Starting phenix.real_space_refine
on Fri Aug 22 14:37:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8c02_16353/08_2025/8c02_16353.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8c02_16353/08_2025/8c02_16353.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8c02_16353/08_2025/8c02_16353.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8c02_16353/08_2025/8c02_16353.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8c02_16353/08_2025/8c02_16353.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8c02_16353/08_2025/8c02_16353.map"
  }
  resolution = 4.09
  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=   0.001 sd=   0.027
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      31      5.16       5
     C    2767      2.51       5
     N     695      2.21       5
     O     749      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4242
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3300
          Classifications: {'peptide': 429}
          Link IDs: {'PTRANS': 9, 'TRANS': 419}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 942
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 942
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
  Time building chain proxies: 0.89, per 1000 atoms: 0.21
  Number of scatterers: 4242
  At special positions: 0
  Unit cell: (76.818, 100.254, 72.912, 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      31     16.00
     O     749      8.00
     N     695      7.00
     C    2767      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  98 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 169.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1004

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 3 sheets defined
      72.5% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 22
    Processing helix  chain 'A' and resid 23 through 54
    Processing helix  chain 'A' and resid 57 through 86
      removed outlier: 3.897A  pdb=" N   THR A  61 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   ALA A  77 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   ILE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
    Processing helix  chain 'A' and resid 116 through 122
    Processing helix  chain 'A' and resid 127 through 164
    Processing helix  chain 'A' and resid 166 through 199
      Proline residue:  A 189  - end of helix
    Processing helix  chain 'A' and resid 200 through 230
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 4.077A  pdb=" N   VAL A 235 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   LYS A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 231 through 236'
    Processing helix  chain 'A' and resid 288 through 305
      removed outlier: 3.856A  pdb=" N   PHE A 292 " --> pdb=" O   MET A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 318
    Processing helix  chain 'A' and resid 331 through 336
    Processing helix  chain 'A' and resid 338 through 367
      removed outlier: 3.695A  pdb=" N   ARG A 365 " --> pdb=" O   THR A 361 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LYS A 366 " --> pdb=" O   TRP A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 393
    Processing helix  chain 'A' and resid 451 through 483
      removed outlier: 3.642A  pdb=" N   VAL A 455 " --> pdb=" O   PRO A 451 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ILE A 467 " --> pdb=" O   ILE A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 514
    Processing helix  chain 'A' and resid 519 through 546
    Processing helix  chain 'B' and resid 89 through 93
    Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 9
    Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 15
      removed outlier: 6.523A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ARG B  37 " --> pdb=" O   ASN B  99 " (cutoff:3.500A)
      removed outlier: 7.060A  pdb=" N   MET B  36 " --> pdb=" O   ALA B  52 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   ALA B  52 " --> pdb=" O   MET B  36 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   TRP B  38 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 15
      removed outlier: 6.523A  pdb=" N   VAL B  14 " --> pdb=" O   SER B 148 " (cutoff:3.500A)
      removed outlier: 5.615A  pdb=" N   LYS B 101 " --> pdb=" O   TYR B 112 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   TYR B 112 " --> pdb=" O   LYS B 101 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   TYR B 103 " --> pdb=" O   TYR B 110 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    1014 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: 0.44

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1312
        1.34 -     1.46: 1032
        1.46 -     1.58: 1939
        1.58 -     1.70: 0
        1.70 -     1.81: 52
  Bond restraints: 4335
  Sorted by residual:
  bond pdb=" N   MET A 288 "
       pdb=" CA  MET A 288 "
    ideal  model  delta    sigma   weight residual
    1.455  1.493 -0.037 1.25e-02 6.40e+03 8.87e+00
  bond pdb=" N   TYR A 318 "
       pdb=" CA  TYR A 318 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.031 1.32e-02 5.74e+03 5.40e+00
  bond pdb=" CG  GLN A  93 "
       pdb=" CD  GLN A  93 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.31e+00
  bond pdb=" CG1 ILE A 136 "
       pdb=" CD1 ILE A 136 "
    ideal  model  delta    sigma   weight residual
    1.513  1.456  0.057 3.90e-02 6.57e+02 2.14e+00
  bond pdb=" CG  LEU A 222 "
       pdb=" CD1 LEU A 222 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.88e+00
  ... (remaining 4330 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 5701
        1.98 -     3.97: 149
        3.97 -     5.95: 33
        5.95 -     7.94: 12
        7.94 -     9.92: 3
  Bond angle restraints: 5898
  Sorted by residual:
  angle pdb=" CA  LYS B  78 "
        pdb=" CB  LYS B  78 "
        pdb=" CG  LYS B  78 "
      ideal   model   delta    sigma   weight residual
     114.10  121.78   -7.68 2.00e+00 2.50e-01 1.48e+01
  angle pdb=" CA  GLU A 486 "
        pdb=" CB  GLU A 486 "
        pdb=" CG  GLU A 486 "
      ideal   model   delta    sigma   weight residual
     114.10  121.55   -7.45 2.00e+00 2.50e-01 1.39e+01
  angle pdb=" N   GLN A  93 "
        pdb=" CA  GLN A  93 "
        pdb=" CB  GLN A  93 "
      ideal   model   delta    sigma   weight residual
     110.28  115.21   -4.93 1.55e+00 4.16e-01 1.01e+01
  angle pdb=" CB  LYS A 549 "
        pdb=" CG  LYS A 549 "
        pdb=" CD  LYS A 549 "
      ideal   model   delta    sigma   weight residual
     111.30  118.34   -7.04 2.30e+00 1.89e-01 9.36e+00
  angle pdb=" CA  GLU A 290 "
        pdb=" CB  GLU A 290 "
        pdb=" CG  GLU A 290 "
      ideal   model   delta    sigma   weight residual
     114.10  120.04   -5.94 2.00e+00 2.50e-01 8.81e+00
  ... (remaining 5893 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.19: 2262
       16.19 -    32.38: 187
       32.38 -    48.57: 43
       48.57 -    64.76: 7
       64.76 -    80.95: 5
  Dihedral angle restraints: 2504
    sinusoidal: 930
      harmonic: 1574
  Sorted by residual:
  dihedral pdb=" CA  THR A 122 "
           pdb=" C   THR A 122 "
           pdb=" N   MET A 123 "
           pdb=" CA  MET A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.55  -17.45     0      5.00e+00 4.00e-02 1.22e+01
  dihedral pdb=" CA  GLU B  46 "
           pdb=" C   GLU B  46 "
           pdb=" N   ARG B  47 "
           pdb=" CA  ARG B  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.72  -17.28     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  MET B 105 "
           pdb=" C   MET B 105 "
           pdb=" N   ALA B 106 "
           pdb=" CA  ALA B 106 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.97   17.03     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 2501 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 473
       0.039 -    0.077: 164
       0.077 -    0.116: 48
       0.116 -    0.155: 7
       0.155 -    0.193: 4
  Chirality restraints: 696
  Sorted by residual:
  chirality pdb=" CA  GLU A 290 "
            pdb=" N   GLU A 290 "
            pdb=" C   GLU A 290 "
            pdb=" CB  GLU A 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.36e-01
  chirality pdb=" CA  GLN A  93 "
            pdb=" N   GLN A  93 "
            pdb=" C   GLN A  93 "
            pdb=" CB  GLN A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.84e-01
  chirality pdb=" CB  ILE B  56 "
            pdb=" CA  ILE B  56 "
            pdb=" CG1 ILE B  56 "
            pdb=" CG2 ILE B  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.81e-01
  ... (remaining 693 not shown)

  Planarity restraints: 719
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 514 "   -0.054 5.00e-02 4.00e+02   8.30e-02 1.10e+01
        pdb=" N   PRO A 515 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO A 515 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 515 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B  29 "   -0.044 5.00e-02 4.00e+02   6.61e-02 6.99e+00
        pdb=" N   PRO B  30 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B  30 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B  30 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 317 "   -0.013 2.00e-02 2.50e+03   2.57e-02 6.62e+00
        pdb=" C   LEU A 317 "    0.044 2.00e-02 2.50e+03
        pdb=" O   LEU A 317 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   TYR A 318 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 716 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 718
        2.76 -     3.29: 4563
        3.29 -     3.83: 7381
        3.83 -     4.36: 7786
        4.36 -     4.90: 13676
  Nonbonded interactions: 34124
  Sorted by model distance:
  nonbonded pdb=" O   CYS B  24 "
            pdb=" OG1 THR B  80 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   VAL A 358 "
            pdb=" OG1 THR A 361 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   ALA B  54 "
            pdb=" NH2 ARG B  74 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" N   MET B 105 "
            pdb=" O   TRP B 108 "
     model   vdw
     2.323 3.120
  nonbonded pdb=" O   THR A 230 "
            pdb=" OG1 THR A 230 "
     model   vdw
     2.339 3.040
  ... (remaining 34119 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.360
  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:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.730
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
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   0.057   4336  Z= 0.188
  Angle     :  0.833   9.920   5900  Z= 0.419
  Chirality :  0.045   0.193    696
  Planarity :  0.007   0.083    719
  Dihedral  : 13.159  80.949   1497
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 19.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  0.00 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.51 (0.35), residues: 541
  helix:  2.10 (0.26), residues: 367
  sheet: -1.31 (0.64), residues: 39
  loop : -1.40 (0.53), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  88 
 TYR   0.030   0.002   TYR A  29 
 PHE   0.016   0.002   PHE A 530 
 TRP   0.030   0.002   TRP B  38 
 HIS   0.002   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 4335)
  covalent geometry    : angle       0.83181 ( 5898)
  SS BOND              : bond        0.00047 (    1)
  SS BOND              : angle       2.16103 (    2)
  hydrogen bonds       : bond        0.12218 (  344)
  hydrogen bonds       : angle       5.58573 ( 1014)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 192
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8755 (t80) cc_final: 0.8459 (t80)
REVERT: A   36 THR cc_start: 0.9349 (m) cc_final: 0.9145 (t)
REVERT: A  111 MET cc_start: 0.8545 (tpt) cc_final: 0.8277 (mmm)
REVERT: A  184 THR cc_start: 0.9334 (m) cc_final: 0.8956 (t)
REVERT: A  290 GLU cc_start: 0.8139 (pm20) cc_final: 0.7931 (pm20)
REVERT: A  312 MET cc_start: 0.8837 (tpt) cc_final: 0.8058 (tpp)
REVERT: A  473 ASP cc_start: 0.9390 (t70) cc_final: 0.9178 (t0)
REVERT: A  536 ILE cc_start: 0.8342 (mm) cc_final: 0.8104 (mm)
REVERT: B   20 LEU cc_start: 0.8822 (tt) cc_final: 0.8444 (mt)
REVERT: B   70 PHE cc_start: 0.7802 (m-10) cc_final: 0.7432 (m-80)
REVERT: B   92 ASP cc_start: 0.7493 (m-30) cc_final: 0.6928 (m-30)
REVERT: B   97 TYR cc_start: 0.7216 (m-80) cc_final: 0.7016 (m-10)
REVERT: B  119 VAL cc_start: 0.9269 (t) cc_final: 0.8910 (p)
  outliers start: 2
  outliers final: 1
  residues processed: 192
  average time/residue: 0.0500
  time to fit residues: 12.5935
Evaluate side-chains
  159 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0370
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.7464

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 228 GLN
A 335 GLN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  15 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.135670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.106917 restraints weight = 8850.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.110291 restraints weight = 5139.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.112687 restraints weight = 3568.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.114225 restraints weight = 2753.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.115469 restraints weight = 2315.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4336  Z= 0.159
  Angle     :  0.663   7.642   5900  Z= 0.338
  Chirality :  0.041   0.164    696
  Planarity :  0.005   0.063    719
  Dihedral  :  4.102  15.678    590
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 14.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.03 (0.36), residues: 541
  helix:  2.39 (0.26), residues: 371
  sheet: -0.21 (0.73), residues: 43
  loop : -1.35 (0.54), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  40 
 TYR   0.025   0.002   TYR A  29 
 PHE   0.007   0.001   PHE B 107 
 TRP   0.019   0.002   TRP B  38 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4335)
  covalent geometry    : angle       0.66183 ( 5898)
  SS BOND              : bond        0.00284 (    1)
  SS BOND              : angle       1.75171 (    2)
  hydrogen bonds       : bond        0.04525 (  344)
  hydrogen bonds       : angle       4.53064 ( 1014)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8793 (t80) cc_final: 0.8586 (t80)
REVERT: A  111 MET cc_start: 0.8574 (tpt) cc_final: 0.8209 (mmm)
REVERT: A  179 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7960 (mtm-85)
REVERT: A  180 ILE cc_start: 0.8284 (mm) cc_final: 0.8080 (mm)
REVERT: A  488 GLU cc_start: 0.7319 (tp30) cc_final: 0.7058 (tp30)
REVERT: A  536 ILE cc_start: 0.8266 (mm) cc_final: 0.8051 (mm)
REVERT: B    6 LEU cc_start: 0.8587 (pp) cc_final: 0.8305 (pp)
REVERT: B    8 GLU cc_start: 0.7465 (mp0) cc_final: 0.5906 (mp0)
REVERT: B   34 ASN cc_start: 0.8155 (m-40) cc_final: 0.7523 (m110)
REVERT: B   70 PHE cc_start: 0.7697 (m-10) cc_final: 0.7353 (m-80)
REVERT: B   92 ASP cc_start: 0.7352 (m-30) cc_final: 0.6905 (m-30)
REVERT: B   97 TYR cc_start: 0.7572 (m-80) cc_final: 0.7222 (m-10)
REVERT: B  108 TRP cc_start: 0.8167 (t-100) cc_final: 0.7294 (t-100)
REVERT: B  115 GLN cc_start: 0.8243 (pm20) cc_final: 0.7991 (pm20)
REVERT: B  117 THR cc_start: 0.8804 (p) cc_final: 0.8588 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.0585
  time to fit residues: 14.6489
Evaluate side-chains
  164 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 5 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0370
   chunk 38 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7262

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.135678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.107708 restraints weight = 8687.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.111126 restraints weight = 4994.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.113513 restraints weight = 3407.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.115161 restraints weight = 2599.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.116090 restraints weight = 2155.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   4336  Z= 0.155
  Angle     :  0.647   9.167   5900  Z= 0.335
  Chirality :  0.040   0.163    696
  Planarity :  0.004   0.046    719
  Dihedral  :  3.961  16.981    590
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  3.08 %
    Favored  : 96.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.03 (0.36), residues: 541
  helix:  2.37 (0.26), residues: 370
  sheet:  0.39 (0.82), residues: 44
  loop : -1.52 (0.52), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  21 
 TYR   0.016   0.001   TYR B  62 
 PHE   0.009   0.001   PHE A 292 
 TRP   0.033   0.002   TRP B  38 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 4335)
  covalent geometry    : angle       0.64608 ( 5898)
  SS BOND              : bond        0.00177 (    1)
  SS BOND              : angle       1.45506 (    2)
  hydrogen bonds       : bond        0.04362 (  344)
  hydrogen bonds       : angle       4.44133 ( 1014)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 185
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8837 (t80) cc_final: 0.8515 (t80)
REVERT: A   29 TYR cc_start: 0.9298 (m-10) cc_final: 0.9029 (m-10)
REVERT: A  179 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.8071 (ttm110)
REVERT: A  180 ILE cc_start: 0.8313 (mm) cc_final: 0.8081 (mm)
REVERT: A  309 LEU cc_start: 0.8769 (mt) cc_final: 0.8303 (mt)
REVERT: A  536 ILE cc_start: 0.8281 (mm) cc_final: 0.8062 (mm)
REVERT: B   34 ASN cc_start: 0.8103 (m-40) cc_final: 0.7595 (m110)
REVERT: B   36 MET cc_start: 0.8900 (mmm) cc_final: 0.8691 (mmm)
REVERT: B   92 ASP cc_start: 0.7361 (m-30) cc_final: 0.6822 (m-30)
REVERT: B   97 TYR cc_start: 0.7936 (m-80) cc_final: 0.7523 (m-10)
REVERT: B  108 TRP cc_start: 0.8374 (t-100) cc_final: 0.7780 (t-100)
REVERT: B  115 GLN cc_start: 0.8166 (pm20) cc_final: 0.7888 (pm20)
REVERT: B  119 VAL cc_start: 0.8897 (m) cc_final: 0.8594 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 185
  average time/residue: 0.0550
  time to fit residues: 13.0404
Evaluate side-chains
  159 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 158
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   chunk 35 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 305 GLN
** A 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.135825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.108792 restraints weight = 8719.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.112022 restraints weight = 5008.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.114539 restraints weight = 3454.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.116216 restraints weight = 2580.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.117252 restraints weight = 2113.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4336  Z= 0.157
  Angle     :  0.655   8.549   5900  Z= 0.335
  Chirality :  0.040   0.148    696
  Planarity :  0.004   0.066    719
  Dihedral  :  3.998  15.651    590
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  4.85 %
    Favored  : 94.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.36), residues: 541
  helix:  2.32 (0.26), residues: 371
  sheet:  0.17 (0.89), residues: 38
  loop : -1.12 (0.54), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  88 
 TYR   0.015   0.001   TYR A 318 
 PHE   0.029   0.001   PHE B  70 
 TRP   0.017   0.001   TRP B  38 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 4335)
  covalent geometry    : angle       0.65458 ( 5898)
  SS BOND              : bond        0.00199 (    1)
  SS BOND              : angle       1.31580 (    2)
  hydrogen bonds       : bond        0.04362 (  344)
  hydrogen bonds       : angle       4.48505 ( 1014)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 186
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8710 (t80) cc_final: 0.8352 (t80)
REVERT: A  111 MET cc_start: 0.8141 (mmm) cc_final: 0.7826 (mmm)
REVERT: A  119 GLU cc_start: 0.7987 (pm20) cc_final: 0.7727 (pm20)
REVERT: A  180 ILE cc_start: 0.8282 (mm) cc_final: 0.8072 (mm)
REVERT: A  205 CYS cc_start: 0.7890 (m) cc_final: 0.7246 (m)
REVERT: A  302 TYR cc_start: 0.8516 (t80) cc_final: 0.8202 (t80)
REVERT: A  335 GLN cc_start: 0.7454 (tp40) cc_final: 0.6632 (tt0)
REVERT: A  355 MET cc_start: 0.8088 (tmm) cc_final: 0.7874 (tmm)
REVERT: A  485 ILE cc_start: 0.8876 (mp) cc_final: 0.8555 (mt)
REVERT: A  488 GLU cc_start: 0.7153 (tp30) cc_final: 0.6831 (tp30)
REVERT: B   30 PRO cc_start: 0.9574 (Cg_exo) cc_final: 0.8873 (Cg_endo)
REVERT: B   31 VAL cc_start: 0.8397 (m) cc_final: 0.8084 (m)
REVERT: B   34 ASN cc_start: 0.8070 (m-40) cc_final: 0.7664 (m-40)
REVERT: B   38 TRP cc_start: 0.8323 (m100) cc_final: 0.7833 (m100)
REVERT: B   84 GLN cc_start: 0.8152 (tp40) cc_final: 0.7887 (tp40)
REVERT: B   97 TYR cc_start: 0.7863 (m-80) cc_final: 0.7268 (m-10)
REVERT: B  108 TRP cc_start: 0.8428 (t-100) cc_final: 0.8203 (t-100)
REVERT: B  119 VAL cc_start: 0.8780 (m) cc_final: 0.8390 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 186
  average time/residue: 0.0545
  time to fit residues: 12.9523
Evaluate side-chains
  162 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0030
   chunk 12 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.135035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.107804 restraints weight = 8778.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.111306 restraints weight = 5075.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.113718 restraints weight = 3446.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.115263 restraints weight = 2623.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.116453 restraints weight = 2182.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4336  Z= 0.150
  Angle     :  0.685   9.041   5900  Z= 0.347
  Chirality :  0.040   0.173    696
  Planarity :  0.004   0.038    719
  Dihedral  :  3.944  15.607    590
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  3.52 %
    Favored  : 96.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.36), residues: 541
  helix:  2.33 (0.26), residues: 369
  sheet:  0.35 (0.84), residues: 38
  loop : -1.06 (0.54), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 293 
 TYR   0.015   0.001   TYR A 318 
 PHE   0.009   0.001   PHE A 292 
 TRP   0.014   0.001   TRP B 108 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 4335)
  covalent geometry    : angle       0.68523 ( 5898)
  SS BOND              : bond        0.00259 (    1)
  SS BOND              : angle       0.70647 (    2)
  hydrogen bonds       : bond        0.04261 (  344)
  hydrogen bonds       : angle       4.38176 ( 1014)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 187
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 PHE cc_start: 0.8667 (t80) cc_final: 0.8304 (t80)
REVERT: A  111 MET cc_start: 0.8112 (mmm) cc_final: 0.7835 (mmm)
REVERT: A  119 GLU cc_start: 0.8062 (pm20) cc_final: 0.7836 (pm20)
REVERT: A  180 ILE cc_start: 0.8136 (mm) cc_final: 0.7903 (mm)
REVERT: A  312 MET cc_start: 0.7821 (tpt) cc_final: 0.7381 (tpt)
REVERT: A  335 GLN cc_start: 0.7461 (tp40) cc_final: 0.6425 (tt0)
REVERT: A  355 MET cc_start: 0.8231 (tmm) cc_final: 0.7959 (tmm)
REVERT: A  473 ASP cc_start: 0.9623 (t70) cc_final: 0.9171 (t0)
REVERT: B   21 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.8430 (mmm-85)
REVERT: B   30 PRO cc_start: 0.9502 (Cg_exo) cc_final: 0.8952 (Cg_endo)
REVERT: B   34 ASN cc_start: 0.8416 (m-40) cc_final: 0.8059 (m-40)
REVERT: B   38 TRP cc_start: 0.8346 (m100) cc_final: 0.7903 (m100)
REVERT: B   46 GLU cc_start: 0.7195 (pp20) cc_final: 0.6940 (pp20)
REVERT: B   92 ASP cc_start: 0.7232 (m-30) cc_final: 0.6864 (m-30)
REVERT: B   97 TYR cc_start: 0.7878 (m-80) cc_final: 0.7322 (m-10)
REVERT: B  119 VAL cc_start: 0.8830 (m) cc_final: 0.8446 (m)
  outliers start: 2
  outliers final: 1
  residues processed: 187
  average time/residue: 0.0535
  time to fit residues: 13.0096
Evaluate side-chains
  162 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0060
   chunk 22 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 43 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0670
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.4334

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  79 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.137674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.111195 restraints weight = 8747.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.114535 restraints weight = 5106.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.116831 restraints weight = 3499.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.118505 restraints weight = 2691.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.119593 restraints weight = 2211.306|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.3788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4336  Z= 0.143
  Angle     :  0.681   8.687   5900  Z= 0.347
  Chirality :  0.041   0.151    696
  Planarity :  0.004   0.037    719
  Dihedral  :  3.944  15.017    590
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  1.98 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.04 (0.36), residues: 541
  helix:  2.26 (0.26), residues: 369
  sheet:  0.39 (0.75), residues: 43
  loop : -1.04 (0.56), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 293 
 TYR   0.030   0.001   TYR A 318 
 PHE   0.011   0.001   PHE A 541 
 TRP   0.011   0.001   TRP A  42 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4335)
  covalent geometry    : angle       0.68059 ( 5898)
  SS BOND              : bond        0.00293 (    1)
  SS BOND              : angle       0.51864 (    2)
  hydrogen bonds       : bond        0.04146 (  344)
  hydrogen bonds       : angle       4.35085 ( 1014)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 TYR cc_start: 0.8728 (t80) cc_final: 0.8521 (t80)
REVERT: A  111 MET cc_start: 0.8159 (mmm) cc_final: 0.7859 (mmm)
REVERT: A  119 GLU cc_start: 0.8123 (pm20) cc_final: 0.7837 (pm20)
REVERT: A  180 ILE cc_start: 0.8003 (mm) cc_final: 0.7792 (mm)
REVERT: A  190 MET cc_start: 0.8766 (tmm) cc_final: 0.8475 (tmm)
REVERT: A  335 GLN cc_start: 0.7573 (tp40) cc_final: 0.6709 (tt0)
REVERT: A  355 MET cc_start: 0.8156 (tmm) cc_final: 0.7803 (tmm)
REVERT: A  473 ASP cc_start: 0.9562 (t70) cc_final: 0.9193 (t0)
REVERT: B   30 PRO cc_start: 0.9441 (Cg_exo) cc_final: 0.8892 (Cg_endo)
REVERT: B   34 ASN cc_start: 0.8374 (m-40) cc_final: 0.7831 (m110)
REVERT: B   38 TRP cc_start: 0.8308 (m100) cc_final: 0.7830 (m100)
REVERT: B   97 TYR cc_start: 0.7787 (m-80) cc_final: 0.7217 (m-10)
REVERT: B  119 VAL cc_start: 0.8740 (m) cc_final: 0.8374 (m)
  outliers start: 1
  outliers final: 0
  residues processed: 183
  average time/residue: 0.0532
  time to fit residues: 12.6341
Evaluate side-chains
  155 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 45 optimal weight:    6.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.134511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.106846 restraints weight = 9036.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.110469 restraints weight = 5177.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.112810 restraints weight = 3503.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.114635 restraints weight = 2672.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.115820 restraints weight = 2192.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.3984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   4336  Z= 0.169
  Angle     :  0.710   8.793   5900  Z= 0.363
  Chirality :  0.041   0.152    696
  Planarity :  0.004   0.040    719
  Dihedral  :  3.924  15.393    590
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  2.01 (0.36), residues: 541
  helix:  2.23 (0.26), residues: 369
  sheet:  0.67 (0.75), residues: 43
  loop : -1.15 (0.57), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 293 
 TYR   0.025   0.002   TYR A 318 
 PHE   0.014   0.001   PHE A 292 
 TRP   0.011   0.001   TRP A  42 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4335)
  covalent geometry    : angle       0.71051 ( 5898)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       0.28213 (    2)
  hydrogen bonds       : bond        0.04252 (  344)
  hydrogen bonds       : angle       4.43384 ( 1014)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8700 (mm-30)
REVERT: A  111 MET cc_start: 0.8227 (mmm) cc_final: 0.7870 (mmm)
REVERT: A  119 GLU cc_start: 0.8171 (pm20) cc_final: 0.7856 (pm20)
REVERT: A  190 MET cc_start: 0.8580 (tmm) cc_final: 0.8319 (tmm)
REVERT: A  312 MET cc_start: 0.7634 (tpt) cc_final: 0.7158 (mmp)
REVERT: A  335 GLN cc_start: 0.7588 (tp40) cc_final: 0.6713 (tt0)
REVERT: A  500 ASN cc_start: 0.8627 (m110) cc_final: 0.8382 (m110)
REVERT: B   20 LEU cc_start: 0.8532 (tt) cc_final: 0.8278 (mt)
REVERT: B   30 PRO cc_start: 0.9494 (Cg_exo) cc_final: 0.8862 (Cg_endo)
REVERT: B   34 ASN cc_start: 0.8431 (m-40) cc_final: 0.7776 (m110)
REVERT: B   38 TRP cc_start: 0.8357 (m100) cc_final: 0.7852 (m100)
REVERT: B   97 TYR cc_start: 0.7944 (m-80) cc_final: 0.7501 (m-10)
REVERT: B  119 VAL cc_start: 0.8729 (m) cc_final: 0.8424 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.0521
  time to fit residues: 12.0698
Evaluate side-chains
  153 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.135467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.108294 restraints weight = 8564.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.111705 restraints weight = 4896.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.114124 restraints weight = 3315.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.115487 restraints weight = 2531.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.116671 restraints weight = 2128.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   4336  Z= 0.165
  Angle     :  0.718   9.090   5900  Z= 0.369
  Chirality :  0.042   0.180    696
  Planarity :  0.004   0.042    719
  Dihedral  :  3.979  14.942    590
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.89 (0.36), residues: 541
  helix:  2.15 (0.26), residues: 369
  sheet:  0.68 (0.72), residues: 43
  loop : -1.26 (0.56), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 293 
 TYR   0.022   0.001   TYR A 318 
 PHE   0.016   0.001   PHE A 292 
 TRP   0.012   0.001   TRP A  42 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 4335)
  covalent geometry    : angle       0.71801 ( 5898)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       0.27963 (    2)
  hydrogen bonds       : bond        0.04283 (  344)
  hydrogen bonds       : angle       4.50090 ( 1014)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.8293 (mmm) cc_final: 0.7845 (mmm)
REVERT: A  119 GLU cc_start: 0.8359 (pm20) cc_final: 0.8071 (pm20)
REVERT: A  190 MET cc_start: 0.8560 (tmm) cc_final: 0.8294 (tmm)
REVERT: A  194 GLN cc_start: 0.8259 (tt0) cc_final: 0.7665 (tt0)
REVERT: A  335 GLN cc_start: 0.7577 (tp40) cc_final: 0.6737 (tt0)
REVERT: A  463 ILE cc_start: 0.9050 (mm) cc_final: 0.8839 (mm)
REVERT: A  495 VAL cc_start: 0.9552 (m) cc_final: 0.9202 (m)
REVERT: A  533 MET cc_start: 0.7648 (mmm) cc_final: 0.6945 (ttt)
REVERT: B   30 PRO cc_start: 0.9468 (Cg_exo) cc_final: 0.8841 (Cg_endo)
REVERT: B   34 ASN cc_start: 0.8402 (m-40) cc_final: 0.7769 (m110)
REVERT: B   38 TRP cc_start: 0.8368 (m100) cc_final: 0.7860 (m100)
REVERT: B   97 TYR cc_start: 0.7808 (m-80) cc_final: 0.7524 (m-10)
REVERT: B  119 VAL cc_start: 0.8749 (m) cc_final: 0.8439 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.0510
  time to fit residues: 11.3426
Evaluate side-chains
  148 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 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 = 0.3777 r_free = 0.3777 target = 0.136152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.108566 restraints weight = 8846.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.111955 restraints weight = 5262.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.114360 restraints weight = 3659.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.115902 restraints weight = 2817.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.117121 restraints weight = 2357.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4336  Z= 0.164
  Angle     :  0.746   9.436   5900  Z= 0.380
  Chirality :  0.042   0.181    696
  Planarity :  0.004   0.048    719
  Dihedral  :  4.005  16.279    590
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 13.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.90 (0.36), residues: 541
  helix:  2.12 (0.26), residues: 370
  sheet:  0.72 (0.70), residues: 43
  loop : -1.16 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 293 
 TYR   0.019   0.001   TYR A 318 
 PHE   0.015   0.001   PHE B  70 
 TRP   0.022   0.001   TRP A 470 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 4335)
  covalent geometry    : angle       0.74650 ( 5898)
  SS BOND              : bond        0.00248 (    1)
  SS BOND              : angle       0.33100 (    2)
  hydrogen bonds       : bond        0.04231 (  344)
  hydrogen bonds       : angle       4.47363 ( 1014)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 TYR cc_start: 0.9187 (m-10) cc_final: 0.8887 (m-80)
REVERT: A  111 MET cc_start: 0.8259 (mmm) cc_final: 0.7806 (mmm)
REVERT: A  119 GLU cc_start: 0.8373 (pm20) cc_final: 0.8107 (pm20)
REVERT: A  190 MET cc_start: 0.8565 (tmm) cc_final: 0.8301 (tmm)
REVERT: A  194 GLN cc_start: 0.8242 (tt0) cc_final: 0.7658 (tt0)
REVERT: A  290 GLU cc_start: 0.8126 (pm20) cc_final: 0.7002 (pm20)
REVERT: A  302 TYR cc_start: 0.8657 (t80) cc_final: 0.8386 (t80)
REVERT: A  335 GLN cc_start: 0.7552 (tp40) cc_final: 0.6692 (tt0)
REVERT: A  393 MET cc_start: 0.7942 (mmm) cc_final: 0.7724 (mmt)
REVERT: A  533 MET cc_start: 0.7785 (mmm) cc_final: 0.6922 (ttt)
REVERT: B   21 ARG cc_start: 0.8856 (mmm-85) cc_final: 0.8597 (mmm-85)
REVERT: B   22 LEU cc_start: 0.8829 (mm) cc_final: 0.8608 (mm)
REVERT: B   30 PRO cc_start: 0.9378 (Cg_exo) cc_final: 0.8860 (Cg_endo)
REVERT: B   34 ASN cc_start: 0.8260 (m-40) cc_final: 0.7621 (m110)
REVERT: B   38 TRP cc_start: 0.8357 (m100) cc_final: 0.7828 (m100)
REVERT: B   80 THR cc_start: 0.8131 (t) cc_final: 0.7873 (t)
REVERT: B   82 TYR cc_start: 0.7169 (m-10) cc_final: 0.6887 (m-10)
REVERT: B   97 TYR cc_start: 0.7839 (m-80) cc_final: 0.7532 (m-10)
REVERT: B  119 VAL cc_start: 0.8752 (m) cc_final: 0.8451 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0490
  time to fit residues: 11.2743
Evaluate side-chains
  157 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 47 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0980
   chunk 50 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 212 ASN
A 380 GLN
B  41 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.136047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.108413 restraints weight = 8710.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.111894 restraints weight = 5053.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.114337 restraints weight = 3462.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.115958 restraints weight = 2644.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.116607 restraints weight = 2197.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.4373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4336  Z= 0.163
  Angle     :  0.760   9.676   5900  Z= 0.389
  Chirality :  0.042   0.179    696
  Planarity :  0.004   0.038    719
  Dihedral  :  4.019  15.461    590
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.44 %
    Allowed  :  0.00 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.73 (0.36), residues: 541
  helix:  2.01 (0.26), residues: 371
  sheet:  0.76 (0.72), residues: 43
  loop : -1.38 (0.56), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 293 
 TYR   0.021   0.002   TYR A 302 
 PHE   0.027   0.002   PHE A 292 
 TRP   0.024   0.002   TRP A 470 
 HIS   0.004   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 4335)
  covalent geometry    : angle       0.75976 ( 5898)
  SS BOND              : bond        0.00305 (    1)
  SS BOND              : angle       0.41432 (    2)
  hydrogen bonds       : bond        0.04216 (  344)
  hydrogen bonds       : angle       4.51094 ( 1014)

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

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

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1082 Ramachandran restraints generated.
    541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 175
  time to evaluate  : 0.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 MET cc_start: 0.8267 (mmm) cc_final: 0.7845 (mmm)
REVERT: A  119 GLU cc_start: 0.8412 (pm20) cc_final: 0.8117 (pm20)
REVERT: A  190 MET cc_start: 0.8535 (tmm) cc_final: 0.8254 (tmm)
REVERT: A  194 GLN cc_start: 0.8288 (tt0) cc_final: 0.7707 (tt0)
REVERT: A  302 TYR cc_start: 0.8513 (t80) cc_final: 0.8221 (t80)
REVERT: A  335 GLN cc_start: 0.7557 (tp40) cc_final: 0.6728 (tt0)
REVERT: A  393 MET cc_start: 0.7612 (mmm) cc_final: 0.7356 (mmt)
REVERT: A  466 ARG cc_start: 0.8301 (tpp80) cc_final: 0.8071 (tpp80)
REVERT: A  500 ASN cc_start: 0.8584 (m110) cc_final: 0.8345 (m-40)
REVERT: B   30 PRO cc_start: 0.9363 (Cg_exo) cc_final: 0.8843 (Cg_endo)
REVERT: B   34 ASN cc_start: 0.8252 (m-40) cc_final: 0.7581 (m110)
REVERT: B   38 TRP cc_start: 0.8349 (m100) cc_final: 0.7791 (m100)
REVERT: B   97 TYR cc_start: 0.7867 (m-80) cc_final: 0.7586 (m-10)
REVERT: B  119 VAL cc_start: 0.8785 (m) cc_final: 0.8480 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0522
  time to fit residues: 12.1169
Evaluate side-chains
  157 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0980
   chunk 17 optimal weight:    0.1980
   chunk 10 optimal weight:    7.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.138443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.111054 restraints weight = 8537.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.114566 restraints weight = 4881.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.116926 restraints weight = 3331.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.118811 restraints weight = 2559.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.119998 restraints weight = 2095.508|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.4527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4336  Z= 0.153
  Angle     :  0.758   9.770   5900  Z= 0.386
  Chirality :  0.042   0.182    696
  Planarity :  0.004   0.032    719
  Dihedral  :  3.960  17.733    590
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 13.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.44 %
    Favored  : 99.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 aren not related in a simple way.
  whole:  1.94 (0.37), residues: 541
  helix:  2.16 (0.27), residues: 370
  sheet:  0.95 (0.74), residues: 43
  loop : -1.29 (0.57), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 293 
 TYR   0.019   0.001   TYR A  29 
 PHE   0.026   0.001   PHE A 292 
 TRP   0.015   0.001   TRP A 470 
 HIS   0.003   0.001   HIS A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 4335)
  covalent geometry    : angle       0.75807 ( 5898)
  SS BOND              : bond        0.00221 (    1)
  SS BOND              : angle       0.48051 (    2)
  hydrogen bonds       : bond        0.04115 (  344)
  hydrogen bonds       : angle       4.40118 ( 1014)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 784.23 seconds
wall clock time: 14 minutes 9.96 seconds (849.96 seconds total)