Starting phenix.real_space_refine
on Tue Feb 11 00:18:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t01_25574/02_2025/7t01_25574.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t01_25574/02_2025/7t01_25574.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.69
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t01_25574/02_2025/7t01_25574.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t01_25574/02_2025/7t01_25574.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t01_25574/02_2025/7t01_25574.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t01_25574/02_2025/7t01_25574.cif"
  }
  resolution = 2.69
  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=   0.015
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      16      5.16       5
     C    2136      2.51       5
     N     555      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3343
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1595
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "H"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 924
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 6, 'TRANS': 113}
    Chain: "L"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 107, 824
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
  Time building chain proxies: 5.06, per 1000 atoms: 1.51
  Number of scatterers: 3343
  At special positions: 0
  Unit cell: (68.85, 62.37, 101.25, 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      16     16.00
     O     636      8.00
     N     555      7.00
     C    2136      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  97 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Conformation dependent library (CDL) restraints added in 383.5 milliseconds
  

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  790

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 9 sheets defined
      13.1% alpha, 32.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 385 through 390
      removed outlier: 4.007A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.380A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.572A  pdb=" N   SER A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 63 through 66
    Processing helix  chain 'H' and resid 88 through 92
    Processing helix  chain 'L' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.297A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLU A 516 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.732A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'H' and resid 4 through 7
      removed outlier: 3.596A  pdb=" N   GLN H  79 " --> pdb=" O   ASP H  74 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   THR H  70 " --> pdb=" O   THR H  83 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 59 through 61
      removed outlier: 6.602A  pdb=" N   TRP H  38 " --> pdb=" O   LEU H  50 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   LEU H  52 " --> pdb=" O   VAL H  36 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL H  36 " --> pdb=" O   LEU H  52 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   TYR H  54 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   VAL H  34 " --> pdb=" O   TYR H  54 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   VAL H 112 " --> pdb=" O   HIS H  99 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 59 through 61
      removed outlier: 6.602A  pdb=" N   TRP H  38 " --> pdb=" O   LEU H  50 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   LEU H  52 " --> pdb=" O   VAL H  36 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL H  36 " --> pdb=" O   LEU H  52 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   TYR H  54 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 7.480A  pdb=" N   VAL H  34 " --> pdb=" O   TYR H  54 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6
      removed outlier: 3.714A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.722A  pdb=" N   LEU L  11 " --> pdb=" O   ASP L 105 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.515A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ALA L  50 " --> pdb=" O   ARG L  53 " (cutoff:3.500A)

    111 hydrogen bonds defined for protein.
    255 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: 0.90

  Time building geometry restraints manager: 0.72 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: 1049
        1.34 -     1.46: 894
        1.46 -     1.59: 1469
        1.59 -     1.71: 0
        1.71 -     1.83: 20
  Bond restraints: 3432
  Sorted by residual:
  bond pdb=" C   THR L  94 "
       pdb=" N   PRO L  95 "
    ideal  model  delta    sigma   weight residual
    1.334  1.373 -0.039 2.34e-02 1.83e+03 2.75e+00
  bond pdb=" C   SER L   7 "
       pdb=" N   PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.334  1.365 -0.031 2.34e-02 1.83e+03 1.75e+00
  bond pdb=" C   LYS H  13 "
       pdb=" N   PRO H  14 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.07e+00
  bond pdb=" CB  ILE L  48 "
       pdb=" CG2 ILE L  48 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.06e+00
  bond pdb=" C   ALA A 520 "
       pdb=" N   PRO A 521 "
    ideal  model  delta    sigma   weight residual
    1.334  1.357 -0.023 2.34e-02 1.83e+03 1.00e+00
  ... (remaining 3427 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 4592
        2.62 -     5.24: 69
        5.24 -     7.86: 10
        7.86 -    10.48: 1
       10.48 -    13.09: 1
  Bond angle restraints: 4673
  Sorted by residual:
  angle pdb=" CA  LEU H  29 "
        pdb=" CB  LEU H  29 "
        pdb=" CG  LEU H  29 "
      ideal   model   delta    sigma   weight residual
     116.30  129.39  -13.09 3.50e+00 8.16e-02 1.40e+01
  angle pdb=" CA  TYR L  49 "
        pdb=" CB  TYR L  49 "
        pdb=" CG  TYR L  49 "
      ideal   model   delta    sigma   weight residual
     113.90  120.52   -6.62 1.80e+00 3.09e-01 1.35e+01
  angle pdb=" CA  VAL L  29 "
        pdb=" CB  VAL L  29 "
        pdb=" CG1 VAL L  29 "
      ideal   model   delta    sigma   weight residual
     110.40  116.34   -5.94 1.70e+00 3.46e-01 1.22e+01
  angle pdb=" N   VAL L  29 "
        pdb=" CA  VAL L  29 "
        pdb=" CB  VAL L  29 "
      ideal   model   delta    sigma   weight residual
     112.08  107.07    5.01 1.68e+00 3.54e-01 8.90e+00
  angle pdb=" C   TYR L  49 "
        pdb=" CA  TYR L  49 "
        pdb=" CB  TYR L  49 "
      ideal   model   delta    sigma   weight residual
     110.90  106.38    4.52 1.58e+00 4.01e-01 8.19e+00
  ... (remaining 4668 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.74: 1810
       14.74 -    29.48: 171
       29.48 -    44.22: 29
       44.22 -    58.96: 5
       58.96 -    73.70: 4
  Dihedral angle restraints: 2019
    sinusoidal: 781
      harmonic: 1238
  Sorted by residual:
  dihedral pdb=" CA  TYR H  54 "
           pdb=" C   TYR H  54 "
           pdb=" N   TRP H  55 "
           pdb=" CA  TRP H  55 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.28   28.72     0      5.00e+00 4.00e-02 3.30e+01
  dihedral pdb=" CA  SER L   9 "
           pdb=" C   SER L   9 "
           pdb=" N   SER L  10 "
           pdb=" CA  SER L  10 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.91   27.09     0      5.00e+00 4.00e-02 2.93e+01
  dihedral pdb=" CA  LEU L  78 "
           pdb=" C   LEU L  78 "
           pdb=" N   GLN L  79 "
           pdb=" CA  GLN L  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.01   26.99     0      5.00e+00 4.00e-02 2.91e+01
  ... (remaining 2016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 311
       0.043 -    0.085: 143
       0.085 -    0.128: 51
       0.128 -    0.171: 8
       0.171 -    0.214: 2
  Chirality restraints: 515
  Sorted by residual:
  chirality pdb=" CA  THR L  94 "
            pdb=" N   THR L  94 "
            pdb=" C   THR L  94 "
            pdb=" CB  THR L  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality pdb=" CA ASER L   7 "
            pdb=" N   SER L   7 "
            pdb=" C   SER L   7 "
            pdb=" CB ASER L   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.54e-01
  chirality pdb=" CA  PRO H  14 "
            pdb=" N   PRO H  14 "
            pdb=" C   PRO H  14 "
            pdb=" CB  PRO H  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 6.85e-01
  ... (remaining 512 not shown)

  Planarity restraints: 598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  49 "   -0.025 2.00e-02 2.50e+03   2.08e-02 8.61e+00
        pdb=" CG  TYR L  49 "    0.047 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  49 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  49 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  49 "    0.011 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  49 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  49 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR L  49 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL L  29 "   -0.014 2.00e-02 2.50e+03   2.87e-02 8.23e+00
        pdb=" C   VAL L  29 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL L  29 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   PHE L  30 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  60 "   -0.167 9.50e-02 1.11e+02   7.55e-02 4.40e+00
        pdb=" NE  ARG H  60 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  60 "   -0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  60 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  60 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 595 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.85: 1135
        2.85 -     3.36: 3020
        3.36 -     3.87: 5498
        3.87 -     4.39: 6364
        4.39 -     4.90: 10848
  Nonbonded interactions: 26865
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP H  74 "
            pdb=" OG  SER H  76 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" O   ALA L  25 "
            pdb=" OG1 THR L  69 "
     model   vdw
     2.379 3.040
  nonbonded pdb=" ND2 ASN A 394 "
            pdb=" OE2 GLU A 516 "
     model   vdw
     2.419 3.120
  nonbonded pdb=" OG  SER A 438 "
            pdb=" OD2 ASP A 442 "
     model   vdw
     2.485 3.040
  nonbonded pdb=" NH1 ARG H  60 "
            pdb=" OG1 THR L  94 "
     model   vdw
     2.508 3.120
  ... (remaining 26860 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.560
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.570
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:12.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
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      :  0.004   0.039   3432  Z= 0.241
  Angle     :  0.870  13.094   4673  Z= 0.469
  Chirality :  0.054   0.214    515
  Planarity :  0.008   0.075    598
  Dihedral  : 12.300  73.703   1220
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 1.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  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: -1.08 (0.38), residues: 422
  helix: -3.82 (0.72), residues: 19
  sheet: -0.35 (0.44), residues: 125
  loop : -0.63 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 436 
 HIS   0.002   0.001   HIS H  99 
 PHE   0.020   0.002   PHE L  83 
 TYR   0.047   0.005   TYR L  49 
 ARG   0.017   0.003   ARG H  60 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8549 (m) cc_final: 0.8312 (p)
REVERT: A  362 VAL cc_start: 0.8512 (t) cc_final: 0.8165 (p)
REVERT: A  421 TYR cc_start: 0.8398 (m-10) cc_final: 0.7723 (m-10)
REVERT: A  425 LEU cc_start: 0.8830 (mt) cc_final: 0.8604 (mt)
REVERT: A  442 ASP cc_start: 0.8082 (m-30) cc_final: 0.7821 (m-30)
REVERT: A  454 ARG cc_start: 0.9020 (ttm-80) cc_final: 0.8736 (ttm110)
REVERT: A  456 PHE cc_start: 0.7839 (m-80) cc_final: 0.7590 (m-80)
REVERT: H   61 TYR cc_start: 0.8953 (m-80) cc_final: 0.8675 (m-80)
REVERT: L    2 MET cc_start: 0.8511 (tpt) cc_final: 0.8181 (tpt)
REVERT: L   14 SER cc_start: 0.8801 (m) cc_final: 0.8560 (m)
REVERT: L   22 THR cc_start: 0.7998 (p) cc_final: 0.7726 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.8185
  time to fit residues: 143.6211
Evaluate side-chains
  149 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 31 optimal weight:    0.1980
   chunk 17 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 11 optimal weight:    0.3980
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.091659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.079317 restraints weight = 7158.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 2.92
r_work: 0.3236 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3246
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3246 r_free = 0.3246    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3245 r_free = 0.3245    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3245
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3432  Z= 0.258
  Angle     :  0.763  10.125   4673  Z= 0.378
  Chirality :  0.049   0.187    515
  Planarity :  0.004   0.031    598
  Dihedral  :  6.525  24.130    465
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 20.11 %
    Favored  : 77.21 %
  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: -0.92 (0.37), residues: 422
  helix: -2.21 (1.28), residues: 18
  sheet: -0.13 (0.46), residues: 119
  loop : -0.71 (0.33), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 436 
 HIS   0.002   0.001   HIS H  99 
 PHE   0.020   0.002   PHE L  83 
 TYR   0.012   0.002   TYR L  49 
 ARG   0.005   0.001   ARG L  61 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 156
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  349 SER cc_start: 0.8703 (m) cc_final: 0.8493 (p)
REVERT: A  362 VAL cc_start: 0.8715 (t) cc_final: 0.8483 (p)
REVERT: A  425 LEU cc_start: 0.8949 (mt) cc_final: 0.8681 (mt)
REVERT: A  442 ASP cc_start: 0.8519 (m-30) cc_final: 0.8195 (m-30)
REVERT: A  454 ARG cc_start: 0.9121 (ttm-80) cc_final: 0.8758 (ttm110)
REVERT: A  456 PHE cc_start: 0.7983 (m-80) cc_final: 0.7720 (m-80)
REVERT: A  489 TYR cc_start: 0.7892 (m-80) cc_final: 0.7672 (m-10)
REVERT: H   24 PHE cc_start: 0.8870 (p90) cc_final: 0.8661 (p90)
REVERT: H   27 PHE cc_start: 0.8756 (p90) cc_final: 0.8471 (p90)
REVERT: H   61 TYR cc_start: 0.9079 (m-80) cc_final: 0.8764 (m-80)
REVERT: L    3 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7762 (mm-40)
REVERT: L   18 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8299 (ttm170)
REVERT: L   55 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8564 (tm-30)
REVERT: L   61 ARG cc_start: 0.8844 (ptt-90) cc_final: 0.8624 (ptt-90)
REVERT: L   86 TYR cc_start: 0.8455 (m-80) cc_final: 0.8230 (m-10)
  outliers start: 10
  outliers final: 3
  residues processed: 157
  average time/residue: 0.7877
  time to fit residues: 128.5381
Evaluate side-chains
  142 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 137
  time to evaluate  : 0.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   74 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    0.3980
   chunk 20 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 40 optimal weight:    0.4980
   chunk 27 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** L   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.088321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.076547 restraints weight = 7299.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.80
r_work: 0.3204 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3206
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3206 r_free = 0.3206    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3206
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   3432  Z= 0.370
  Angle     :  0.763  10.489   4673  Z= 0.383
  Chirality :  0.051   0.204    515
  Planarity :  0.005   0.042    598
  Dihedral  :  6.302  23.946    465
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 24.66 %
    Favored  : 69.97 %
  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: -1.14 (0.38), residues: 422
  helix: -2.38 (1.24), residues: 18
  sheet: -0.53 (0.46), residues: 121
  loop : -0.73 (0.34), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP H  55 
 HIS   0.003   0.001   HIS H  99 
 PHE   0.020   0.002   PHE H  96 
 TYR   0.014   0.002   TYR A 421 
 ARG   0.004   0.001   ARG H  68 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8511 (ptm-80)
REVERT: A  421 TYR cc_start: 0.8693 (m-10) cc_final: 0.8404 (m-10)
REVERT: A  425 LEU cc_start: 0.8977 (mt) cc_final: 0.8770 (mt)
REVERT: A  442 ASP cc_start: 0.8657 (m-30) cc_final: 0.8329 (m-30)
REVERT: A  454 ARG cc_start: 0.9175 (ttm-80) cc_final: 0.8868 (ttm-80)
REVERT: A  456 PHE cc_start: 0.8065 (m-80) cc_final: 0.7812 (m-80)
REVERT: A  489 TYR cc_start: 0.7969 (m-80) cc_final: 0.7716 (m-10)
REVERT: H  119 VAL cc_start: 0.9101 (OUTLIER) cc_final: 0.8872 (p)
REVERT: L    2 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.8085 (tpt)
REVERT: L   55 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8631 (tm-30)
  outliers start: 20
  outliers final: 7
  residues processed: 155
  average time/residue: 0.8884
  time to fit residues: 142.7620
Evaluate side-chains
  144 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 133
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  119 VAL
Chi-restraints excluded: chain L residue    2 MET
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue  102 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 18 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 25 optimal weight:    0.3980
   chunk 2 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.087532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.076006 restraints weight = 7498.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.83
r_work: 0.3194 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.52   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.3497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028   3432  Z= 0.323
  Angle     :  0.768  11.634   4673  Z= 0.378
  Chirality :  0.050   0.195    515
  Planarity :  0.005   0.048    598
  Dihedral  :  6.065  24.773    465
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  7.24 %
    Allowed  : 27.35 %
    Favored  : 65.42 %
  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: -1.26 (0.39), residues: 422
  helix: -2.17 (1.73), residues: 12
  sheet: -0.68 (0.46), residues: 124
  loop : -0.85 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP H  55 
 HIS   0.005   0.002   HIS H  99 
 PHE   0.039   0.003   PHE H  27 
 TYR   0.014   0.002   TYR L  87 
 ARG   0.006   0.001   ARG L  61 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  390 LEU cc_start: 0.8863 (mm) cc_final: 0.8640 (mp)
REVERT: A  408 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8573 (ptm-80)
REVERT: A  421 TYR cc_start: 0.8663 (m-10) cc_final: 0.8444 (m-80)
REVERT: A  425 LEU cc_start: 0.8958 (mt) cc_final: 0.8697 (mt)
REVERT: A  442 ASP cc_start: 0.8670 (m-30) cc_final: 0.8351 (m-30)
REVERT: A  454 ARG cc_start: 0.9184 (ttm-80) cc_final: 0.8767 (ttm-80)
REVERT: A  456 PHE cc_start: 0.8083 (m-80) cc_final: 0.7788 (m-80)
REVERT: H   80 VAL cc_start: 0.9131 (t) cc_final: 0.8917 (t)
REVERT: H   81 VAL cc_start: 0.9264 (m) cc_final: 0.9007 (p)
REVERT: H  106 ASP cc_start: 0.8233 (m-30) cc_final: 0.8004 (m-30)
REVERT: L    3 GLN cc_start: 0.8157 (mm110) cc_final: 0.7892 (mm110)
REVERT: L   18 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8570 (ptm160)
REVERT: L   27 GLN cc_start: 0.7716 (mm-40) cc_final: 0.7435 (mm-40)
REVERT: L   55 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8727 (tm-30)
  outliers start: 27
  outliers final: 12
  residues processed: 159
  average time/residue: 0.8156
  time to fit residues: 134.5687
Evaluate side-chains
  168 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   60 SER
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 35 optimal weight:    0.1980
   chunk 25 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    0.3980
   chunk 0 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.4980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.087420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.075836 restraints weight = 7389.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.82
r_work: 0.3201 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3201
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3201 r_free = 0.3201    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3201
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.3725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3432  Z= 0.338
  Angle     :  0.770  10.763   4673  Z= 0.381
  Chirality :  0.050   0.196    515
  Planarity :  0.005   0.044    598
  Dihedral  :  6.004  25.386    465
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  7.24 %
    Allowed  : 28.95 %
    Favored  : 63.81 %
  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: -1.24 (0.40), residues: 422
  helix: -2.11 (1.77), residues: 12
  sheet: -0.50 (0.48), residues: 120
  loop : -0.92 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP H  55 
 HIS   0.003   0.001   HIS H  99 
 PHE   0.036   0.002   PHE H  27 
 TYR   0.010   0.002   TYR L  36 
 ARG   0.004   0.001   ARG L  61 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8454 (t)
REVERT: A  408 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8570 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9062 (mt0) cc_final: 0.8739 (tt0)
REVERT: A  425 LEU cc_start: 0.8919 (mt) cc_final: 0.8643 (mt)
REVERT: A  442 ASP cc_start: 0.8657 (m-30) cc_final: 0.8325 (m-30)
REVERT: A  456 PHE cc_start: 0.8078 (m-80) cc_final: 0.7808 (m-80)
REVERT: H   55 TRP cc_start: 0.8637 (p90) cc_final: 0.8416 (p90)
REVERT: H   80 VAL cc_start: 0.9137 (t) cc_final: 0.8926 (t)
REVERT: H   81 VAL cc_start: 0.9236 (m) cc_final: 0.9010 (p)
REVERT: H  106 ASP cc_start: 0.8285 (m-30) cc_final: 0.8027 (m-30)
REVERT: L   18 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8523 (ptm160)
REVERT: L   55 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8709 (tm-30)
REVERT: L   90 GLN cc_start: 0.8955 (pp30) cc_final: 0.8692 (pp30)
  outliers start: 27
  outliers final: 11
  residues processed: 158
  average time/residue: 0.8300
  time to fit residues: 136.0464
Evaluate side-chains
  158 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  458 LYS
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   60 SER
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.0970
   chunk 30 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    0.1980
   chunk 16 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.3356

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.088644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.076850 restraints weight = 7547.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.93
r_work: 0.3214 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.4003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3432  Z= 0.273
  Angle     :  0.798  12.424   4673  Z= 0.388
  Chirality :  0.049   0.184    515
  Planarity :  0.005   0.045    598
  Dihedral  :  5.855  25.604    465
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 33.24 %
    Favored  : 61.13 %
  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: -1.26 (0.40), residues: 422
  helix: -2.06 (1.82), residues: 12
  sheet: -0.69 (0.47), residues: 126
  loop : -0.84 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP H  38 
 HIS   0.001   0.000   HIS H  99 
 PHE   0.029   0.002   PHE H  27 
 TYR   0.017   0.002   TYR A 421 
 ARG   0.007   0.001   ARG A 454 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 153
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8440 (t)
REVERT: A  355 ARG cc_start: 0.8744 (tpp-160) cc_final: 0.8481 (tpp-160)
REVERT: A  390 LEU cc_start: 0.8886 (mm) cc_final: 0.8679 (mp)
REVERT: A  392 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8852 (m-80)
REVERT: A  408 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8593 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9046 (mt0) cc_final: 0.8720 (tt0)
REVERT: A  425 LEU cc_start: 0.8861 (mt) cc_final: 0.8660 (mt)
REVERT: A  442 ASP cc_start: 0.8643 (m-30) cc_final: 0.8294 (m-30)
REVERT: A  456 PHE cc_start: 0.7985 (m-80) cc_final: 0.7741 (m-80)
REVERT: H  106 ASP cc_start: 0.8293 (m-30) cc_final: 0.8039 (m-30)
REVERT: L    3 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8152 (mm110)
REVERT: L   18 ARG cc_start: 0.8729 (ttm170) cc_final: 0.8496 (ptm160)
REVERT: L   55 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8606 (tm-30)
REVERT: L   75 ILE cc_start: 0.8730 (mp) cc_final: 0.8460 (tp)
REVERT: L   90 GLN cc_start: 0.8950 (pp30) cc_final: 0.8717 (pp30)
  outliers start: 21
  outliers final: 12
  residues processed: 160
  average time/residue: 0.8007
  time to fit residues: 133.1047
Evaluate side-chains
  167 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   32 ILE
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   60 SER
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 14 optimal weight:    0.1980
   chunk 2 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 35 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0770
   overall best weight:    0.3338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.088423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.076560 restraints weight = 7398.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3340 rms_B_bonded: 2.92
r_work: 0.3218 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3220
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3432  Z= 0.265
  Angle     :  0.831  12.926   4673  Z= 0.399
  Chirality :  0.050   0.182    515
  Planarity :  0.005   0.046    598
  Dihedral  :  5.715  24.982    465
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 33.24 %
    Favored  : 60.86 %
  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 (0.41), residues: 422
  helix: -1.91 (1.88), residues: 12
  sheet: -0.79 (0.47), residues: 127
  loop : -0.84 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP H  38 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.025   0.002   PHE H  27 
 TYR   0.012   0.001   TYR L  36 
 ARG   0.009   0.001   ARG L  61 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 152
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8448 (t)
REVERT: A  355 ARG cc_start: 0.8739 (tpp-160) cc_final: 0.8514 (tpp-160)
REVERT: A  390 LEU cc_start: 0.8888 (mm) cc_final: 0.8676 (mp)
REVERT: A  392 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8805 (m-80)
REVERT: A  408 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8588 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9029 (mt0) cc_final: 0.8719 (tt0)
REVERT: A  442 ASP cc_start: 0.8642 (m-30) cc_final: 0.8342 (m-30)
REVERT: A  456 PHE cc_start: 0.8008 (m-80) cc_final: 0.7725 (m-80)
REVERT: H   81 VAL cc_start: 0.9210 (m) cc_final: 0.8886 (p)
REVERT: H  106 ASP cc_start: 0.8292 (m-30) cc_final: 0.8040 (m-30)
REVERT: L    3 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8156 (mm110)
REVERT: L   18 ARG cc_start: 0.8709 (ttm170) cc_final: 0.8492 (ptm160)
REVERT: L   55 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8586 (tm-30)
REVERT: L   75 ILE cc_start: 0.8732 (mp) cc_final: 0.8472 (tp)
REVERT: L   90 GLN cc_start: 0.8976 (pp30) cc_final: 0.8765 (pp30)
  outliers start: 22
  outliers final: 13
  residues processed: 160
  average time/residue: 0.8377
  time to fit residues: 139.0986
Evaluate side-chains
  167 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 150
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   72 THR
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   60 SER
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    0.2980
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0980
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.4580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.087985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.076273 restraints weight = 7388.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.90
r_work: 0.3204 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3205
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3205 r_free = 0.3205    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3205
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   3432  Z= 0.326
  Angle     :  0.852  12.399   4673  Z= 0.411
  Chirality :  0.050   0.189    515
  Planarity :  0.006   0.054    598
  Dihedral  :  5.785  25.136    465
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 33.24 %
    Favored  : 59.79 %
  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: -1.37 (0.41), residues: 422
  helix: -1.95 (1.84), residues: 12
  sheet: -0.74 (0.47), residues: 126
  loop : -0.94 (0.37), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP H  38 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.024   0.002   PHE H  24 
 TYR   0.028   0.002   TYR A 380 
 ARG   0.012   0.001   ARG L  61 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8703 (OUTLIER) cc_final: 0.8443 (t)
REVERT: A  355 ARG cc_start: 0.8741 (tpp-160) cc_final: 0.8502 (tpp-160)
REVERT: A  392 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8826 (m-80)
REVERT: A  408 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8583 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9046 (mt0) cc_final: 0.8792 (tt0)
REVERT: A  442 ASP cc_start: 0.8679 (m-30) cc_final: 0.8355 (m-30)
REVERT: A  456 PHE cc_start: 0.8040 (m-80) cc_final: 0.7757 (m-80)
REVERT: A  516 GLU cc_start: 0.7270 (tm-30) cc_final: 0.6998 (tm-30)
REVERT: H  106 ASP cc_start: 0.8314 (m-30) cc_final: 0.8054 (m-30)
REVERT: L   18 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8528 (ptm160)
REVERT: L   55 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8628 (tm-30)
REVERT: L   90 GLN cc_start: 0.9035 (pp30) cc_final: 0.8830 (pp30)
  outliers start: 26
  outliers final: 15
  residues processed: 164
  average time/residue: 0.8090
  time to fit residues: 137.7237
Evaluate side-chains
  168 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   19 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain L residue   12 SER
Chi-restraints excluded: chain L residue   14 SER
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   37 GLN
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   60 SER
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 24 optimal weight:    0.2980
   chunk 11 optimal weight:    0.8980
   chunk 2 optimal weight:    0.3980
   chunk 29 optimal weight:    0.4980
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.3980
   chunk 28 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0470
   chunk 16 optimal weight:    0.8980
   chunk 35 optimal weight:    0.3980
   overall best weight:    0.3078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.089373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.077454 restraints weight = 7390.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.95
r_work: 0.3227 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3226
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3226 r_free = 0.3226    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3226
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.4370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3432  Z= 0.264
  Angle     :  0.889  12.963   4673  Z= 0.420
  Chirality :  0.050   0.179    515
  Planarity :  0.006   0.062    598
  Dihedral  :  5.665  24.112    465
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 36.46 %
    Favored  : 58.45 %
  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: -1.43 (0.41), residues: 422
  helix: -1.89 (1.86), residues: 12
  sheet: -0.82 (0.47), residues: 127
  loop : -0.97 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP H  38 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.026   0.002   PHE L  71 
 TYR   0.021   0.002   TYR A 380 
 ARG   0.013   0.001   ARG L  61 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 157
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8676 (OUTLIER) cc_final: 0.8414 (t)
REVERT: A  355 ARG cc_start: 0.8712 (tpp-160) cc_final: 0.8507 (tpp-160)
REVERT: A  392 PHE cc_start: 0.9103 (OUTLIER) cc_final: 0.8827 (m-80)
REVERT: A  408 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8570 (ptm-80)
REVERT: A  409 GLN cc_start: 0.9006 (mt0) cc_final: 0.8751 (tt0)
REVERT: A  442 ASP cc_start: 0.8670 (m-30) cc_final: 0.8343 (m-30)
REVERT: A  456 PHE cc_start: 0.7968 (m-80) cc_final: 0.7729 (m-80)
REVERT: H   13 LYS cc_start: 0.7004 (tptt) cc_final: 0.6798 (tptp)
REVERT: H  106 ASP cc_start: 0.8301 (m-30) cc_final: 0.8030 (m-30)
REVERT: L   55 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8527 (tm-30)
REVERT: L   61 ARG cc_start: 0.8595 (ptt-90) cc_final: 0.8135 (ptp-170)
REVERT: L   90 GLN cc_start: 0.9051 (pp30) cc_final: 0.8807 (pp30)
  outliers start: 19
  outliers final: 11
  residues processed: 162
  average time/residue: 0.8148
  time to fit residues: 137.0709
Evaluate side-chains
  163 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  335 LEU
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  408 ARG
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  453 TYR
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0970
   chunk 4 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 35 optimal weight:    0.3980
   chunk 5 optimal weight:    0.0970
   chunk 26 optimal weight:    0.2980
   chunk 15 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0670
   chunk 19 optimal weight:    0.0970
   chunk 31 optimal weight:    0.1980
   overall best weight:    0.1112

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

Flipped N/Q/H residues before XYZ refinement:
L   3 GLN
** L  79 GLN ** 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 = 0.3585 r_free = 0.3585 target = 0.091657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.079736 restraints weight = 7318.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 2.98
r_work: 0.3265 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3263
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3263 r_free = 0.3263    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3263
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3432  Z= 0.227
  Angle     :  0.894  12.846   4673  Z= 0.427
  Chirality :  0.050   0.181    515
  Planarity :  0.006   0.053    598
  Dihedral  :  5.580  26.550    465
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 37.80 %
    Favored  : 58.71 %
  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 (0.41), residues: 422
  helix: -3.48 (1.06), residues: 18
  sheet: -0.92 (0.46), residues: 127
  loop : -0.95 (0.38), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.003   TRP H  38 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.025   0.002   PHE H  27 
 TYR   0.022   0.002   TYR A 453 
 ARG   0.012   0.001   ARG L  61 

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

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

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  844 Ramachandran restraints generated.
    422 Oldfield, 0 Emsley, 422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: A  333 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8425 (t)
REVERT: A  392 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8768 (m-80)
REVERT: A  409 GLN cc_start: 0.8926 (mt0) cc_final: 0.8699 (tt0)
REVERT: A  442 ASP cc_start: 0.8618 (m-30) cc_final: 0.8317 (m-30)
REVERT: H  106 ASP cc_start: 0.8259 (m-30) cc_final: 0.7988 (m-30)
REVERT: L   10 SER cc_start: 0.8739 (t) cc_final: 0.8368 (p)
REVERT: L   55 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8457 (tm-30)
REVERT: L   61 ARG cc_start: 0.8595 (ptt-90) cc_final: 0.8090 (ptt-90)
REVERT: L   79 GLN cc_start: 0.8587 (mm-40) cc_final: 0.7505 (mm-40)
REVERT: L   81 GLU cc_start: 0.8624 (pm20) cc_final: 0.7784 (pp20)
REVERT: L   82 ASP cc_start: 0.8400 (m-30) cc_final: 0.7641 (m-30)
  outliers start: 13
  outliers final: 6
  residues processed: 147
  average time/residue: 0.8309
  time to fit residues: 126.7773
Evaluate side-chains
  148 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 139
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain H residue   25 SER
Chi-restraints excluded: chain H residue   36 VAL
Chi-restraints excluded: chain H residue   84 LEU
Chi-restraints excluded: chain L residue   55 GLN
Chi-restraints excluded: chain L residue   94 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 37 optimal weight:    0.0670
   chunk 36 optimal weight:    0.7980
   chunk 15 optimal weight:    0.3980
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 30 optimal weight:    0.2980
   overall best weight:    0.3518

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

Flipped N/Q/H residues before XYZ refinement:
** L  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.089285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.077503 restraints weight = 7424.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.99
r_work: 0.3228 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3228 r_free = 0.3228    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.4756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   3432  Z= 0.301
  Angle     :  0.894  12.379   4673  Z= 0.425
  Chirality :  0.052   0.274    515
  Planarity :  0.006   0.051    598
  Dihedral  :  5.618  24.261    465
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 37.53 %
    Favored  : 58.71 %
  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 (0.42), residues: 422
  helix: -3.18 (1.11), residues: 18
  sheet: -0.91 (0.46), residues: 126
  loop : -0.88 (0.39), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.003   TRP H  38 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.021   0.002   PHE H  27 
 TYR   0.024   0.002   TYR A 380 
 ARG   0.011   0.001   ARG L  61 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3807.90 seconds
wall clock time: 67 minutes 56.21 seconds (4076.21 seconds total)