Starting phenix.real_space_refine
on Wed Mar 12 02:47:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vk1_21223/03_2025/6vk1_21223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vk1_21223/03_2025/6vk1_21223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vk1_21223/03_2025/6vk1_21223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vk1_21223/03_2025/6vk1_21223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vk1_21223/03_2025/6vk1_21223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vk1_21223/03_2025/6vk1_21223.cif"
  }
  resolution = 3.9
  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=   0.008
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    4712      2.51       5
     N    1203      2.21       5
     O    1310      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 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: 7259
  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: 4916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4916
          Classifications: {'peptide': 602}
          Link IDs: {'PTRANS': 20, 'TRANS': 581}
          Chain breaks: 5
  Time building chain proxies: 4.23, per 1000 atoms: 0.58
  Number of scatterers: 7259
  At special positions: 0
  Unit cell: (78.3, 99.9, 152.55, 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    1310      8.00
     N    1203      7.00
     C    4712      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: 1.70
  Conformation dependent library (CDL) restraints added in 950.8 milliseconds
  

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1700

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 0 sheets defined
      79.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  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 71
    Processing helix  chain 'B' and resid 75 through 98
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 99 through 100
      No H-bonds generated for 'chain 'B' and resid 99 through 100'
    Processing helix  chain 'B' and resid 101 through 104
    Processing helix  chain 'B' and resid 105 through 135
      removed outlier: 3.856A  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: 3.560A  pdb=" N   THR B 183 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 294
      removed outlier: 4.022A  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 297 through 324
    Processing helix  chain 'A' and resid 27 through 35
    Processing helix  chain 'A' and resid 42 through 47
    Processing helix  chain 'A' and resid 66 through 81
    Processing helix  chain 'A' and resid 83 through 100
      removed outlier: 3.583A  pdb=" N   PHE A 100 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 116
      removed outlier: 3.877A  pdb=" N   THR A 108 " --> pdb=" O   GLU A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 138
    Processing helix  chain 'A' and resid 142 through 156
      removed outlier: 3.676A  pdb=" N   ILE A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 184
      removed outlier: 3.604A  pdb=" N   ALA A 174 " --> pdb=" O   ASP A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 200
      removed outlier: 3.601A  pdb=" N   LYS A 190 " --> pdb=" O   ASN A 186 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLY A 200 " --> pdb=" O   LYS A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 224
      removed outlier: 4.131A  pdb=" N   SER A 210 " --> pdb=" O   ASN A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 232
      removed outlier: 3.630A  pdb=" N   TRP A 230 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 329
      removed outlier: 4.318A  pdb=" N   ILE A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 355
      removed outlier: 3.932A  pdb=" N   ALA A 343 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 361
      removed outlier: 5.558A  pdb=" N   ASP A 359 " --> pdb=" O   PRO A 356 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN A 360 " --> pdb=" O   HIS A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 4.058A  pdb=" N   TYR A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 407
      removed outlier: 3.931A  pdb=" N   ARG A 407 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 426
      removed outlier: 3.869A  pdb=" N   TYR A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 441
      removed outlier: 3.995A  pdb=" N   ALA A 433 " --> pdb=" O   ASN A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 461
    Processing helix  chain 'A' and resid 462 through 465
      removed outlier: 4.080A  pdb=" N   LYS A 465 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
      No H-bonds generated for '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: 3.708A  pdb=" N   TYR A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 517
      removed outlier: 3.767A  pdb=" N   THR A 505 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   GLU A 517 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 532
      removed outlier: 3.911A  pdb=" N   THR A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 548
      removed outlier: 4.023A  pdb=" N   ALA A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   GLU A 548 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 563
    Processing helix  chain 'A' and resid 576 through 594
      removed outlier: 3.805A  pdb=" N   SER A 585 " --> pdb=" O   THR A 581 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLY A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 609
      removed outlier: 3.683A  pdb=" N   VAL A 600 " --> pdb=" O   ILE A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 624
      removed outlier: 3.662A  pdb=" N   LEU A 618 " --> pdb=" O   LYS A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 647 through 662
      removed outlier: 3.686A  pdb=" N   ASP A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 682

    498 hydrogen bonds defined for protein.
    1488 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: 2.05 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: 2267
        1.34 -     1.46: 1464
        1.46 -     1.58: 3645
        1.58 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 7437
  Sorted by residual:
  bond pdb=" N   HIS B 101 "
       pdb=" CA  HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.29e-02 6.01e+03 7.91e+00
  bond pdb=" N   GLU B 102 "
       pdb=" CA  GLU B 102 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.031 1.27e-02 6.20e+03 6.07e+00
  bond pdb=" N   ARG B 103 "
       pdb=" CA  ARG B 103 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.028 1.16e-02 7.43e+03 5.72e+00
  bond pdb=" CE1 HIS B 101 "
       pdb=" NE2 HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.321  1.338 -0.017 1.00e-02 1.00e+04 3.03e+00
  bond pdb=" CA  HIS B 101 "
       pdb=" C   HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.523  1.538 -0.015 1.34e-02 5.57e+03 1.30e+00
  ... (remaining 7432 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 9622
        1.28 -     2.57: 370
        2.57 -     3.85: 56
        3.85 -     5.14: 13
        5.14 -     6.42: 4
  Bond angle restraints: 10065
  Sorted by residual:
  angle pdb=" N   GLY A 253 "
        pdb=" CA  GLY A 253 "
        pdb=" C   GLY A 253 "
      ideal   model   delta    sigma   weight residual
     112.48  118.47   -5.99 1.21e+00 6.83e-01 2.45e+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  127.96   -6.42 1.91e+00 2.74e-01 1.13e+01
  angle pdb=" C   PHE A 201 "
        pdb=" N   ASN A 202 "
        pdb=" CA  ASN A 202 "
      ideal   model   delta    sigma   weight residual
     121.54  127.39   -5.85 1.91e+00 2.74e-01 9.38e+00
  angle pdb=" CA  ARG B 103 "
        pdb=" C   ARG B 103 "
        pdb=" O   ARG B 103 "
      ideal   model   delta    sigma   weight residual
     121.07  117.91    3.16 1.10e+00 8.26e-01 8.26e+00
  angle pdb=" C   PHE B 214 "
        pdb=" N   TYR B 215 "
        pdb=" CA  TYR B 215 "
      ideal   model   delta    sigma   weight residual
     120.79  124.54   -3.75 1.39e+00 5.18e-01 7.29e+00
  ... (remaining 10060 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 3880
       17.65 -    35.31: 440
       35.31 -    52.96: 64
       52.96 -    70.61: 14
       70.61 -    88.26: 5
  Dihedral angle restraints: 4403
    sinusoidal: 1772
      harmonic: 2631
  Sorted by residual:
  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  157.61   22.39     0      5.00e+00 4.00e-02 2.01e+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 -160.05  -19.95     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  SER A 245 "
           pdb=" C   SER A 245 "
           pdb=" N   ASP A 246 "
           pdb=" CA  ASP A 246 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.30   19.70     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 4400 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 784
       0.037 -    0.075: 265
       0.075 -    0.112: 46
       0.112 -    0.149: 10
       0.149 -    0.187: 1
  Chirality restraints: 1106
  Sorted by residual:
  chirality pdb=" CA  LEU A 252 "
            pdb=" N   LEU A 252 "
            pdb=" C   LEU A 252 "
            pdb=" CB  LEU A 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.70e-01
  chirality pdb=" CB  VAL B 155 "
            pdb=" CA  VAL B 155 "
            pdb=" CG1 VAL B 155 "
            pdb=" CG2 VAL B 155 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.79e-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    2.57   -0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 1103 not shown)

  Planarity restraints: 1257
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 295 "   -0.029 5.00e-02 4.00e+02   4.33e-02 3.01e+00
        pdb=" N   PRO B 296 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO B 296 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 296 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B   2 "    0.027 5.00e-02 4.00e+02   4.15e-02 2.76e+00
        pdb=" N   PRO B   3 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B   3 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B   3 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 102 "   -0.008 2.00e-02 2.50e+03   1.55e-02 2.41e+00
        pdb=" C   GLU B 102 "    0.027 2.00e-02 2.50e+03
        pdb=" O   GLU B 102 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ARG B 103 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1254 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1500
        2.78 -     3.31: 7437
        3.31 -     3.84: 11683
        3.84 -     4.37: 12815
        4.37 -     4.90: 21844
  Nonbonded interactions: 55279
  Sorted by model distance:
  nonbonded pdb=" O   THR B 144 "
            pdb=" OG  SER B 148 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" CD1 LEU B 285 "
            pdb=" ND1 HIS B 286 "
     model   vdw
     2.250 3.540
  nonbonded pdb=" O   ASP B 179 "
            pdb=" OG  SER B 182 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR A 425 "
            pdb=" OE1 GLN A 453 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OH  TYR B 104 "
            pdb=" OD2 ASP B 179 "
     model   vdw
     2.296 3.040
  ... (remaining 55274 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:             0.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.790
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
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   0.036   7437  Z= 0.174
  Angle     :  0.590   6.422  10065  Z= 0.362
  Chirality :  0.038   0.187   1106
  Planarity :  0.004   0.043   1257
  Dihedral  : 14.769  88.262   2703
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  5.08 %
    Favored  : 94.80 %
  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: -1.86 (0.25), residues: 866
  helix: -0.46 (0.18), residues: 659
  sheet:  None (None), residues: 0
  loop : -3.52 (0.32), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  27 
 HIS   0.004   0.001   HIS A 143 
 PHE   0.013   0.001   PHE B 147 
 TYR   0.011   0.001   TYR A  74 
 ARG   0.003   0.000   ARG A 265 

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 237
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8411 (mt0) cc_final: 0.8099 (tm-30)
REVERT: B   60 THR cc_start: 0.9237 (p) cc_final: 0.8945 (p)
REVERT: B   85 ARG cc_start: 0.8645 (mmt180) cc_final: 0.7809 (mmm160)
REVERT: B  103 ARG cc_start: 0.5868 (mpp80) cc_final: 0.4330 (ptm-80)
REVERT: B  118 LEU cc_start: 0.8831 (mt) cc_final: 0.8259 (mt)
REVERT: B  119 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8932 (mtpp)
REVERT: B  122 HIS cc_start: 0.8242 (m90) cc_final: 0.7997 (m170)
REVERT: B  124 ILE cc_start: 0.9062 (pt) cc_final: 0.8740 (pt)
REVERT: B  197 LEU cc_start: 0.9220 (tp) cc_final: 0.8927 (tp)
REVERT: B  202 ASN cc_start: 0.7890 (t0) cc_final: 0.7326 (t0)
REVERT: B  206 GLN cc_start: 0.7832 (mt0) cc_final: 0.7278 (mt0)
REVERT: A  149 LEU cc_start: 0.9375 (tp) cc_final: 0.9067 (mm)
REVERT: A  238 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7682 (mt-10)
REVERT: A  416 CYS cc_start: 0.8270 (m) cc_final: 0.8053 (m)
REVERT: A  639 GLU cc_start: 0.8036 (pp20) cc_final: 0.7656 (pt0)
REVERT: A  642 LEU cc_start: 0.6236 (pp) cc_final: 0.5211 (pp)
REVERT: A  676 LEU cc_start: 0.7656 (tp) cc_final: 0.7311 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 238
  average time/residue: 0.2023
  time to fit residues: 62.4631
Evaluate side-chains
  169 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 66 optimal weight:    0.4980
   chunk 37 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 44 optimal weight:   10.0000
   chunk 35 optimal weight:    7.9990
   chunk 68 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
B  79 HIS
B 189 GLN
A  86 GLN
A 101 ASN
A 113 HIS
A 202 ASN
A 593 GLN
A 620 GLN
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.154375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.123300 restraints weight = 12454.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.120017 restraints weight = 10227.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.121437 restraints weight = 10369.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7437  Z= 0.219
  Angle     :  0.623  13.932  10065  Z= 0.323
  Chirality :  0.040   0.200   1106
  Planarity :  0.004   0.047   1257
  Dihedral  :  4.476  21.221    973
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 14.21 %
    Favored  : 83.25 %
  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:  0.20 (0.27), residues: 866
  helix:  1.06 (0.19), residues: 663
  sheet:  None (None), residues: 0
  loop : -3.05 (0.35), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 305 
 HIS   0.009   0.001   HIS B 122 
 PHE   0.019   0.001   PHE B 293 
 TYR   0.017   0.002   TYR A 486 
 ARG   0.002   0.000   ARG B  75 

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 176
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8620 (mt0) cc_final: 0.8153 (tm-30)
REVERT: B   60 THR cc_start: 0.9220 (p) cc_final: 0.8974 (p)
REVERT: B   83 PHE cc_start: 0.6932 (t80) cc_final: 0.6659 (t80)
REVERT: B   85 ARG cc_start: 0.8978 (mmt180) cc_final: 0.7711 (mmm160)
REVERT: B  103 ARG cc_start: 0.6073 (mpp80) cc_final: 0.4004 (ttp-170)
REVERT: B  118 LEU cc_start: 0.8863 (mt) cc_final: 0.8570 (mm)
REVERT: B  123 TRP cc_start: 0.8123 (m-10) cc_final: 0.7630 (m100)
REVERT: B  128 ARG cc_start: 0.7888 (mmm160) cc_final: 0.7634 (mmm160)
REVERT: B  189 GLN cc_start: 0.8985 (mp10) cc_final: 0.8637 (mp10)
REVERT: B  197 LEU cc_start: 0.9373 (tp) cc_final: 0.8960 (tp)
REVERT: A   74 TYR cc_start: 0.7430 (t80) cc_final: 0.7094 (t80)
REVERT: A  149 LEU cc_start: 0.9374 (tp) cc_final: 0.9036 (mm)
REVERT: A  248 GLU cc_start: 0.7501 (mp0) cc_final: 0.7149 (mp0)
REVERT: A  416 CYS cc_start: 0.8456 (m) cc_final: 0.8087 (m)
REVERT: A  423 ASN cc_start: 0.8453 (p0) cc_final: 0.8218 (p0)
REVERT: A  656 ASP cc_start: 0.7685 (m-30) cc_final: 0.7392 (m-30)
  outliers start: 20
  outliers final: 8
  residues processed: 181
  average time/residue: 0.1930
  time to fit residues: 47.7268
Evaluate side-chains
  171 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 163
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  147 PHE
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  631 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 46 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 374 GLN
A 638 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.150842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.119906 restraints weight = 12711.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.118104 restraints weight = 11580.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.119256 restraints weight = 11717.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   7437  Z= 0.306
  Angle     :  0.651  11.460  10065  Z= 0.341
  Chirality :  0.041   0.134   1106
  Planarity :  0.004   0.052   1257
  Dihedral  :  4.614  23.641    973
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.64 %
    Favored  : 79.31 %
  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:  0.58 (0.28), residues: 866
  helix:  1.34 (0.19), residues: 663
  sheet:  None (None), residues: 0
  loop : -2.91 (0.36), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 541 
 HIS   0.006   0.001   HIS B  79 
 PHE   0.025   0.002   PHE A 367 
 TYR   0.014   0.002   TYR A 636 
 ARG   0.004   0.000   ARG A 406 

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.816 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8699 (mt0) cc_final: 0.8243 (tm-30)
REVERT: B   60 THR cc_start: 0.9223 (p) cc_final: 0.8982 (p)
REVERT: B   83 PHE cc_start: 0.6739 (t80) cc_final: 0.6498 (t80)
REVERT: B   85 ARG cc_start: 0.8859 (mmt180) cc_final: 0.7798 (mmm160)
REVERT: B  103 ARG cc_start: 0.6136 (mpp80) cc_final: 0.3618 (ttp-170)
REVERT: B  128 ARG cc_start: 0.7961 (mmm160) cc_final: 0.7705 (mmm160)
REVERT: B  142 MET cc_start: 0.4929 (tpt) cc_final: 0.4687 (tpt)
REVERT: B  195 MET cc_start: 0.8195 (mtp) cc_final: 0.7665 (mtp)
REVERT: B  197 LEU cc_start: 0.9376 (tp) cc_final: 0.9023 (tp)
REVERT: A   74 TYR cc_start: 0.7646 (t80) cc_final: 0.7242 (t80)
REVERT: A  416 CYS cc_start: 0.8471 (m) cc_final: 0.8055 (m)
REVERT: A  423 ASN cc_start: 0.8439 (p0) cc_final: 0.8203 (p0)
REVERT: A  620 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7137 (tm130)
REVERT: A  656 ASP cc_start: 0.7731 (m-30) cc_final: 0.7481 (m-30)
  outliers start: 24
  outliers final: 12
  residues processed: 180
  average time/residue: 0.1762
  time to fit residues: 43.1867
Evaluate side-chains
  167 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 154
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   77 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  620 GLN
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  658 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 77 optimal weight:    0.4980
   chunk 68 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9990
   chunk 32 optimal weight:    8.9990
   chunk 27 optimal weight:   10.0000
   chunk 78 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   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 286 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.155416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.124235 restraints weight = 12740.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.121864 restraints weight = 11239.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.123333 restraints weight = 10257.134|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7437  Z= 0.165
  Angle     :  0.599  11.084  10065  Z= 0.303
  Chirality :  0.039   0.244   1106
  Planarity :  0.004   0.051   1257
  Dihedral  :  4.366  27.279    973
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.16 %
    Favored  : 78.43 %
  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:  1.27 (0.28), residues: 866
  helix:  1.83 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -2.49 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 632 
 HIS   0.008   0.001   HIS B 122 
 PHE   0.034   0.001   PHE B 277 
 TYR   0.011   0.001   TYR A  90 
 ARG   0.002   0.000   ARG A 406 

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 180
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8593 (mt0) cc_final: 0.8099 (tm-30)
REVERT: B   60 THR cc_start: 0.9059 (p) cc_final: 0.8847 (p)
REVERT: B   83 PHE cc_start: 0.6795 (t80) cc_final: 0.6529 (t80)
REVERT: B   85 ARG cc_start: 0.8830 (mmt180) cc_final: 0.7765 (mmm160)
REVERT: B  128 ARG cc_start: 0.7742 (mmm160) cc_final: 0.7525 (mmm160)
REVERT: B  192 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7943 (mm-30)
REVERT: B  195 MET cc_start: 0.8023 (mtp) cc_final: 0.7708 (mtp)
REVERT: B  197 LEU cc_start: 0.9369 (tp) cc_final: 0.8953 (tp)
REVERT: B  271 GLU cc_start: 0.7696 (pt0) cc_final: 0.7171 (pt0)
REVERT: B  272 LYS cc_start: 0.8307 (mptt) cc_final: 0.7894 (mmtm)
REVERT: A  248 GLU cc_start: 0.7445 (mp0) cc_final: 0.6954 (mp0)
REVERT: A  406 ARG cc_start: 0.8446 (mtm110) cc_final: 0.8077 (mtm110)
REVERT: A  423 ASN cc_start: 0.8354 (p0) cc_final: 0.8091 (p0)
REVERT: A  473 MET cc_start: 0.8541 (mmt) cc_final: 0.8312 (mmt)
REVERT: A  656 ASP cc_start: 0.7635 (m-30) cc_final: 0.7400 (m-30)
  outliers start: 19
  outliers final: 9
  residues processed: 191
  average time/residue: 0.1689
  time to fit residues: 44.5903
Evaluate side-chains
  170 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 161
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue   82 ILE
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  639 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 64 optimal weight:    5.9990
   chunk 37 optimal weight:    0.6980
   chunk 39 optimal weight:    6.9990
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 633 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.154169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.122707 restraints weight = 12667.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.120611 restraints weight = 10354.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.121730 restraints weight = 10634.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7437  Z= 0.208
  Angle     :  0.626  10.312  10065  Z= 0.320
  Chirality :  0.041   0.288   1106
  Planarity :  0.004   0.050   1257
  Dihedral  :  4.392  26.406    973
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 19.54 %
    Favored  : 76.90 %
  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:  1.31 (0.28), residues: 866
  helix:  1.85 (0.20), residues: 659
  sheet:  None (None), residues: 0
  loop : -2.49 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  78 
 HIS   0.006   0.001   HIS B 122 
 PHE   0.033   0.002   PHE B 147 
 TYR   0.016   0.001   TYR A 436 
 ARG   0.002   0.000   ARG B  75 

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 176
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8627 (mt0) cc_final: 0.8075 (tm-30)
REVERT: B   60 THR cc_start: 0.9080 (p) cc_final: 0.8866 (p)
REVERT: B   75 ARG cc_start: 0.7950 (ptm-80) cc_final: 0.7432 (ptp90)
REVERT: B   78 GLU cc_start: 0.8430 (pt0) cc_final: 0.8077 (pt0)
REVERT: B   83 PHE cc_start: 0.6870 (t80) cc_final: 0.6648 (t80)
REVERT: B   85 ARG cc_start: 0.8853 (mmt180) cc_final: 0.7772 (mmm160)
REVERT: B  191 MET cc_start: 0.7625 (tmm) cc_final: 0.7413 (tmm)
REVERT: B  192 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7959 (mm-30)
REVERT: B  195 MET cc_start: 0.8027 (mtp) cc_final: 0.7587 (mtp)
REVERT: B  197 LEU cc_start: 0.9350 (tp) cc_final: 0.8940 (tp)
REVERT: B  318 TRP cc_start: 0.6736 (t-100) cc_final: 0.5914 (t-100)
REVERT: A   74 TYR cc_start: 0.7984 (t80) cc_final: 0.7654 (t80)
REVERT: A  152 MET cc_start: 0.8995 (tpp) cc_final: 0.8579 (tpp)
REVERT: A  344 LYS cc_start: 0.9026 (ttpp) cc_final: 0.8601 (ttpt)
REVERT: A  465 LYS cc_start: 0.7151 (mptt) cc_final: 0.6787 (tptt)
REVERT: A  473 MET cc_start: 0.8545 (mmt) cc_final: 0.8322 (mmt)
REVERT: A  624 LEU cc_start: 0.8922 (mp) cc_final: 0.8618 (mt)
REVERT: A  656 ASP cc_start: 0.7669 (m-30) cc_final: 0.7435 (m-30)
  outliers start: 28
  outliers final: 17
  residues processed: 193
  average time/residue: 0.1622
  time to fit residues: 43.6357
Evaluate side-chains
  181 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  633 ASN
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  682 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 56 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 52 optimal weight:    0.3980
   chunk 80 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 29 optimal weight:    8.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
A 633 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.152999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.121284 restraints weight = 12732.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.119630 restraints weight = 10796.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.120692 restraints weight = 10332.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   7437  Z= 0.253
  Angle     :  0.681  10.095  10065  Z= 0.349
  Chirality :  0.042   0.288   1106
  Planarity :  0.004   0.051   1257
  Dihedral  :  4.395  24.850    973
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 20.30 %
    Favored  : 75.51 %
  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:  1.23 (0.28), residues: 866
  helix:  1.79 (0.20), residues: 660
  sheet:  None (None), residues: 0
  loop : -2.57 (0.39), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  78 
 HIS   0.005   0.001   HIS B 122 
 PHE   0.028   0.002   PHE B 277 
 TYR   0.016   0.002   TYR A 436 
 ARG   0.002   0.000   ARG B  75 

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 163
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8602 (mt0) cc_final: 0.8081 (tm-30)
REVERT: B   75 ARG cc_start: 0.7857 (ptm-80) cc_final: 0.7635 (ptp90)
REVERT: B   78 GLU cc_start: 0.8407 (pt0) cc_final: 0.8105 (pt0)
REVERT: B   85 ARG cc_start: 0.8783 (mmt180) cc_final: 0.7832 (mmm160)
REVERT: B  192 GLU cc_start: 0.8319 (mm-30) cc_final: 0.8020 (mm-30)
REVERT: B  195 MET cc_start: 0.7981 (mtp) cc_final: 0.7502 (mtp)
REVERT: B  197 LEU cc_start: 0.9363 (tp) cc_final: 0.8939 (tp)
REVERT: B  318 TRP cc_start: 0.6676 (t-100) cc_final: 0.5843 (t-100)
REVERT: A  344 LYS cc_start: 0.8955 (ttpp) cc_final: 0.8573 (ttpt)
REVERT: A  465 LYS cc_start: 0.7228 (mptt) cc_final: 0.6801 (tptt)
REVERT: A  656 ASP cc_start: 0.7746 (m-30) cc_final: 0.7508 (m-30)
  outliers start: 33
  outliers final: 24
  residues processed: 182
  average time/residue: 0.1625
  time to fit residues: 41.3450
Evaluate side-chains
  183 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 159
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  113 LEU
Chi-restraints excluded: chain B residue  156 LEU
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  633 ASN
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  671 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 85 optimal weight:    0.5980
   chunk 17 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 62 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 4 optimal weight:    0.9980
   chunk 75 optimal weight:    0.7980
   chunk 55 optimal weight:    9.9990
   chunk 78 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 504 ASN
A 633 ASN
** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.156164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.123677 restraints weight = 12704.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.123323 restraints weight = 9438.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.124565 restraints weight = 8860.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7437  Z= 0.182
  Angle     :  0.661   9.747  10065  Z= 0.337
  Chirality :  0.040   0.267   1106
  Planarity :  0.004   0.051   1257
  Dihedral  :  4.326  26.837    973
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 21.57 %
    Favored  : 75.00 %
  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:  1.51 (0.29), residues: 866
  helix:  2.05 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -2.55 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A  78 
 HIS   0.004   0.001   HIS B 122 
 PHE   0.039   0.001   PHE B 147 
 TYR   0.016   0.001   TYR A 436 
 ARG   0.009   0.000   ARG B  75 

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 168
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8447 (mt0) cc_final: 0.8090 (tm-30)
REVERT: B   85 ARG cc_start: 0.8620 (mmt180) cc_final: 0.7671 (mmm160)
REVERT: B   92 ASN cc_start: 0.8694 (t0) cc_final: 0.8389 (t0)
REVERT: B  191 MET cc_start: 0.7584 (tmm) cc_final: 0.7183 (tmm)
REVERT: B  192 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7917 (mm-30)
REVERT: B  195 MET cc_start: 0.7783 (mtp) cc_final: 0.7264 (mtp)
REVERT: B  197 LEU cc_start: 0.9303 (tp) cc_final: 0.8950 (tp)
REVERT: B  318 TRP cc_start: 0.6593 (t-100) cc_final: 0.5752 (t-100)
REVERT: A   74 TYR cc_start: 0.7978 (t80) cc_final: 0.7526 (t80)
REVERT: A  248 GLU cc_start: 0.6989 (mp0) cc_final: 0.6776 (mp0)
REVERT: A  344 LYS cc_start: 0.8827 (ttpp) cc_final: 0.8505 (ttpt)
REVERT: A  465 LYS cc_start: 0.7136 (mptt) cc_final: 0.6752 (tptt)
REVERT: A  656 ASP cc_start: 0.7527 (m-30) cc_final: 0.7314 (m-30)
  outliers start: 27
  outliers final: 17
  residues processed: 185
  average time/residue: 0.1580
  time to fit residues: 40.9180
Evaluate side-chains
  174 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 157
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  285 LEU
Chi-restraints excluded: chain B residue  297 MET
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  639 GLU
Chi-restraints excluded: chain A residue  671 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 40 optimal weight:    0.2980
   chunk 35 optimal weight:   10.0000
   chunk 10 optimal weight:    0.0770
   chunk 64 optimal weight:    0.0980
   chunk 59 optimal weight:    0.8980
   chunk 77 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 32 optimal weight:    0.2980
   chunk 69 optimal weight:    9.9990
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    0.3338

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

Flipped N/Q/H residues before XYZ refinement:
A 117 GLN
A 633 ASN
A 638 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.158809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.126754 restraints weight = 12622.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.127418 restraints weight = 10836.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.128489 restraints weight = 11504.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.3898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7437  Z= 0.166
  Angle     :  0.675  11.490  10065  Z= 0.340
  Chirality :  0.040   0.308   1106
  Planarity :  0.004   0.052   1257
  Dihedral  :  4.148  27.691    973
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 22.46 %
    Favored  : 75.13 %
  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:  1.79 (0.29), residues: 866
  helix:  2.24 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -2.37 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  78 
 HIS   0.004   0.001   HIS B 122 
 PHE   0.043   0.001   PHE B 147 
 TYR   0.015   0.001   TYR A 436 
 ARG   0.002   0.000   ARG A 535 

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 GLN cc_start: 0.8351 (mt0) cc_final: 0.8000 (tm-30)
REVERT: B   85 ARG cc_start: 0.8573 (mmt180) cc_final: 0.7842 (mmm160)
REVERT: B  191 MET cc_start: 0.7381 (tmm) cc_final: 0.7011 (tmm)
REVERT: B  195 MET cc_start: 0.7440 (mtp) cc_final: 0.7037 (mtp)
REVERT: B  197 LEU cc_start: 0.9243 (tp) cc_final: 0.8854 (tp)
REVERT: B  297 MET cc_start: 0.6309 (mtt) cc_final: 0.6056 (ptm)
REVERT: B  318 TRP cc_start: 0.6331 (t-100) cc_final: 0.5515 (t-100)
REVERT: A  465 LYS cc_start: 0.7030 (mptt) cc_final: 0.6720 (tptt)
REVERT: A  656 ASP cc_start: 0.7629 (m-30) cc_final: 0.7336 (m-30)
  outliers start: 19
  outliers final: 14
  residues processed: 178
  average time/residue: 0.1730
  time to fit residues: 42.7277
Evaluate side-chains
  169 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 155
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  633 ASN
Chi-restraints excluded: chain A residue  638 HIS
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  682 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 ASN
** A 638 HIS ** 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 = 0.3832 r_free = 0.3832 target = 0.155583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.123877 restraints weight = 12776.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.123251 restraints weight = 11391.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.124833 restraints weight = 10244.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.3937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   7437  Z= 0.222
  Angle     :  0.719  12.030  10065  Z= 0.366
  Chirality :  0.043   0.328   1106
  Planarity :  0.004   0.049   1257
  Dihedral  :  4.194  29.127    973
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.27 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 24.11 %
    Favored  : 73.73 %
  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: 866
  helix:  2.19 (0.20), residues: 654
  sheet:  None (None), residues: 0
  loop : -2.51 (0.38), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A  78 
 HIS   0.009   0.001   HIS A 638 
 PHE   0.037   0.002   PHE B 147 
 TYR   0.016   0.001   TYR A 436 
 ARG   0.004   0.000   ARG B  75 

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.3200 (pmm) cc_final: 0.2468 (ptt)
REVERT: B    9 GLN cc_start: 0.8457 (mt0) cc_final: 0.8019 (tm-30)
REVERT: B   85 ARG cc_start: 0.8593 (mmt180) cc_final: 0.7853 (mmm160)
REVERT: B  195 MET cc_start: 0.7610 (mtp) cc_final: 0.7372 (mtp)
REVERT: B  197 LEU cc_start: 0.9298 (tp) cc_final: 0.8940 (tp)
REVERT: B  318 TRP cc_start: 0.6446 (t-100) cc_final: 0.5620 (t-100)
REVERT: A   74 TYR cc_start: 0.7974 (t80) cc_final: 0.7671 (t80)
REVERT: A  344 LYS cc_start: 0.8968 (ttpp) cc_final: 0.8510 (ptmm)
REVERT: A  465 LYS cc_start: 0.7058 (mptt) cc_final: 0.6685 (tptt)
REVERT: A  656 ASP cc_start: 0.7601 (m-30) cc_final: 0.7346 (m-30)
  outliers start: 17
  outliers final: 14
  residues processed: 168
  average time/residue: 0.1704
  time to fit residues: 39.8136
Evaluate side-chains
  173 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 159
  time to evaluate  : 0.804 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  633 ASN
Chi-restraints excluded: chain A residue  671 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 0 optimal weight:   20.0000
   chunk 30 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 34 optimal weight:    8.9990
   chunk 27 optimal weight:    5.9990
   chunk 6 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 21 optimal weight:    9.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 ASN
** A 638 HIS ** 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 = 0.3860 r_free = 0.3860 target = 0.157790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.126562 restraints weight = 12851.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.128055 restraints weight = 10681.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.128946 restraints weight = 8405.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7437  Z= 0.183
  Angle     :  0.737  11.933  10065  Z= 0.365
  Chirality :  0.042   0.323   1106
  Planarity :  0.004   0.050   1257
  Dihedral  :  4.137  27.697    973
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 24.75 %
    Favored  : 73.22 %
  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:  1.74 (0.29), residues: 866
  helix:  2.22 (0.20), residues: 653
  sheet:  None (None), residues: 0
  loop : -2.47 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A  78 
 HIS   0.003   0.001   HIS B 122 
 PHE   0.042   0.002   PHE B 277 
 TYR   0.016   0.001   TYR A 436 
 ARG   0.003   0.000   ARG B  75 

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

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

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1732 Ramachandran restraints generated.
    866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 161
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    1 MET cc_start: 0.3115 (pmm) cc_final: 0.2440 (ptt)
REVERT: B    9 GLN cc_start: 0.8466 (mt0) cc_final: 0.8040 (tm-30)
REVERT: B   85 ARG cc_start: 0.8692 (mmt180) cc_final: 0.7941 (mmm160)
REVERT: B   92 ASN cc_start: 0.8713 (t0) cc_final: 0.8419 (t0)
REVERT: B  195 MET cc_start: 0.7391 (mtp) cc_final: 0.7147 (mtp)
REVERT: B  197 LEU cc_start: 0.9277 (tp) cc_final: 0.8940 (tp)
REVERT: B  318 TRP cc_start: 0.6413 (t-100) cc_final: 0.5570 (t-100)
REVERT: A  248 GLU cc_start: 0.7409 (mp0) cc_final: 0.7143 (mp0)
REVERT: A  465 LYS cc_start: 0.6959 (mptt) cc_final: 0.6681 (tptt)
REVERT: A  656 ASP cc_start: 0.7544 (m-30) cc_final: 0.7272 (m-30)
  outliers start: 16
  outliers final: 13
  residues processed: 170
  average time/residue: 0.1882
  time to fit residues: 44.7476
Evaluate side-chains
  170 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   65 LEU
Chi-restraints excluded: chain B residue  161 ASP
Chi-restraints excluded: chain B residue  209 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  372 CYS
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  443 THR
Chi-restraints excluded: chain A residue  461 PHE
Chi-restraints excluded: chain A residue  633 ASN
Chi-restraints excluded: chain A residue  671 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 66 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0030
   chunk 0 optimal weight:   20.0000
   chunk 83 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   overall best weight:    1.0794

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

Flipped N/Q/H residues before XYZ refinement:
** A 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 633 ASN
** A 638 HIS ** 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 = 0.3844 r_free = 0.3844 target = 0.156446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.125456 restraints weight = 12710.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.125991 restraints weight = 10799.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.126903 restraints weight = 9391.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7437  Z= 0.195
  Angle     :  0.740  12.194  10065  Z= 0.369
  Chirality :  0.043   0.331   1106
  Planarity :  0.004   0.049   1257
  Dihedral  :  4.148  29.343    973
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 25.51 %
    Favored  : 72.46 %
  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:  1.68 (0.29), residues: 866
  helix:  2.18 (0.20), residues: 653
  sheet:  None (None), residues: 0
  loop : -2.47 (0.38), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A  78 
 HIS   0.003   0.001   HIS B 122 
 PHE   0.038   0.001   PHE B 147 
 TYR   0.015   0.001   TYR A 436 
 ARG   0.005   0.000   ARG B  75 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2209.00 seconds
wall clock time: 39 minutes 18.30 seconds (2358.30 seconds total)