAL B  25 "
            pdb=" OG1 THR B  29 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OE2 GLU A 639 "
            pdb=" ND1 HIS A 640 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OE1 GLN A 424 "
            pdb=" OH  TYR A 437 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   PHE B 147 "
            pdb=" OG  SER B 151 "
     model   vdw
     2.298 3.040
  ... (remaining 55538 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 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:             0.610
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     20.770
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
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   0.025   7445  Z= 0.224
  Angle     :  0.641   9.861  10078  Z= 0.388
  Chirality :  0.039   0.181   1108
  Planarity :  0.003   0.042   1259
  Dihedral  : 14.400  88.885   2706
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  5.83 %
    Favored  : 94.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.62 (0.25), residues: 869
  helix: -0.34 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop : -3.25 (0.35), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 632 
 HIS   0.005   0.001   HIS A 661 
 PHE   0.018   0.001   PHE A 528 
 TYR   0.017   0.001   TYR A 107 
 ARG   0.006   0.000   ARG A 589 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.9330 (tt) cc_final: 0.8903 (mt)
REVERT: B   81 HIS cc_start: 0.8819 (m170) cc_final: 0.8303 (m170)
REVERT: B  125 LEU cc_start: 0.9264 (tp) cc_final: 0.9036 (mt)
REVERT: B  130 GLU cc_start: 0.8918 (tp30) cc_final: 0.8542 (tm-30)
REVERT: B  152 PHE cc_start: 0.7690 (t80) cc_final: 0.7376 (t80)
REVERT: B  203 LEU cc_start: 0.9441 (mm) cc_final: 0.9146 (mm)
REVERT: B  307 ILE cc_start: 0.6196 (mm) cc_final: 0.5664 (mm)
REVERT: A  215 ARG cc_start: 0.9131 (ttm110) cc_final: 0.8898 (ttp80)
REVERT: A  238 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7915 (mt-10)
REVERT: A  317 ARG cc_start: 0.7755 (tpt170) cc_final: 0.7223 (mmp80)
REVERT: A  499 LYS cc_start: 0.8357 (mmmt) cc_final: 0.8052 (tmtt)
REVERT: A  510 LYS cc_start: 0.9133 (tttt) cc_final: 0.8695 (tttp)
REVERT: A  552 GLU cc_start: 0.8745 (pp20) cc_final: 0.8474 (pp20)
REVERT: A  593 GLN cc_start: 0.8803 (tt0) cc_final: 0.8397 (tm-30)
REVERT: A  609 MET cc_start: 0.8575 (ttt) cc_final: 0.8139 (tmm)
REVERT: A  666 TYR cc_start: 0.8388 (t80) cc_final: 0.7445 (t80)
REVERT: A  670 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8554 (mptt)
  outliers start: 1
  outliers final: 0
  residues processed: 213
  average time/residue: 0.2089
  time to fit residues: 58.4831
Evaluate side-chains
  138 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.5980
   chunk 66 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 101 HIS
B 218 GLN
A  86 GLN
A 123 ASN
A 179 GLN
A 186 ASN
A 191 GLN
A 257 ASN
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 GLN
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.107919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.081722 restraints weight = 22519.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.082322 restraints weight = 12429.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.082255 restraints weight = 8930.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7445  Z= 0.157
  Angle     :  0.587   9.975  10078  Z= 0.307
  Chirality :  0.038   0.214   1108
  Planarity :  0.004   0.044   1259
  Dihedral  :  4.458  20.341    975
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  3.68 %
    Favored  : 95.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.52 (0.28), residues: 869
  helix:  1.28 (0.20), residues: 661
  sheet:  None (None), residues: 0
  loop : -2.78 (0.38), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP B 321 
 HIS   0.012   0.001   HIS A 378 
 PHE   0.031   0.001   PHE B 214 
 TYR   0.022   0.001   TYR B 117 
 ARG   0.004   0.000   ARG B 279 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 192
  time to evaluate  : 0.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.9350 (tt) cc_final: 0.8983 (mt)
REVERT: B   81 HIS cc_start: 0.8867 (m170) cc_final: 0.8656 (m170)
REVERT: B  117 TYR cc_start: 0.8806 (m-80) cc_final: 0.8517 (m-80)
REVERT: B  127 ASP cc_start: 0.8275 (t0) cc_final: 0.7772 (t0)
REVERT: B  130 GLU cc_start: 0.8945 (tp30) cc_final: 0.8707 (tm-30)
REVERT: B  152 PHE cc_start: 0.7727 (t80) cc_final: 0.7377 (t80)
REVERT: B  307 ILE cc_start: 0.5613 (mm) cc_final: 0.5361 (mm)
REVERT: A   34 LEU cc_start: 0.9189 (mt) cc_final: 0.8982 (mt)
REVERT: A   72 LYS cc_start: 0.9278 (mttt) cc_final: 0.8688 (mptt)
REVERT: A  169 GLN cc_start: 0.9055 (pm20) cc_final: 0.8536 (pp30)
REVERT: A  215 ARG cc_start: 0.9178 (ttm110) cc_final: 0.8895 (ttp80)
REVERT: A  217 ILE cc_start: 0.9582 (mt) cc_final: 0.9192 (tp)
REVERT: A  349 LEU cc_start: 0.9709 (tp) cc_final: 0.9464 (tp)
REVERT: A  371 ARG cc_start: 0.8887 (ttm170) cc_final: 0.8641 (ttm110)
REVERT: A  466 ILE cc_start: 0.7977 (pt) cc_final: 0.7760 (tp)
REVERT: A  510 LYS cc_start: 0.9051 (tttt) cc_final: 0.8802 (tttp)
REVERT: A  609 MET cc_start: 0.8655 (ttt) cc_final: 0.8158 (tmm)
REVERT: A  666 TYR cc_start: 0.8603 (t80) cc_final: 0.8047 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 194
  average time/residue: 0.2146
  time to fit residues: 55.3624
Evaluate side-chains
  145 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 59 optimal weight:    9.9990
   chunk 80 optimal weight:    6.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 17 optimal weight:    8.9990
   chunk 18 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
B  79 HIS
B 218 GLN
A 111 GLN
A 123 ASN
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.106351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.080466 restraints weight = 23032.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.081177 restraints weight = 12558.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.081655 restraints weight = 8410.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7445  Z= 0.198
  Angle     :  0.583   8.996  10078  Z= 0.305
  Chirality :  0.039   0.223   1108
  Planarity :  0.003   0.038   1259
  Dihedral  :  4.368  21.035    975
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.68 %
    Favored  : 96.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.97 (0.28), residues: 869
  helix:  1.58 (0.19), residues: 663
  sheet:  None (None), residues: 0
  loop : -2.57 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP B 321 
 HIS   0.003   0.001   HIS A  88 
 PHE   0.022   0.001   PHE B 214 
 TYR   0.021   0.001   TYR A  74 
 ARG   0.006   0.000   ARG B  85 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 182
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.9371 (tt) cc_final: 0.9005 (mt)
REVERT: B  117 TYR cc_start: 0.8832 (m-80) cc_final: 0.8618 (m-80)
REVERT: B  127 ASP cc_start: 0.8231 (t0) cc_final: 0.7390 (t70)
REVERT: B  130 GLU cc_start: 0.8944 (tp30) cc_final: 0.8739 (tm-30)
REVERT: B  134 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8492 (tm-30)
REVERT: B  152 PHE cc_start: 0.7707 (t80) cc_final: 0.7317 (t80)
REVERT: A   34 LEU cc_start: 0.9196 (mt) cc_final: 0.8941 (mt)
REVERT: A   72 LYS cc_start: 0.9235 (mttt) cc_final: 0.8678 (mptt)
REVERT: A  169 GLN cc_start: 0.9067 (pm20) cc_final: 0.8615 (pp30)
REVERT: A  215 ARG cc_start: 0.9179 (ttm110) cc_final: 0.8767 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9563 (mt) cc_final: 0.9240 (tp)
REVERT: A  317 ARG cc_start: 0.8576 (mmp80) cc_final: 0.8369 (mmp80)
REVERT: A  321 ARG cc_start: 0.8563 (ptt-90) cc_final: 0.7888 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8829 (tm-30)
REVERT: A  466 ILE cc_start: 0.8033 (pt) cc_final: 0.7749 (tp)
REVERT: A  510 LYS cc_start: 0.9027 (tttt) cc_final: 0.8570 (tmtt)
REVERT: A  609 MET cc_start: 0.8584 (ttt) cc_final: 0.8080 (tmm)
REVERT: A  666 TYR cc_start: 0.8537 (t80) cc_final: 0.7983 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1996
  time to fit residues: 48.3799
Evaluate side-chains
  135 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 69 optimal weight:    7.9990
   chunk 78 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 51 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 14 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 64 optimal weight:    0.0980
   chunk 6 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
B  79 HIS
B  81 HIS
B 218 GLN
** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.106921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.081395 restraints weight = 23139.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.082291 restraints weight = 11070.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.082485 restraints weight = 9027.804|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7445  Z= 0.168
  Angle     :  0.570   8.948  10078  Z= 0.294
  Chirality :  0.038   0.214   1108
  Planarity :  0.003   0.033   1259
  Dihedral  :  4.218  20.960    975
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.68 %
    Favored  : 96.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.25 (0.28), residues: 869
  helix:  1.74 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.36 (0.41), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP B 321 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.019   0.001   PHE B 214 
 TYR   0.013   0.001   TYR A  74 
 ARG   0.004   0.000   ARG B  85 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 180
  time to evaluate  : 0.871 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 ASN cc_start: 0.8820 (m-40) cc_final: 0.8563 (m-40)
REVERT: B   69 LEU cc_start: 0.9375 (tt) cc_final: 0.9168 (pp)
REVERT: B  117 TYR cc_start: 0.8799 (m-80) cc_final: 0.8568 (m-80)
REVERT: B  127 ASP cc_start: 0.8260 (t0) cc_final: 0.7316 (t70)
REVERT: B  134 GLN cc_start: 0.8722 (tm-30) cc_final: 0.8469 (tm-30)
REVERT: B  152 PHE cc_start: 0.7652 (t80) cc_final: 0.7255 (t80)
REVERT: A   72 LYS cc_start: 0.9242 (mttt) cc_final: 0.8720 (mptt)
REVERT: A  215 ARG cc_start: 0.9160 (ttm110) cc_final: 0.8740 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9562 (mt) cc_final: 0.9258 (tp)
REVERT: A  321 ARG cc_start: 0.8590 (ptt-90) cc_final: 0.7876 (tmm-80)
REVERT: A  344 LYS cc_start: 0.9531 (tmtt) cc_final: 0.9277 (tmtt)
REVERT: A  353 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8811 (tm-30)
REVERT: A  371 ARG cc_start: 0.8864 (ttm170) cc_final: 0.8620 (ttm110)
REVERT: A  418 ASP cc_start: 0.9364 (m-30) cc_final: 0.9136 (m-30)
REVERT: A  609 MET cc_start: 0.8552 (ttt) cc_final: 0.8101 (tmm)
REVERT: A  666 TYR cc_start: 0.8514 (t80) cc_final: 0.7943 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 180
  average time/residue: 0.1974
  time to fit residues: 47.5228
Evaluate side-chains
  137 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 46 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0770
   chunk 79 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0570
   chunk 54 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    0.8260

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

Flipped N/Q/H residues before XYZ refinement:
B  79 HIS
B  81 HIS
B 163 GLN
B 218 GLN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 ASN
A 640 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.107590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.081417 restraints weight = 22750.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.082106 restraints weight = 11501.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.082703 restraints weight = 9056.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7445  Z= 0.165
  Angle     :  0.585   8.749  10078  Z= 0.298
  Chirality :  0.038   0.159   1108
  Planarity :  0.003   0.033   1259
  Dihedral  :  4.166  20.384    975
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.35 (0.28), residues: 869
  helix:  1.81 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -2.25 (0.41), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.002   TRP B 321 
 HIS   0.004   0.001   HIS A 122 
 PHE   0.020   0.001   PHE B 214 
 TYR   0.011   0.001   TYR B 117 
 ARG   0.005   0.000   ARG A 653 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 MET cc_start: 0.8478 (ptt) cc_final: 0.8270 (tmm)
REVERT: B   69 LEU cc_start: 0.9397 (tt) cc_final: 0.9168 (pp)
REVERT: B  127 ASP cc_start: 0.8249 (t0) cc_final: 0.8010 (t70)
REVERT: B  134 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8481 (tm-30)
REVERT: B  152 PHE cc_start: 0.7570 (t80) cc_final: 0.7202 (t80)
REVERT: A   72 LYS cc_start: 0.9305 (mttt) cc_final: 0.8760 (mptt)
REVERT: A  131 LEU cc_start: 0.8883 (mm) cc_final: 0.8607 (tp)
REVERT: A  215 ARG cc_start: 0.9168 (ttm110) cc_final: 0.8769 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9526 (mt) cc_final: 0.9241 (tp)
REVERT: A  353 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8799 (tm-30)
REVERT: A  371 ARG cc_start: 0.8877 (ttm170) cc_final: 0.8660 (ttm110)
REVERT: A  393 MET cc_start: 0.8851 (ppp) cc_final: 0.8567 (ppp)
REVERT: A  418 ASP cc_start: 0.9222 (m-30) cc_final: 0.9021 (m-30)
REVERT: A  441 MET cc_start: 0.9035 (tmm) cc_final: 0.8667 (tmm)
REVERT: A  514 ASP cc_start: 0.8414 (m-30) cc_final: 0.8171 (m-30)
REVERT: A  562 MET cc_start: 0.9037 (mtt) cc_final: 0.8598 (mmm)
REVERT: A  609 MET cc_start: 0.8546 (ttt) cc_final: 0.8119 (tmm)
REVERT: A  666 TYR cc_start: 0.8506 (t80) cc_final: 0.7964 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.1894
  time to fit residues: 45.6283
Evaluate side-chains
  140 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   chunk 68 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 23 optimal weight:    9.9990
   chunk 56 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
B 189 GLN
B 218 GLN
A 113 HIS
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.107514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.081537 restraints weight = 23250.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.081231 restraints weight = 13651.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.081892 restraints weight = 10932.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7445  Z= 0.153
  Angle     :  0.580   8.653  10078  Z= 0.296
  Chirality :  0.038   0.224   1108
  Planarity :  0.003   0.040   1259
  Dihedral  :  4.067  20.535    975
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  2.03 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.60 (0.29), residues: 869
  helix:  1.96 (0.19), residues: 665
  sheet:  None (None), residues: 0
  loop : -2.11 (0.42), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.002   TRP B 321 
 HIS   0.006   0.001   HIS A 122 
 PHE   0.016   0.001   PHE B 214 
 TYR   0.036   0.001   TYR B 117 
 ARG   0.005   0.000   ARG A 653 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 172
  time to evaluate  : 0.793 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 MET cc_start: 0.8412 (ptt) cc_final: 0.8155 (tmm)
REVERT: B   69 LEU cc_start: 0.9403 (tt) cc_final: 0.9160 (pp)
REVERT: B  117 TYR cc_start: 0.8819 (m-80) cc_final: 0.8494 (m-80)
REVERT: B  127 ASP cc_start: 0.8981 (t0) cc_final: 0.8045 (t70)
REVERT: B  134 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8479 (tm-30)
REVERT: B  215 TYR cc_start: 0.4277 (t80) cc_final: 0.3963 (t80)
REVERT: A   72 LYS cc_start: 0.9285 (mttt) cc_final: 0.8791 (mptt)
REVERT: A  215 ARG cc_start: 0.9157 (ttm110) cc_final: 0.8734 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9535 (mt) cc_final: 0.9261 (tp)
REVERT: A  321 ARG cc_start: 0.8651 (ppt170) cc_final: 0.8147 (tmm-80)
REVERT: A  345 ASN cc_start: 0.9492 (m-40) cc_final: 0.9147 (m-40)
REVERT: A  353 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8778 (tm-30)
REVERT: A  371 ARG cc_start: 0.8820 (ttm170) cc_final: 0.8611 (ttm110)
REVERT: A  441 MET cc_start: 0.8995 (tmm) cc_final: 0.8617 (tmm)
REVERT: A  514 ASP cc_start: 0.8399 (m-30) cc_final: 0.8132 (m-30)
REVERT: A  555 GLN cc_start: 0.8981 (mt0) cc_final: 0.8574 (mt0)
REVERT: A  562 MET cc_start: 0.9084 (mtt) cc_final: 0.8639 (mmm)
REVERT: A  609 MET cc_start: 0.8588 (ttt) cc_final: 0.8189 (tmm)
REVERT: A  666 TYR cc_start: 0.8440 (t80) cc_final: 0.7843 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 175
  average time/residue: 0.1751
  time to fit residues: 41.4176
Evaluate side-chains
  135 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 7 optimal weight:    9.9990
   chunk 44 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
B 189 GLN
B 218 GLN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.108074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.081841 restraints weight = 22807.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.082846 restraints weight = 13615.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.083471 restraints weight = 8567.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7445  Z= 0.156
  Angle     :  0.604   9.363  10078  Z= 0.307
  Chirality :  0.038   0.166   1108
  Planarity :  0.003   0.044   1259
  Dihedral  :  4.086  28.523    975
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.52 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.67 (0.29), residues: 869
  helix:  1.99 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -2.00 (0.43), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.002   TRP B 321 
 HIS   0.005   0.001   HIS A 122 
 PHE   0.015   0.001   PHE B 214 
 TYR   0.029   0.001   TYR B 117 
 ARG   0.006   0.000   ARG A 653 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   49 MET cc_start: 0.8449 (ptt) cc_final: 0.8171 (tmm)
REVERT: B   69 LEU cc_start: 0.9412 (tt) cc_final: 0.9156 (pp)
REVERT: B  117 TYR cc_start: 0.8911 (m-80) cc_final: 0.8580 (m-80)
REVERT: B  127 ASP cc_start: 0.8931 (t0) cc_final: 0.7962 (t70)
REVERT: B  134 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8460 (tm-30)
REVERT: B  215 TYR cc_start: 0.4163 (t80) cc_final: 0.3815 (t80)
REVERT: A   78 TRP cc_start: 0.9199 (m100) cc_final: 0.8978 (m100)
REVERT: A  131 LEU cc_start: 0.8879 (mm) cc_final: 0.8619 (tp)
REVERT: A  215 ARG cc_start: 0.9147 (ttm110) cc_final: 0.8713 (ttp-110)
REVERT: A  321 ARG cc_start: 0.8592 (ppt170) cc_final: 0.8034 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8750 (tm-30)
REVERT: A  418 ASP cc_start: 0.9234 (m-30) cc_final: 0.8996 (m-30)
REVERT: A  441 MET cc_start: 0.9049 (tmm) cc_final: 0.8665 (tmm)
REVERT: A  514 ASP cc_start: 0.8439 (m-30) cc_final: 0.8174 (m-30)
REVERT: A  562 MET cc_start: 0.9032 (mtt) cc_final: 0.8604 (mmm)
REVERT: A  609 MET cc_start: 0.8531 (ttt) cc_final: 0.8103 (tmm)
REVERT: A  666 TYR cc_start: 0.8385 (t80) cc_final: 0.7821 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1833
  time to fit residues: 42.5295
Evaluate side-chains
  125 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   chunk 11 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
B 218 GLN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 453 GLN
A 611 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.107493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.080884 restraints weight = 23551.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.080797 restraints weight = 13636.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.081502 restraints weight = 10939.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7445  Z= 0.173
  Angle     :  0.645   9.339  10078  Z= 0.327
  Chirality :  0.040   0.257   1108
  Planarity :  0.003   0.044   1259
  Dihedral  :  4.038  22.443    975
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.69 (0.29), residues: 869
  helix:  2.00 (0.19), residues: 665
  sheet:  None (None), residues: 0
  loop : -1.97 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.071   0.002   TRP B 321 
 HIS   0.005   0.001   HIS A 122 
 PHE   0.016   0.001   PHE B 214 
 TYR   0.027   0.001   TYR B 117 
 ARG   0.006   0.000   ARG A 653 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.811 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 LEU cc_start: 0.9426 (tt) cc_final: 0.9197 (pp)
REVERT: B  117 TYR cc_start: 0.8960 (m-80) cc_final: 0.8639 (m-80)
REVERT: B  118 LEU cc_start: 0.9500 (mt) cc_final: 0.9293 (mt)
REVERT: B  122 HIS cc_start: 0.9348 (m90) cc_final: 0.9123 (m90)
REVERT: B  127 ASP cc_start: 0.8941 (t0) cc_final: 0.7956 (t70)
REVERT: B  134 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8521 (tm-30)
REVERT: B  215 TYR cc_start: 0.4169 (t80) cc_final: 0.3827 (t80)
REVERT: A  124 MET cc_start: 0.8590 (mmt) cc_final: 0.8266 (mmt)
REVERT: A  131 LEU cc_start: 0.8901 (mm) cc_final: 0.8596 (tp)
REVERT: A  215 ARG cc_start: 0.9187 (ttm110) cc_final: 0.8811 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9527 (mt) cc_final: 0.9163 (tp)
REVERT: A  321 ARG cc_start: 0.8621 (ppt170) cc_final: 0.8059 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8767 (tm-30)
REVERT: A  361 LEU cc_start: 0.9486 (mp) cc_final: 0.9266 (mm)
REVERT: A  418 ASP cc_start: 0.9238 (m-30) cc_final: 0.8953 (m-30)
REVERT: A  441 MET cc_start: 0.9031 (tmm) cc_final: 0.8640 (tmm)
REVERT: A  514 ASP cc_start: 0.8437 (m-30) cc_final: 0.8164 (m-30)
REVERT: A  520 MET cc_start: 0.8732 (mmp) cc_final: 0.8399 (mmm)
REVERT: A  562 MET cc_start: 0.9096 (mtt) cc_final: 0.8728 (mmm)
REVERT: A  609 MET cc_start: 0.8580 (ttt) cc_final: 0.8134 (tmm)
REVERT: A  666 TYR cc_start: 0.8433 (t80) cc_final: 0.7796 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1777
  time to fit residues: 39.8287
Evaluate side-chains
  124 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 69 optimal weight:    0.3980
   chunk 17 optimal weight:   30.0000
   chunk 27 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 86 optimal weight:    1.9990
   chunk 54 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0270
   overall best weight:    1.4844

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
B 189 GLN
B 218 GLN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.105716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.078858 restraints weight = 23211.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.080038 restraints weight = 14771.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.081072 restraints weight = 8874.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7445  Z= 0.195
  Angle     :  0.672   9.343  10078  Z= 0.341
  Chirality :  0.041   0.247   1108
  Planarity :  0.003   0.046   1259
  Dihedral  :  4.131  24.537    975
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.89 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.65 (0.29), residues: 869
  helix:  1.96 (0.19), residues: 665
  sheet:  None (None), residues: 0
  loop : -1.94 (0.43), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.074   0.002   TRP B 321 
 HIS   0.005   0.001   HIS A 122 
 PHE   0.013   0.001   PHE B 214 
 TYR   0.025   0.001   TYR B 117 
 ARG   0.006   0.000   ARG A 653 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 160
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 ASN cc_start: 0.8933 (m-40) cc_final: 0.8541 (m-40)
REVERT: B   69 LEU cc_start: 0.9418 (tt) cc_final: 0.9179 (pp)
REVERT: B  117 TYR cc_start: 0.8991 (m-80) cc_final: 0.8559 (m-80)
REVERT: B  127 ASP cc_start: 0.8858 (t70) cc_final: 0.8539 (t0)
REVERT: B  215 TYR cc_start: 0.4177 (t80) cc_final: 0.3830 (t80)
REVERT: A  124 MET cc_start: 0.8560 (mmt) cc_final: 0.8301 (mmt)
REVERT: A  131 LEU cc_start: 0.8920 (mm) cc_final: 0.8531 (tp)
REVERT: A  152 MET cc_start: 0.7541 (tpt) cc_final: 0.6259 (tpt)
REVERT: A  215 ARG cc_start: 0.9212 (ttm110) cc_final: 0.8808 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9524 (mt) cc_final: 0.9301 (tp)
REVERT: A  321 ARG cc_start: 0.8596 (ppt170) cc_final: 0.7925 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8720 (tm-30)
REVERT: A  361 LEU cc_start: 0.9478 (mp) cc_final: 0.9265 (mm)
REVERT: A  418 ASP cc_start: 0.9254 (m-30) cc_final: 0.8971 (m-30)
REVERT: A  520 MET cc_start: 0.8736 (mmp) cc_final: 0.8433 (mmm)
REVERT: A  562 MET cc_start: 0.9044 (mtt) cc_final: 0.8662 (mmm)
REVERT: A  609 MET cc_start: 0.8554 (ttt) cc_final: 0.8104 (tmm)
REVERT: A  666 TYR cc_start: 0.8436 (t80) cc_final: 0.7796 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 160
  average time/residue: 0.1792
  time to fit residues: 39.2522
Evaluate side-chains
  120 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 84 optimal weight:    0.3980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
B 189 GLN
B 218 GLN
A 186 ASN
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 453 GLN
A 611 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.107530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.081632 restraints weight = 23818.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.080087 restraints weight = 15307.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.081139 restraints weight = 12064.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7445  Z= 0.172
  Angle     :  0.660  10.223  10078  Z= 0.334
  Chirality :  0.040   0.228   1108
  Planarity :  0.003   0.046   1259
  Dihedral  :  4.069  20.953    975
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.13 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.65 (0.29), residues: 869
  helix:  2.00 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -2.01 (0.43), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.072   0.002   TRP B 321 
 HIS   0.005   0.001   HIS A 122 
 PHE   0.013   0.001   PHE B 214 
 TYR   0.026   0.001   TYR B 117 
 ARG   0.005   0.000   ARG A 317 

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

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

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1738 Ramachandran restraints generated.
    869 Oldfield, 0 Emsley, 869 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 163
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 ASN cc_start: 0.8935 (m-40) cc_final: 0.8650 (m-40)
REVERT: B   49 MET cc_start: 0.8466 (ptt) cc_final: 0.8176 (tmm)
REVERT: B   69 LEU cc_start: 0.9429 (tt) cc_final: 0.9198 (pp)
REVERT: B  117 TYR cc_start: 0.8950 (m-80) cc_final: 0.8545 (m-80)
REVERT: B  118 LEU cc_start: 0.9519 (mt) cc_final: 0.9317 (mt)
REVERT: B  122 HIS cc_start: 0.9362 (m90) cc_final: 0.9079 (m90)
REVERT: B  130 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8367 (mm-30)
REVERT: B  215 TYR cc_start: 0.4183 (t80) cc_final: 0.3831 (t80)
REVERT: A   72 LYS cc_start: 0.9237 (mttt) cc_final: 0.8680 (mmtm)
REVERT: A  124 MET cc_start: 0.8510 (mmt) cc_final: 0.8248 (mmt)
REVERT: A  152 MET cc_start: 0.7362 (tpt) cc_final: 0.6132 (tpt)
REVERT: A  215 ARG cc_start: 0.9189 (ttm110) cc_final: 0.8765 (ttp-110)
REVERT: A  217 ILE cc_start: 0.9515 (mt) cc_final: 0.9298 (tp)
REVERT: A  321 ARG cc_start: 0.8604 (ppt170) cc_final: 0.7928 (tmm-80)
REVERT: A  353 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8759 (tm-30)
REVERT: A  361 LEU cc_start: 0.9487 (mp) cc_final: 0.9262 (mm)
REVERT: A  418 ASP cc_start: 0.9226 (m-30) cc_final: 0.8966 (m-30)
REVERT: A  473 MET cc_start: 0.8568 (mmp) cc_final: 0.7360 (mmp)
REVERT: A  520 MET cc_start: 0.8701 (mmp) cc_final: 0.8396 (mmm)
REVERT: A  562 MET cc_start: 0.9064 (mtt) cc_final: 0.8737 (mmm)
REVERT: A  609 MET cc_start: 0.8547 (ttt) cc_final: 0.8082 (tmm)
  outliers start: 2
  outliers final: 1
  residues processed: 165
  average time/residue: 0.1746
  time to fit residues: 40.2531
Evaluate side-chains
  125 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 30 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 17 optimal weight:   30.0000
   chunk 6 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 65 optimal weight:    1.9990
   chunk 25 optimal weight:    0.1980
   chunk 14 optimal weight:    0.0170
   overall best weight:    0.7822

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

Flipped N/Q/H residues before XYZ refinement:
B  81 HIS
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.107994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.081043 restraints weight = 23316.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.082369 restraints weight = 14305.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.082716 restraints weight = 8914.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.4161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7445  Z= 0.164
  Angle     :  0.656   9.628  10078  Z= 0.331
  Chirality :  0.040   0.213   1108
  Planarity :  0.003   0.045   1259
  Dihedral  :  4.033  22.217    975
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.70 (0.29), residues: 869
  helix:  2.03 (0.19), residues: 660
  sheet:  None (None), residues: 0
  loop : -1.94 (0.43), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.076   0.002   TRP B 321 
 HIS   0.005   0.001   HIS A 122 
 PHE   0.010   0.001   PHE B 110 
 TYR   0.026   0.001   TYR B 117 
 ARG   0.005   0.000   ARG A 317 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2388.91 seconds
wall clock time: 42 minutes 41.64 seconds (2561.64 seconds total)