Starting phenix.real_space_refine
on Tue Aug  4 12:43:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k8y_62182/08_2026/9k8y_62182.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k8y_62182/08_2026/9k8y_62182.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k8y_62182/08_2026/9k8y_62182.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k8y_62182/08_2026/9k8y_62182.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k8y_62182/08_2026/9k8y_62182.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k8y_62182/08_2026/9k8y_62182.map"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.028
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      24      5.16       5
     C    1933      2.51       5
     N     447      2.21       5
     O     484      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 2888
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2869
          Classifications: {'peptide': 361}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 351}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'NOS%rna2p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna2p': 1}
  Time building chain proxies: 0.56, per 1000 atoms: 0.19
  Number of scatterers: 2888
  At special positions: 0
  Unit cell: (77, 55, 74.8, 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      24     16.00
     O     484      8.00
     N     447      7.00
     C    1933      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 144 " - pdb=" SG  CYS A 375 " 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: 0.15
  Conformation dependent library (CDL) restraints added in 63.6 milliseconds
  

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  680

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      90.6% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 59
      removed outlier: 3.643A  pdb=" N   LEU A  50 " --> pdb=" O   GLY A  46 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   VAL A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   TRP A  53 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 83
      removed outlier: 3.981A  pdb=" N   ASN A  66 " --> pdb=" O   ASN A  62 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   PHE A  82 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 88
      No H-bonds generated for 'chain 'A' and resid 86 through 88'
    Processing helix  chain 'A' and resid 89 through 111
      removed outlier: 3.588A  pdb=" N   SER A 109 " --> pdb=" O   GLN A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 145
      removed outlier: 3.791A  pdb=" N   ILE A 125 " --> pdb=" O   LEU A 121 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   CYS A 144 " --> pdb=" O   ASN A 140 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   MET A 145 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 175
      removed outlier: 4.277A  pdb=" N   GLY A 161 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   VAL A 162 " --> pdb=" O   GLY A 158 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLN A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 210
    Processing helix  chain 'A' and resid 231 through 257
      removed outlier: 5.968A  pdb=" N   LYS A 241 " --> pdb=" O   LYS A 237 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ALA A 242 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ASN A 250 " --> pdb=" O   MET A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 270
    Processing helix  chain 'A' and resid 272 through 292
      removed outlier: 3.724A  pdb=" N   ARG A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   TYR A 292 " --> pdb=" O   PHE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 297
      removed outlier: 3.667A  pdb=" N   THR A 297 " --> pdb=" O   PRO A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 306
      removed outlier: 4.541A  pdb=" N   ASN A 304 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   THR A 306 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 319
    Processing helix  chain 'A' and resid 321 through 332
      removed outlier: 3.676A  pdb=" N   TRP A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 339
    Processing helix  chain 'A' and resid 339 through 358
    Processing helix  chain 'A' and resid 359 through 368
      removed outlier: 3.630A  pdb=" N   LEU A 363 " --> pdb=" O   THR A 359 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   VAL A 366 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   LYS A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 400
    Processing helix  chain 'A' and resid 401 through 406
    Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 180

    231 hydrogen bonds defined for protein.
    669 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: 0.30

  Time building geometry restraints manager: 0.20 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 846
        1.35 -     1.47: 775
        1.47 -     1.59: 1308
        1.59 -     1.71: 0
        1.71 -     1.83: 35
  Bond restraints: 2964
  Sorted by residual:
  bond pdb=" N   VAL A  52 "
       pdb=" CA  VAL A  52 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.17e-02 7.31e+03 8.41e+00
  bond pdb=" N   ILE A 137 "
       pdb=" CA  ILE A 137 "
    ideal  model  delta    sigma   weight residual
    1.462  1.494 -0.032 1.14e-02 7.69e+03 7.82e+00
  bond pdb=" N   ASN A  51 "
       pdb=" CA  ASN A  51 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.23e-02 6.61e+03 7.06e+00
  bond pdb=" N   ASN A 354 "
       pdb=" CA  ASN A 354 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.23e-02 6.61e+03 6.23e+00
  bond pdb=" N   LEU A  50 "
       pdb=" CA  LEU A  50 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.032 1.31e-02 5.83e+03 6.15e+00
  ... (remaining 2959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 3764
        1.10 -     2.21: 187
        2.21 -     3.31: 47
        3.31 -     4.41: 14
        4.41 -     5.51: 11
  Bond angle restraints: 4023
  Sorted by residual:
  angle pdb=" N   ASN A 250 "
        pdb=" CA  ASN A 250 "
        pdb=" C   ASN A 250 "
      ideal   model   delta    sigma   weight residual
     111.14  105.63    5.51 1.08e+00 8.57e-01 2.61e+01
  angle pdb=" N   ASP A 287 "
        pdb=" CA  ASP A 287 "
        pdb=" C   ASP A 287 "
      ideal   model   delta    sigma   weight residual
     111.07  105.73    5.34 1.07e+00 8.73e-01 2.49e+01
  angle pdb=" C   VAL A 249 "
        pdb=" N   ASN A 250 "
        pdb=" CA  ASN A 250 "
      ideal   model   delta    sigma   weight residual
     120.44  115.25    5.19 1.36e+00 5.41e-01 1.46e+01
  angle pdb=" C   GLN A 135 "
        pdb=" CA  GLN A 135 "
        pdb=" CB  GLN A 135 "
      ideal   model   delta    sigma   weight residual
     110.92  116.20   -5.28 1.59e+00 3.96e-01 1.10e+01
  angle pdb=" O   LEU A 133 "
        pdb=" C   LEU A 133 "
        pdb=" N   ALA A 134 "
      ideal   model   delta    sigma   weight residual
     122.07  125.39   -3.32 1.03e+00 9.43e-01 1.04e+01
  ... (remaining 4018 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.92: 1540
       12.92 -    25.84: 127
       25.84 -    38.76: 43
       38.76 -    51.69: 8
       51.69 -    64.61: 2
  Dihedral angle restraints: 1720
    sinusoidal: 670
      harmonic: 1050
  Sorted by residual:
  dihedral pdb=" CB  CYS A 144 "
           pdb=" SG  CYS A 144 "
           pdb=" SG  CYS A 375 "
           pdb=" CB  CYS A 375 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -128.16   42.16     1      1.00e+01 1.00e-02 2.48e+01
  dihedral pdb=" CD  ARG A 291 "
           pdb=" NE  ARG A 291 "
           pdb=" CZ  ARG A 291 "
           pdb=" NH1 ARG A 291 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -31.93   31.93     1      1.00e+01 1.00e-02 1.45e+01
  dihedral pdb=" CA  PHE A 307 "
           pdb=" C   PHE A 307 "
           pdb=" N   SER A 308 "
           pdb=" CA  SER A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.56   15.44     0      5.00e+00 4.00e-02 9.54e+00
  ... (remaining 1717 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 323
       0.041 -    0.081: 116
       0.081 -    0.122: 33
       0.122 -    0.162: 1
       0.162 -    0.203: 2
  Chirality restraints: 475
  Sorted by residual:
  chirality pdb=" CA  ILE A 137 "
            pdb=" N   ILE A 137 "
            pdb=" C   ILE A 137 "
            pdb=" CB  ILE A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  VAL A  52 "
            pdb=" N   VAL A  52 "
            pdb=" C   VAL A  52 "
            pdb=" CB  VAL A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.86e-01
  chirality pdb=" CA  ASN A 354 "
            pdb=" N   ASN A 354 "
            pdb=" C   ASN A 354 "
            pdb=" CB  ASN A 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.32e-01
  ... (remaining 472 not shown)

  Planarity restraints: 482
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 291 "   -0.592 9.50e-02 1.11e+02   2.65e-01 4.30e+01
        pdb=" NE  ARG A 291 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 291 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 291 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 291 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 353 "    0.014 2.00e-02 2.50e+03   2.75e-02 7.56e+00
        pdb=" C   THR A 353 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   THR A 353 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ASN A 354 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 249 "   -0.009 2.00e-02 2.50e+03   1.87e-02 3.48e+00
        pdb=" C   VAL A 249 "    0.032 2.00e-02 2.50e+03
        pdb=" O   VAL A 249 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASN A 250 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 479 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 1051
        2.87 -     3.38: 3041
        3.38 -     3.88: 4853
        3.88 -     4.39: 5427
        4.39 -     4.90: 8976
  Nonbonded interactions: 23348
  Sorted by model distance:
  nonbonded pdb=" O   GLY A  46 "
            pdb=" OG  SER A  49 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" OD1 ASP A 172 "
            pdb=" NZ  LYS A 187 "
     model   vdw
     2.378 3.120
  nonbonded pdb=" NZ  LYS A 241 "
            pdb=" OD1 ASN A 310 "
     model   vdw
     2.483 3.120
  nonbonded pdb=" OH  TYR A  65 "
            pdb=" OD1 ASP A 117 "
     model   vdw
     2.527 3.040
  nonbonded pdb=" O   LEU A 133 "
            pdb=" C   ALA A 134 "
     model   vdw
     2.533 3.270
  ... (remaining 23343 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  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:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     3.030
  Find NCS groups from input model:        0.010
  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:1.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5525
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   0.034   2965  Z= 0.257
  Angle     :  0.662   5.515   4025  Z= 0.434
  Chirality :  0.044   0.203    475
  Planarity :  0.013   0.265    482
  Dihedral  : 11.184  64.608   1037
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.77 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.43), residues: 357
  helix:  1.55 (0.29), residues: 286
  sheet:  None (None), residues: 0
  loop : -0.22 (0.80), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 319 
 TYR   0.009   0.001   TYR A 119 
 PHE   0.019   0.002   PHE A 394 
 TRP   0.014   0.002   TRP A 398 
 HIS   0.004   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.26 ( 2964)
  covalent geometry    : angle       0.66167 /  0.43 ( 4023)
  SS BOND              : bond        0.00575 /  0.30 (    1)
  SS BOND              : angle       1.30890 /  0.72 (    2)
  hydrogen bonds       : bond        0.14383 /  9.48 (  231)
  hydrogen bonds       : angle       5.71250 /  4.13 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.062 
Fit side-chains
REVERT: A   59 LEU cc_start: 0.6340 (mt) cc_final: 0.5497 (tt)
REVERT: A   67 THR cc_start: 0.7711 (m) cc_final: 0.7509 (p)
REVERT: A  115 GLN cc_start: 0.4352 (mt0) cc_final: 0.3862 (mm-40)
REVERT: A  326 PHE cc_start: 0.8155 (m-80) cc_final: 0.7864 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 117
  average time/residue: 0.0419
  time to fit residues: 5.9877
Evaluate side-chains
  64 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0270
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0670
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.2776

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  34 GLN
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 HIS
A 316 ASN
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.217711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.191430 restraints weight = 5019.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4495 r_free = 0.4495 target = 0.196890 restraints weight = 2811.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.200830 restraints weight = 1816.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.203684 restraints weight = 1290.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.205552 restraints weight = 981.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.4546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5863
moved from start:          0.3589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2965  Z= 0.153
  Angle     :  0.645   7.584   4025  Z= 0.334
  Chirality :  0.045   0.191    475
  Planarity :  0.004   0.034    482
  Dihedral  :  5.484  59.348    398
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 14.15 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.44), residues: 357
  helix:  1.98 (0.29), residues: 293
  sheet:  None (None), residues: 0
  loop :  0.52 (0.93), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 291 
 TYR   0.018   0.002   TYR A 181 
 PHE   0.018   0.001   PHE A 104 
 TRP   0.015   0.001   TRP A 356 
 HIS   0.009   0.002   HIS A 262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.15 ( 2964)
  covalent geometry    : angle       0.64545 /  0.33 ( 4023)
  SS BOND              : bond        0.00120 /  0.06 (    1)
  SS BOND              : angle       0.33897 /  0.19 (    2)
  hydrogen bonds       : bond        0.05497 /  3.64 (  231)
  hydrogen bonds       : angle       4.24345 /  2.96 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.7556 (m-80) cc_final: 0.7323 (m-80)
REVERT: A   71 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8735 (t)
REVERT: A  153 MET cc_start: 0.7255 (tpp) cc_final: 0.6998 (tpp)
REVERT: A  255 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.5847 (tp40)
REVERT: A  398 TRP cc_start: 0.7553 (m100) cc_final: 0.6744 (t-100)
  outliers start: 17
  outliers final: 9
  residues processed: 74
  average time/residue: 0.0307
  time to fit residues: 2.9852
Evaluate side-chains
  68 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  306 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    0.2980
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0870
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.5358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 108 HIS
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 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 = 0.4614 r_free = 0.4614 target = 0.209600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.184620 restraints weight = 5262.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.190249 restraints weight = 2894.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4472 r_free = 0.4472 target = 0.193960 restraints weight = 1828.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4492 r_free = 0.4492 target = 0.196446 restraints weight = 1293.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.198383 restraints weight = 994.027|
|-----------------------------------------------------------------------------|
r_work (final): 0.4495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6059
moved from start:          0.4585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2965  Z= 0.153
  Angle     :  0.589   8.236   4025  Z= 0.312
  Chirality :  0.042   0.138    475
  Planarity :  0.004   0.035    482
  Dihedral  :  5.414  59.412    398
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 17.30 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.44), residues: 357
  helix:  2.01 (0.28), residues: 296
  sheet:  None (None), residues: 0
  loop :  0.25 (0.95), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  60 
 TYR   0.015   0.002   TYR A 181 
 PHE   0.023   0.002   PHE A 236 
 TRP   0.015   0.001   TRP A 356 
 HIS   0.003   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.15 ( 2964)
  covalent geometry    : angle       0.58904 /  0.31 ( 4023)
  SS BOND              : bond        0.00272 /  0.14 (    1)
  SS BOND              : angle       0.39241 /  0.23 (    2)
  hydrogen bonds       : bond        0.05034 /  3.42 (  231)
  hydrogen bonds       : angle       4.14370 /  2.96 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A   71 THR cc_start: 0.9154 (OUTLIER) cc_final: 0.8744 (t)
REVERT: A   85 ILE cc_start: 0.7552 (OUTLIER) cc_final: 0.7203 (tp)
REVERT: A  100 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6607 (mt)
REVERT: A  153 MET cc_start: 0.7135 (tpp) cc_final: 0.6850 (tpp)
REVERT: A  255 GLN cc_start: 0.6855 (OUTLIER) cc_final: 0.5303 (tp40)
REVERT: A  398 TRP cc_start: 0.7455 (m100) cc_final: 0.6692 (t-100)
  outliers start: 16
  outliers final: 9
  residues processed: 69
  average time/residue: 0.0426
  time to fit residues: 3.7443
Evaluate side-chains
  63 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 50
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  360 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0050
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 105 GLN
A 184 ASN
** A 342 GLN ** 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 = 0.4552 r_free = 0.4552 target = 0.201726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.177650 restraints weight = 5413.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.182677 restraints weight = 3018.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.186213 restraints weight = 1932.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.188485 restraints weight = 1359.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.190286 restraints weight = 1052.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.4449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6211
moved from start:          0.5492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   2965  Z= 0.154
  Angle     :  0.598   9.384   4025  Z= 0.314
  Chirality :  0.043   0.180    475
  Planarity :  0.004   0.035    482
  Dihedral  :  5.472  54.237    398
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 18.87 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.34 (0.44), residues: 357
  helix:  1.89 (0.29), residues: 295
  sheet:  None (None), residues: 0
  loop :  0.01 (0.94), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.016   0.002   TYR A 119 
 PHE   0.015   0.001   PHE A 104 
 TRP   0.014   0.001   TRP A 356 
 HIS   0.004   0.001   HIS A 180 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 ( 2964)
  covalent geometry    : angle       0.59815 /  0.31 ( 4023)
  SS BOND              : bond        0.00182 /  0.10 (    1)
  SS BOND              : angle       0.29527 /  0.17 (    2)
  hydrogen bonds       : bond        0.04995 /  3.31 (  231)
  hydrogen bonds       : angle       4.11585 /  2.94 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.064 
Fit side-chains
REVERT: A   71 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8833 (t)
REVERT: A  153 MET cc_start: 0.7452 (tpp) cc_final: 0.7026 (tpp)
REVERT: A  201 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7733 (tp)
REVERT: A  255 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6399 (tp40)
REVERT: A  347 MET cc_start: 0.5756 (OUTLIER) cc_final: 0.5457 (tpt)
REVERT: A  398 TRP cc_start: 0.7209 (m100) cc_final: 0.6509 (t-100)
  outliers start: 19
  outliers final: 10
  residues processed: 68
  average time/residue: 0.0334
  time to fit residues: 3.0347
Evaluate side-chains
  63 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 49
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain A residue  360 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0470
   chunk 25 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.8682

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 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 = 0.4473 r_free = 0.4473 target = 0.192581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.169985 restraints weight = 5323.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.174726 restraints weight = 2909.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.177936 restraints weight = 1854.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.180256 restraints weight = 1319.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.181777 restraints weight = 1000.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.4377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6429
moved from start:          0.6755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   2965  Z= 0.166
  Angle     :  0.638   9.617   4025  Z= 0.335
  Chirality :  0.044   0.172    475
  Planarity :  0.004   0.038    482
  Dihedral  :  5.918  57.070    398
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 20.75 %
    Favored  : 72.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.08 (0.43), residues: 357
  helix:  1.80 (0.28), residues: 290
  sheet:  None (None), residues: 0
  loop : -0.38 (0.83), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  60 
 TYR   0.014   0.002   TYR A 119 
 PHE   0.016   0.002   PHE A 326 
 TRP   0.016   0.002   TRP A 356 
 HIS   0.005   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00355 /  0.17 ( 2964)
  covalent geometry    : angle       0.63794 /  0.34 ( 4023)
  SS BOND              : bond        0.00187 /  0.10 (    1)
  SS BOND              : angle       0.33847 /  0.20 (    2)
  hydrogen bonds       : bond        0.05815 /  3.88 (  231)
  hydrogen bonds       : angle       4.33059 /  3.09 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 59
  time to evaluate  : 0.061 
Fit side-chains
REVERT: A   71 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.8921 (t)
REVERT: A  114 THR cc_start: 0.5108 (p) cc_final: 0.4819 (t)
REVERT: A  119 TYR cc_start: 0.5968 (t80) cc_final: 0.5749 (t80)
REVERT: A  153 MET cc_start: 0.7576 (tpp) cc_final: 0.7209 (tpp)
REVERT: A  201 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7849 (tp)
REVERT: A  255 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6626 (tp40)
REVERT: A  347 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5533 (tpt)
REVERT: A  398 TRP cc_start: 0.7147 (m100) cc_final: 0.6385 (t-100)
  outliers start: 21
  outliers final: 10
  residues processed: 69
  average time/residue: 0.0269
  time to fit residues: 2.4640
Evaluate side-chains
  66 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 52
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain A residue  360 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 209 ASN
** A 342 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 = 0.4453 r_free = 0.4453 target = 0.190750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.168766 restraints weight = 5438.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.173478 restraints weight = 2945.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.176680 restraints weight = 1871.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.178684 restraints weight = 1324.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.180281 restraints weight = 1032.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.4354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6472
moved from start:          0.7156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2965  Z= 0.159
  Angle     :  0.611   7.664   4025  Z= 0.320
  Chirality :  0.043   0.155    475
  Planarity :  0.004   0.039    482
  Dihedral  :  6.028  55.018    398
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 23.58 %
    Favored  : 70.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.43), residues: 357
  helix:  1.85 (0.29), residues: 290
  sheet:  None (None), residues: 0
  loop : -0.49 (0.80), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  60 
 TYR   0.013   0.002   TYR A 119 
 PHE   0.017   0.001   PHE A 326 
 TRP   0.013   0.002   TRP A 356 
 HIS   0.004   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.16 ( 2964)
  covalent geometry    : angle       0.61070 /  0.32 ( 4023)
  SS BOND              : bond        0.00094 /  0.05 (    1)
  SS BOND              : angle       0.36253 /  0.21 (    2)
  hydrogen bonds       : bond        0.05491 /  3.68 (  231)
  hydrogen bonds       : angle       4.28462 /  3.10 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 57
  time to evaluate  : 0.065 
Fit side-chains
REVERT: A   71 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8894 (t)
REVERT: A  119 TYR cc_start: 0.6141 (t80) cc_final: 0.5893 (t80)
REVERT: A  153 MET cc_start: 0.7590 (tpp) cc_final: 0.7200 (tpp)
REVERT: A  201 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7858 (tp)
REVERT: A  231 SER cc_start: 0.6210 (t) cc_final: 0.5952 (m)
REVERT: A  232 TYR cc_start: 0.7829 (m-80) cc_final: 0.7559 (m-80)
REVERT: A  255 GLN cc_start: 0.6969 (OUTLIER) cc_final: 0.6494 (tp40)
REVERT: A  347 MET cc_start: 0.5700 (OUTLIER) cc_final: 0.5441 (tpt)
REVERT: A  398 TRP cc_start: 0.7092 (m100) cc_final: 0.6352 (t-100)
  outliers start: 20
  outliers final: 14
  residues processed: 69
  average time/residue: 0.0326
  time to fit residues: 2.9549
Evaluate side-chains
  69 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 51
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  274 TYR
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain A residue  360 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0670
   chunk 9 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.6118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 209 ASN
** A 342 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 = 0.4505 r_free = 0.4505 target = 0.193379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.170177 restraints weight = 5379.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.174451 restraints weight = 2960.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.177240 restraints weight = 1939.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.179373 restraints weight = 1445.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.180724 restraints weight = 1149.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.4407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6474
moved from start:          0.7440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2965  Z= 0.144
  Angle     :  0.607   7.705   4025  Z= 0.316
  Chirality :  0.042   0.145    475
  Planarity :  0.004   0.040    482
  Dihedral  :  6.014  55.721    398
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  6.29 %
    Allowed  : 25.16 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.26 (0.44), residues: 357
  helix:  1.97 (0.29), residues: 290
  sheet:  None (None), residues: 0
  loop : -0.54 (0.82), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.013   0.001   TYR A 119 
 PHE   0.016   0.001   PHE A 326 
 TRP   0.011   0.002   TRP A 251 
 HIS   0.004   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 ( 2964)
  covalent geometry    : angle       0.60689 /  0.32 ( 4023)
  SS BOND              : bond        0.00014 /  0.01 (    1)
  SS BOND              : angle       0.70519 /  0.39 (    2)
  hydrogen bonds       : bond        0.05215 /  3.53 (  231)
  hydrogen bonds       : angle       4.21719 /  3.03 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 59
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8870 (t)
REVERT: A  119 TYR cc_start: 0.6199 (t80) cc_final: 0.5973 (t80)
REVERT: A  145 MET cc_start: 0.7102 (tmm) cc_final: 0.6853 (tmm)
REVERT: A  153 MET cc_start: 0.7528 (tpp) cc_final: 0.7122 (tpp)
REVERT: A  201 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7804 (tp)
REVERT: A  232 TYR cc_start: 0.7811 (m-80) cc_final: 0.7437 (m-10)
REVERT: A  255 GLN cc_start: 0.7122 (OUTLIER) cc_final: 0.6813 (tp40)
REVERT: A  347 MET cc_start: 0.5638 (OUTLIER) cc_final: 0.5386 (tpt)
REVERT: A  398 TRP cc_start: 0.6997 (m100) cc_final: 0.6304 (t-100)
  outliers start: 20
  outliers final: 12
  residues processed: 70
  average time/residue: 0.0270
  time to fit residues: 2.5479
Evaluate side-chains
  70 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 54
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  209 ASN
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  274 TYR
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain A residue  360 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0370
   chunk 2 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.5058

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 209 ASN
** A 342 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 = 0.4540 r_free = 0.4540 target = 0.196463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.172951 restraints weight = 5495.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.177179 restraints weight = 3036.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.180165 restraints weight = 2003.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.182194 restraints weight = 1475.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.183710 restraints weight = 1181.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.4593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6470
moved from start:          0.7618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   2965  Z= 0.136
  Angle     :  0.607   8.268   4025  Z= 0.317
  Chirality :  0.042   0.149    475
  Planarity :  0.004   0.039    482
  Dihedral  :  6.113  55.837    398
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 23.90 %
    Favored  : 69.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.44), residues: 357
  helix:  1.89 (0.29), residues: 290
  sheet:  None (None), residues: 0
  loop : -0.59 (0.82), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.012   0.001   TYR A 119 
 PHE   0.021   0.001   PHE A 165 
 TRP   0.010   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.14 ( 2964)
  covalent geometry    : angle       0.60669 /  0.32 ( 4023)
  SS BOND              : bond        0.00026 /  0.01 (    1)
  SS BOND              : angle       0.55770 /  0.31 (    2)
  hydrogen bonds       : bond        0.04987 /  3.35 (  231)
  hydrogen bonds       : angle       4.14526 /  2.98 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 55
  time to evaluate  : 0.063 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 THR cc_start: 0.9270 (OUTLIER) cc_final: 0.8878 (t)
REVERT: A  145 MET cc_start: 0.7102 (tmm) cc_final: 0.6839 (tmm)
REVERT: A  153 MET cc_start: 0.7508 (tpp) cc_final: 0.7108 (tpp)
REVERT: A  201 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7775 (tp)
REVERT: A  255 GLN cc_start: 0.7141 (OUTLIER) cc_final: 0.6853 (tp40)
REVERT: A  329 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7981 (m-40)
REVERT: A  398 TRP cc_start: 0.6926 (m100) cc_final: 0.6287 (t-100)
  outliers start: 22
  outliers final: 16
  residues processed: 67
  average time/residue: 0.0376
  time to fit residues: 3.2993
Evaluate side-chains
  70 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 50
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  209 ASN
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  360 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    0.0570
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.7098

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 209 ASN
** A 342 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 = 0.4442 r_free = 0.4442 target = 0.191691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.171148 restraints weight = 5667.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.175735 restraints weight = 2926.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.178963 restraints weight = 1830.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.180966 restraints weight = 1275.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.182361 restraints weight = 980.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.4359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6482
moved from start:          0.7863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2965  Z= 0.147
  Angle     :  0.646   9.068   4025  Z= 0.336
  Chirality :  0.043   0.149    475
  Planarity :  0.004   0.038    482
  Dihedral  :  6.177  55.826    398
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 25.79 %
    Favored  : 67.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.44), residues: 357
  helix:  1.83 (0.29), residues: 290
  sheet:  None (None), residues: 0
  loop : -0.71 (0.82), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.013   0.001   TYR A 119 
 PHE   0.018   0.001   PHE A 326 
 TRP   0.010   0.002   TRP A 356 
 HIS   0.004   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.15 ( 2964)
  covalent geometry    : angle       0.64651 /  0.34 ( 4023)
  SS BOND              : bond        0.00071 /  0.04 (    1)
  SS BOND              : angle       0.51070 /  0.29 (    2)
  hydrogen bonds       : bond        0.05142 /  3.44 (  231)
  hydrogen bonds       : angle       4.19168 /  3.03 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8889 (t)
REVERT: A  145 MET cc_start: 0.7050 (tmm) cc_final: 0.6763 (tmm)
REVERT: A  153 MET cc_start: 0.7521 (tpp) cc_final: 0.7128 (tpp)
REVERT: A  201 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7833 (tp)
REVERT: A  255 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.6803 (tp40)
REVERT: A  329 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7985 (m-40)
REVERT: A  398 TRP cc_start: 0.6878 (m100) cc_final: 0.6193 (t-100)
  outliers start: 21
  outliers final: 14
  residues processed: 69
  average time/residue: 0.0307
  time to fit residues: 2.9123
Evaluate side-chains
  71 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 53
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  209 ASN
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  271 ILE
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  360 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0040
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6392

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 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 = 0.4440 r_free = 0.4440 target = 0.191016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.170950 restraints weight = 5624.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.175680 restraints weight = 2915.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.178793 restraints weight = 1796.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.180676 restraints weight = 1243.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.181971 restraints weight = 959.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.4362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6491
moved from start:          0.8035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2965  Z= 0.146
  Angle     :  0.657   9.216   4025  Z= 0.344
  Chirality :  0.043   0.149    475
  Planarity :  0.004   0.038    482
  Dihedral  :  6.174  55.815    398
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 26.42 %
    Favored  : 68.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.44), residues: 357
  helix:  1.80 (0.29), residues: 290
  sheet:  None (None), residues: 0
  loop : -0.85 (0.80), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.011   0.001   TYR A 119 
 PHE   0.016   0.001   PHE A 326 
 TRP   0.011   0.002   TRP A 251 
 HIS   0.003   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.15 ( 2964)
  covalent geometry    : angle       0.65664 /  0.34 ( 4023)
  SS BOND              : bond        0.00005 /  0.00 (    1)
  SS BOND              : angle       0.52851 /  0.30 (    2)
  hydrogen bonds       : bond        0.05178 /  3.47 (  231)
  hydrogen bonds       : angle       4.27472 /  3.08 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 53
  time to evaluate  : 0.062 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8871 (t)
REVERT: A  145 MET cc_start: 0.7093 (tmm) cc_final: 0.6803 (tmm)
REVERT: A  153 MET cc_start: 0.7492 (tpp) cc_final: 0.7095 (tpp)
REVERT: A  201 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7799 (tp)
REVERT: A  255 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6848 (tp40)
REVERT: A  329 ASN cc_start: 0.8237 (OUTLIER) cc_final: 0.7901 (m-40)
REVERT: A  398 TRP cc_start: 0.6866 (m100) cc_final: 0.6203 (t-100)
  outliers start: 15
  outliers final: 11
  residues processed: 61
  average time/residue: 0.0329
  time to fit residues: 2.7242
Evaluate side-chains
  67 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 52
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  360 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    0.3980
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 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 = 0.4520 r_free = 0.4520 target = 0.193583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.173029 restraints weight = 5467.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.177624 restraints weight = 2905.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.180580 restraints weight = 1826.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.182701 restraints weight = 1304.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.184074 restraints weight = 993.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.4469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
moved from start:          0.8300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2965  Z= 0.155
  Angle     :  0.674   8.896   4025  Z= 0.351
  Chirality :  0.043   0.166    475
  Planarity :  0.004   0.037    482
  Dihedral  :  6.263  56.003    398
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 26.10 %
    Favored  : 68.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.44), residues: 357
  helix:  1.74 (0.29), residues: 291
  sheet:  None (None), residues: 0
  loop : -1.14 (0.80), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  60 
 TYR   0.011   0.002   TYR A 119 
 PHE   0.012   0.001   PHE A 326 
 TRP   0.013   0.002   TRP A 251 
 HIS   0.004   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.15 ( 2964)
  covalent geometry    : angle       0.67380 /  0.35 ( 4023)
  SS BOND              : bond        0.00000 /  0.00 (    1)
  SS BOND              : angle       0.47309 /  0.27 (    2)
  hydrogen bonds       : bond        0.05522 /  3.75 (  231)
  hydrogen bonds       : angle       4.36454 /  3.14 (  669)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 539.93 seconds
wall clock time: 9 minutes 57.35 seconds (597.35 seconds total)