Starting phenix.real_space_refine
on Tue Aug  4 22:46:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9s0s_54419/08_2026/9s0s_54419.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9s0s_54419/08_2026/9s0s_54419.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9s0s_54419/08_2026/9s0s_54419.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9s0s_54419/08_2026/9s0s_54419.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9s0s_54419/08_2026/9s0s_54419.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9s0s_54419/08_2026/9s0s_54419.map"
  }
  resolution = 3.4
  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=   0.002
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      42      5.16       5
     C    4696      2.51       5
     N    1134      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  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: 7062
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 3531
          Classifications: {'peptide': 445}
          Link IDs: {'PTRANS': 8, 'TRANS': 436}
          Chain breaks: 2
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.11, per 1000 atoms: 0.30
  Number of scatterers: 7062
  At special positions: 0
  Unit cell: (90.625, 99.325, 74.675, 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      42     16.00
     O    1190      8.00
     N    1134      7.00
     C    4696      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 302.0 milliseconds
  

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1644

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 0 sheets defined
      83.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 94
      removed outlier: 4.749A  pdb=" N   LEU A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE A  91 " --> pdb=" O   THR A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 119
    Processing helix  chain 'A' and resid 170 through 177
    Processing helix  chain 'A' and resid 179 through 181
      No H-bonds generated for 'chain 'A' and resid 179 through 181'
    Processing helix  chain 'A' and resid 182 through 187
    Processing helix  chain 'A' and resid 187 through 198
      removed outlier: 3.809A  pdb=" N   ILE A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 206
      No H-bonds generated for 'chain 'A' and resid 204 through 206'
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.801A  pdb=" N   ALA A 213 " --> pdb=" O   GLY A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 241
    Processing helix  chain 'A' and resid 248 through 260
    Processing helix  chain 'A' and resid 264 through 275
    Processing helix  chain 'A' and resid 277 through 305
    Processing helix  chain 'A' and resid 316 through 352
    Processing helix  chain 'A' and resid 357 through 380
      removed outlier: 4.279A  pdb=" N   PHE A 373 " --> pdb=" O   SER A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 397
    Processing helix  chain 'A' and resid 397 through 402
      removed outlier: 3.634A  pdb=" N   ASN A 401 " --> pdb=" O   TYR A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 436
      removed outlier: 3.936A  pdb=" N   LEU A 433 " --> pdb=" O   MET A 429 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   PHE A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 469
      removed outlier: 3.641A  pdb=" N   PHE A 454 " --> pdb=" O   PHE A 450 " (cutoff:3.500A)
      Proline residue:  A 463  - end of helix
    Processing helix  chain 'A' and resid 477 through 487
    Processing helix  chain 'A' and resid 491 through 501
      removed outlier: 4.535A  pdb=" N   ASP A 501 " --> pdb=" O   LEU A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 536
      removed outlier: 3.606A  pdb=" N   TRP A 523 " --> pdb=" O   PHE A 519 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   THR A 530 " --> pdb=" O   GLY A 526 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   ALA A 531 " --> pdb=" O   GLY A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 575
    Processing helix  chain 'B' and resid 75 through 94
      removed outlier: 4.749A  pdb=" N   LEU B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE B  91 " --> pdb=" O   THR B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 119
    Processing helix  chain 'B' and resid 170 through 177
    Processing helix  chain 'B' and resid 179 through 181
      No H-bonds generated for 'chain 'B' and resid 179 through 181'
    Processing helix  chain 'B' and resid 182 through 187
    Processing helix  chain 'B' and resid 187 through 198
      removed outlier: 3.809A  pdb=" N   ILE B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 206
      No H-bonds generated for 'chain 'B' and resid 204 through 206'
    Processing helix  chain 'B' and resid 207 through 216
      removed outlier: 3.802A  pdb=" N   ALA B 213 " --> pdb=" O   GLY B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 216 through 241
    Processing helix  chain 'B' and resid 248 through 260
    Processing helix  chain 'B' and resid 264 through 275
    Processing helix  chain 'B' and resid 277 through 305
    Processing helix  chain 'B' and resid 316 through 352
    Processing helix  chain 'B' and resid 357 through 380
      removed outlier: 4.279A  pdb=" N   PHE B 373 " --> pdb=" O   SER B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 397
    Processing helix  chain 'B' and resid 397 through 402
      removed outlier: 3.633A  pdb=" N   ASN B 401 " --> pdb=" O   TYR B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 436
      removed outlier: 3.936A  pdb=" N   LEU B 433 " --> pdb=" O   MET B 429 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   PHE B 434 " --> pdb=" O   GLY B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 469
      removed outlier: 3.642A  pdb=" N   PHE B 454 " --> pdb=" O   PHE B 450 " (cutoff:3.500A)
      Proline residue:  B 463  - end of helix
    Processing helix  chain 'B' and resid 477 through 487
    Processing helix  chain 'B' and resid 491 through 501
      removed outlier: 4.535A  pdb=" N   ASP B 501 " --> pdb=" O   LEU B 497 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 536
      removed outlier: 3.606A  pdb=" N   TRP B 523 " --> pdb=" O   PHE B 519 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   THR B 530 " --> pdb=" O   GLY B 526 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   ALA B 531 " --> pdb=" O   GLY B 527 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 575

    541 hydrogen bonds defined for protein.
    1623 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: 0.91

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2130
        1.34 -     1.46: 1976
        1.46 -     1.58: 3068
        1.58 -     1.70: 0
        1.70 -     1.82: 74
  Bond restraints: 7248
  Sorted by residual:
  bond pdb=" CA  ASN A 576 "
       pdb=" CB  ASN A 576 "
    ideal  model  delta    sigma   weight residual
    1.530  1.546 -0.016 1.69e-02 3.50e+03 9.03e-01
  bond pdb=" CB  ASN B 576 "
       pdb=" CG  ASN B 576 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 2.50e-02 1.60e+03 8.38e-01
  bond pdb=" CA  ASN B 576 "
       pdb=" CB  ASN B 576 "
    ideal  model  delta    sigma   weight residual
    1.530  1.545 -0.015 1.69e-02 3.50e+03 8.17e-01
  bond pdb=" CB  ASN A 576 "
       pdb=" CG  ASN A 576 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.79e-01
  bond pdb=" C   LYS B 579 "
       pdb=" N   PRO B 580 "
    ideal  model  delta    sigma   weight residual
    1.334  1.352 -0.018 2.34e-02 1.83e+03 5.94e-01
  ... (remaining 7243 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 9774
        2.02 -     4.04: 44
        4.04 -     6.06: 8
        6.06 -     8.08: 4
        8.08 -    10.10: 2
  Bond angle restraints: 9832
  Sorted by residual:
  angle pdb=" C   HIS A 575 "
        pdb=" N   ASN A 576 "
        pdb=" CA  ASN A 576 "
      ideal   model   delta    sigma   weight residual
     121.54  128.34   -6.80 1.91e+00 2.74e-01 1.27e+01
  angle pdb=" C   HIS B 575 "
        pdb=" N   ASN B 576 "
        pdb=" CA  ASN B 576 "
      ideal   model   delta    sigma   weight residual
     121.54  128.30   -6.76 1.91e+00 2.74e-01 1.25e+01
  angle pdb=" CB  MET A 230 "
        pdb=" CG  MET A 230 "
        pdb=" SD  MET A 230 "
      ideal   model   delta    sigma   weight residual
     112.70  122.80  -10.10 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" CB  MET B 230 "
        pdb=" CG  MET B 230 "
        pdb=" SD  MET B 230 "
      ideal   model   delta    sigma   weight residual
     112.70  122.78  -10.08 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" N   PHE B 204 "
        pdb=" CA  PHE B 204 "
        pdb=" C   PHE B 204 "
      ideal   model   delta    sigma   weight residual
     114.04  110.98    3.06 1.24e+00 6.50e-01 6.10e+00
  ... (remaining 9827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 3626
       17.88 -    35.76: 384
       35.76 -    53.65: 78
       53.65 -    71.53: 8
       71.53 -    89.41: 6
  Dihedral angle restraints: 4102
    sinusoidal: 1542
      harmonic: 2560
  Sorted by residual:
  dihedral pdb=" CA  ASP A 263 "
           pdb=" CB  ASP A 263 "
           pdb=" CG  ASP A 263 "
           pdb=" OD1 ASP A 263 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.53   55.53     1      2.00e+01 2.50e-03 1.04e+01
  dihedral pdb=" CA  ASP B 263 "
           pdb=" CB  ASP B 263 "
           pdb=" CG  ASP B 263 "
           pdb=" OD1 ASP B 263 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.51   55.51     1      2.00e+01 2.50e-03 1.04e+01
  dihedral pdb=" CA  ARG B 539 "
           pdb=" CB  ARG B 539 "
           pdb=" CG  ARG B 539 "
           pdb=" CD  ARG B 539 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.40  -53.60     3      1.50e+01 4.44e-03 9.22e+00
  ... (remaining 4099 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 812
       0.031 -    0.062: 253
       0.062 -    0.094: 55
       0.094 -    0.125: 16
       0.125 -    0.156: 6
  Chirality restraints: 1142
  Sorted by residual:
  chirality pdb=" CB  VAL A 276 "
            pdb=" CA  VAL A 276 "
            pdb=" CG1 VAL A 276 "
            pdb=" CG2 VAL A 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.10e-01
  chirality pdb=" CA  VAL B 276 "
            pdb=" N   VAL B 276 "
            pdb=" C   VAL B 276 "
            pdb=" CB  VAL B 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.15 2.00e-01 2.50e+01 5.99e-01
  chirality pdb=" CA  VAL A 276 "
            pdb=" N   VAL A 276 "
            pdb=" C   VAL A 276 "
            pdb=" CB  VAL A 276 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.15 2.00e-01 2.50e+01 5.94e-01
  ... (remaining 1139 not shown)

  Planarity restraints: 1200
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 188 "   -0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO B 189 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO B 189 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO B 189 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 188 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO A 189 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 575 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.09e+00
        pdb=" C   HIS A 575 "    0.025 2.00e-02 2.50e+03
        pdb=" O   HIS A 575 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ASN A 576 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1197 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1353
        2.76 -     3.30: 6840
        3.30 -     3.83: 12487
        3.83 -     4.37: 13859
        4.37 -     4.90: 24828
  Nonbonded interactions: 59367
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 397 "
            pdb=" OD1 ASP A 574 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OH  TYR B 397 "
            pdb=" OD1 ASP B 574 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG1 THR A 219 "
            pdb=" OD1 ASN A 291 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG1 THR B 219 "
            pdb=" OD1 ASN B 291 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   ILE A 517 "
            pdb=" OG1 THR A 521 "
     model   vdw
     2.295 3.040
  ... (remaining 59362 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.370
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     7.250
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
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      :  0.002   0.025   7248  Z= 0.100
  Angle     :  0.435  10.104   9832  Z= 0.228
  Chirality :  0.034   0.156   1142
  Planarity :  0.003   0.040   1200
  Dihedral  : 15.311  89.411   2458
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 16.31 %
    Favored  : 83.16 %
  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 are not related in a simple way.
  whole:  1.20 (0.28), residues: 878
  helix:  1.37 (0.18), residues: 704
  sheet:  None (None), residues: 0
  loop : -1.49 (0.50), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 500 
 TYR   0.005   0.001   TYR A 231 
 PHE   0.008   0.001   PHE B 414 
 TRP   0.008   0.001   TRP B  89 
 HIS   0.003   0.001   HIS A 100 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00212 /  0.10 ( 7248)
  covalent geometry    : angle       0.43525 /  0.23 ( 9832)
  hydrogen bonds       : bond        0.12398 /  7.68 (  541)
  hydrogen bonds       : angle       5.65535 /  3.87 ( 1623)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 126
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.7495 (mmm-85) cc_final: 0.7262 (mmm160)
REVERT: A  174 ARG cc_start: 0.7746 (mtm180) cc_final: 0.7334 (mtm-85)
REVERT: A  569 MET cc_start: 0.7411 (mmp) cc_final: 0.5887 (tpt)
REVERT: B   94 ARG cc_start: 0.7339 (mmm-85) cc_final: 0.7116 (tpt-90)
REVERT: B  174 ARG cc_start: 0.7742 (mtm180) cc_final: 0.7331 (mtm-85)
REVERT: B  569 MET cc_start: 0.7337 (mmp) cc_final: 0.5953 (tpt)
  outliers start: 4
  outliers final: 2
  residues processed: 126
  average time/residue: 0.0877
  time to fit residues: 14.1032
Evaluate side-chains
  94 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 92
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain B residue  577 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 121 HIS
A 170 ASN
A 242 GLN
A 313 HIS
A 400 ASN
B 170 ASN
B 400 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.130784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.114850 restraints weight = 8415.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 1.48
r_work: 0.3137 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   7248  Z= 0.164
  Angle     :  0.538   7.507   9832  Z= 0.284
  Chirality :  0.038   0.156   1142
  Planarity :  0.004   0.045   1200
  Dihedral  :  4.036  41.507    956
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 17.78 %
    Favored  : 79.55 %
  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 are not related in a simple way.
  whole:  1.55 (0.28), residues: 878
  helix:  1.64 (0.19), residues: 708
  sheet:  None (None), residues: 0
  loop : -1.61 (0.51), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 500 
 TYR   0.019   0.001   TYR B 305 
 PHE   0.016   0.001   PHE A 511 
 TRP   0.007   0.001   TRP B  89 
 HIS   0.004   0.001   HIS B 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.16 ( 7248)
  covalent geometry    : angle       0.53827 /  0.28 ( 9832)
  hydrogen bonds       : bond        0.04147 /  2.75 (  541)
  hydrogen bonds       : angle       4.12412 /  2.92 ( 1623)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A   88 ILE cc_start: 0.8713 (tp) cc_final: 0.8184 (tp)
REVERT: A   94 ARG cc_start: 0.7589 (mmm-85) cc_final: 0.7279 (tpp80)
REVERT: A  174 ARG cc_start: 0.7646 (mtm180) cc_final: 0.7183 (mtm-85)
REVERT: A  230 MET cc_start: 0.8229 (mmm) cc_final: 0.7811 (mmm)
REVERT: A  337 MET cc_start: 0.7679 (tpp) cc_final: 0.7285 (mmm)
REVERT: A  479 ASN cc_start: 0.8158 (OUTLIER) cc_final: 0.7878 (m-40)
REVERT: A  569 MET cc_start: 0.7984 (mmp) cc_final: 0.6355 (tpt)
REVERT: A  572 ASN cc_start: 0.7592 (m-40) cc_final: 0.7376 (t0)
REVERT: B   88 ILE cc_start: 0.8681 (tp) cc_final: 0.8173 (tp)
REVERT: B   94 ARG cc_start: 0.7480 (mmm-85) cc_final: 0.7101 (tpp80)
REVERT: B  174 ARG cc_start: 0.7631 (mtm180) cc_final: 0.7209 (mtm-85)
REVERT: B  230 MET cc_start: 0.8307 (mmm) cc_final: 0.7915 (mmm)
REVERT: B  479 ASN cc_start: 0.8149 (OUTLIER) cc_final: 0.7870 (m-40)
REVERT: B  569 MET cc_start: 0.8019 (mmp) cc_final: 0.6482 (tpt)
REVERT: B  572 ASN cc_start: 0.7608 (m-40) cc_final: 0.7399 (t0)
  outliers start: 20
  outliers final: 8
  residues processed: 104
  average time/residue: 0.0855
  time to fit residues: 11.8205
Evaluate side-chains
  91 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 81
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  502 THR
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  479 ASN
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  577 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 85 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0980
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 170 ASN
A 313 HIS
B 121 HIS
B 242 GLN
B 313 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.131304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.115165 restraints weight = 8281.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 1.51
r_work: 0.3139 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7248  Z= 0.130
  Angle     :  0.471   6.658   9832  Z= 0.249
  Chirality :  0.036   0.147   1142
  Planarity :  0.003   0.043   1200
  Dihedral  :  3.873  41.267    956
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 19.52 %
    Favored  : 78.48 %
  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 are not related in a simple way.
  whole:  1.93 (0.28), residues: 878
  helix:  1.92 (0.19), residues: 710
  sheet:  None (None), residues: 0
  loop : -1.53 (0.51), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 500 
 TYR   0.012   0.001   TYR B 305 
 PHE   0.015   0.001   PHE A 486 
 TRP   0.007   0.001   TRP B 379 
 HIS   0.005   0.001   HIS A 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 ( 7248)
  covalent geometry    : angle       0.47078 /  0.25 ( 9832)
  hydrogen bonds       : bond        0.03861 /  2.52 (  541)
  hydrogen bonds       : angle       3.98770 /  2.83 ( 1623)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A   88 ILE cc_start: 0.8698 (tp) cc_final: 0.8196 (tp)
REVERT: A   94 ARG cc_start: 0.7639 (mmm-85) cc_final: 0.7368 (tpp80)
REVERT: A  174 ARG cc_start: 0.7581 (mtm180) cc_final: 0.7132 (mtm-85)
REVERT: A  337 MET cc_start: 0.7683 (tpp) cc_final: 0.7257 (mmm)
REVERT: A  569 MET cc_start: 0.7993 (mmp) cc_final: 0.6489 (tpt)
REVERT: A  572 ASN cc_start: 0.7513 (m-40) cc_final: 0.7299 (t0)
REVERT: B   94 ARG cc_start: 0.7525 (mmm-85) cc_final: 0.7244 (tpp80)
REVERT: B  174 ARG cc_start: 0.7601 (mtm180) cc_final: 0.7161 (mtm-85)
REVERT: B  353 LYS cc_start: 0.8288 (mttt) cc_final: 0.7653 (mptt)
REVERT: B  569 MET cc_start: 0.8051 (mmp) cc_final: 0.6549 (tpt)
REVERT: B  572 ASN cc_start: 0.7571 (m-40) cc_final: 0.7348 (t0)
  outliers start: 15
  outliers final: 5
  residues processed: 96
  average time/residue: 0.0776
  time to fit residues: 10.1435
Evaluate side-chains
  89 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  577 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0670
   chunk 55 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.6518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.129359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.113134 restraints weight = 8408.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.51
r_work: 0.3107 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.3618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7248  Z= 0.144
  Angle     :  0.486   6.643   9832  Z= 0.258
  Chirality :  0.036   0.152   1142
  Planarity :  0.003   0.044   1200
  Dihedral  :  3.884  40.001    956
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.25 %
    Favored  : 78.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.00 (0.28), residues: 878
  helix:  1.97 (0.19), residues: 710
  sheet:  None (None), residues: 0
  loop : -1.52 (0.51), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 500 
 TYR   0.009   0.001   TYR B 305 
 PHE   0.023   0.001   PHE A 486 
 TRP   0.008   0.001   TRP A 379 
 HIS   0.004   0.001   HIS A 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.14 ( 7248)
  covalent geometry    : angle       0.48604 /  0.26 ( 9832)
  hydrogen bonds       : bond        0.03911 /  2.57 (  541)
  hydrogen bonds       : angle       3.98573 /  2.82 ( 1623)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   88 ILE cc_start: 0.8708 (tp) cc_final: 0.8224 (tp)
REVERT: A   94 ARG cc_start: 0.7679 (mmm-85) cc_final: 0.7335 (tpp80)
REVERT: A  101 GLU cc_start: 0.7163 (OUTLIER) cc_final: 0.6878 (mt-10)
REVERT: A  174 ARG cc_start: 0.7604 (mtm180) cc_final: 0.7187 (mtm-85)
REVERT: A  337 MET cc_start: 0.7811 (tpp) cc_final: 0.7412 (mmm)
REVERT: A  475 LYS cc_start: 0.7984 (mmmt) cc_final: 0.7772 (mmmt)
REVERT: A  569 MET cc_start: 0.8047 (mmp) cc_final: 0.6595 (tpt)
REVERT: A  572 ASN cc_start: 0.7561 (m-40) cc_final: 0.7327 (t0)
REVERT: B   94 ARG cc_start: 0.7626 (mmm-85) cc_final: 0.7309 (tpp80)
REVERT: B  101 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6808 (mp0)
REVERT: B  174 ARG cc_start: 0.7572 (mtm180) cc_final: 0.7110 (mtm-85)
REVERT: B  306 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7952 (mm-40)
REVERT: B  569 MET cc_start: 0.8099 (mmp) cc_final: 0.6668 (tpt)
  outliers start: 19
  outliers final: 11
  residues processed: 105
  average time/residue: 0.0861
  time to fit residues: 11.8699
Evaluate side-chains
  100 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  121 HIS
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  479 ASN
Chi-restraints excluded: chain B residue  577 TYR
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0010
   chunk 31 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.5386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.130208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.113944 restraints weight = 8378.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.52
r_work: 0.3120 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7248  Z= 0.131
  Angle     :  0.472   6.623   9832  Z= 0.251
  Chirality :  0.036   0.150   1142
  Planarity :  0.003   0.043   1200
  Dihedral  :  3.866  40.550    956
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 20.32 %
    Favored  : 77.67 %
  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 are not related in a simple way.
  whole:  2.12 (0.28), residues: 878
  helix:  2.05 (0.19), residues: 710
  sheet:  None (None), residues: 0
  loop : -1.47 (0.51), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 500 
 TYR   0.007   0.001   TYR A 231 
 PHE   0.022   0.001   PHE A 486 
 TRP   0.007   0.001   TRP A 379 
 HIS   0.005   0.001   HIS B 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 ( 7248)
  covalent geometry    : angle       0.47208 /  0.25 ( 9832)
  hydrogen bonds       : bond        0.03795 /  2.49 (  541)
  hydrogen bonds       : angle       3.95656 /  2.80 ( 1623)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.7625 (mmm-85) cc_final: 0.7311 (tpp80)
REVERT: A  101 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6876 (mt-10)
REVERT: A  174 ARG cc_start: 0.7568 (mtm180) cc_final: 0.7024 (mtm-85)
REVERT: A  337 MET cc_start: 0.7731 (tpp) cc_final: 0.7330 (mmm)
REVERT: A  569 MET cc_start: 0.7991 (mmp) cc_final: 0.6557 (tpt)
REVERT: B   94 ARG cc_start: 0.7599 (mmm-85) cc_final: 0.7275 (tpp80)
REVERT: B  101 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6803 (mp0)
REVERT: B  106 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8210 (mtm)
REVERT: B  174 ARG cc_start: 0.7518 (mtm180) cc_final: 0.7006 (mtm-85)
REVERT: B  306 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7913 (mm-40)
REVERT: B  569 MET cc_start: 0.8041 (mmp) cc_final: 0.6594 (tpt)
  outliers start: 15
  outliers final: 10
  residues processed: 96
  average time/residue: 0.0936
  time to fit residues: 11.7599
Evaluate side-chains
  96 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  106 MET
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  479 ASN
Chi-restraints excluded: chain B residue  577 TYR
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 73 optimal weight:    0.9980
   chunk 41 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.7380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.127910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.111933 restraints weight = 8497.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.47
r_work: 0.3100 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7248  Z= 0.154
  Angle     :  0.488   6.645   9832  Z= 0.261
  Chirality :  0.037   0.154   1142
  Planarity :  0.003   0.045   1200
  Dihedral  :  3.900  39.224    956
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.12 %
    Favored  : 78.34 %
  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 are not related in a simple way.
  whole:  2.10 (0.28), residues: 878
  helix:  2.03 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.37 (0.50), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 500 
 TYR   0.008   0.001   TYR A 231 
 PHE   0.024   0.001   PHE A 486 
 TRP   0.007   0.001   TRP B 379 
 HIS   0.004   0.001   HIS A 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.15 ( 7248)
  covalent geometry    : angle       0.48821 /  0.26 ( 9832)
  hydrogen bonds       : bond        0.03952 /  2.61 (  541)
  hydrogen bonds       : angle       4.00902 /  2.84 ( 1623)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.253 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.7655 (mmm-85) cc_final: 0.7378 (tpp80)
REVERT: A  101 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6899 (mt-10)
REVERT: A  174 ARG cc_start: 0.7667 (mtm180) cc_final: 0.7160 (mtm-85)
REVERT: A  337 MET cc_start: 0.7852 (tpp) cc_final: 0.7461 (mmm)
REVERT: A  569 MET cc_start: 0.8071 (mmp) cc_final: 0.6684 (tpt)
REVERT: B   94 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7358 (tpp80)
REVERT: B  101 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6929 (mt-10)
REVERT: B  174 ARG cc_start: 0.7603 (mtm180) cc_final: 0.7036 (mtm-85)
REVERT: B  306 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7992 (mm-40)
REVERT: B  569 MET cc_start: 0.8102 (mmp) cc_final: 0.6693 (tpt)
  outliers start: 19
  outliers final: 14
  residues processed: 99
  average time/residue: 0.0869
  time to fit residues: 11.1312
Evaluate side-chains
  99 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  101 GLU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  467 LEU
Chi-restraints excluded: chain B residue  476 ILE
Chi-restraints excluded: chain B residue  479 ASN
Chi-restraints excluded: chain B residue  577 TYR
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 46 optimal weight:    4.9990
   chunk 54 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.8784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.127197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.111228 restraints weight = 8412.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.48
r_work: 0.3084 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.4015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7248  Z= 0.173
  Angle     :  0.528   8.969   9832  Z= 0.277
  Chirality :  0.037   0.158   1142
  Planarity :  0.003   0.045   1200
  Dihedral  :  3.947  38.858    956
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 19.12 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.01 (0.28), residues: 878
  helix:  1.95 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.33 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 507 
 TYR   0.008   0.001   TYR A 231 
 PHE   0.025   0.001   PHE A 486 
 TRP   0.006   0.001   TRP B  89 
 HIS   0.004   0.001   HIS B 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00400 /  0.17 ( 7248)
  covalent geometry    : angle       0.52836 /  0.28 ( 9832)
  hydrogen bonds       : bond        0.04063 /  2.68 (  541)
  hydrogen bonds       : angle       4.06660 /  2.88 ( 1623)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 86
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.7418 (tpp80)
REVERT: A  101 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6874 (mp0)
REVERT: A  174 ARG cc_start: 0.7665 (mtm180) cc_final: 0.7144 (mtm-85)
REVERT: A  337 MET cc_start: 0.7901 (tpp) cc_final: 0.7510 (mmm)
REVERT: A  569 MET cc_start: 0.8069 (mmp) cc_final: 0.6664 (tpt)
REVERT: B   94 ARG cc_start: 0.7666 (mmm-85) cc_final: 0.7376 (tpp80)
REVERT: B  174 ARG cc_start: 0.7642 (mtm180) cc_final: 0.7150 (mtm-85)
REVERT: B  240 THR cc_start: 0.8510 (m) cc_final: 0.7990 (p)
REVERT: B  306 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7985 (mm-40)
REVERT: B  569 MET cc_start: 0.8099 (mmp) cc_final: 0.6696 (tpt)
  outliers start: 23
  outliers final: 16
  residues processed: 105
  average time/residue: 0.0823
  time to fit residues: 11.2003
Evaluate side-chains
  101 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  476 ILE
Chi-restraints excluded: chain B residue  479 ASN
Chi-restraints excluded: chain B residue  577 TYR
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 86 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.7580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.127666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.111552 restraints weight = 8446.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 1.50
r_work: 0.3090 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7248  Z= 0.157
  Angle     :  0.523   7.324   9832  Z= 0.274
  Chirality :  0.037   0.153   1142
  Planarity :  0.003   0.045   1200
  Dihedral  :  3.967  39.075    956
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 19.25 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.97 (0.28), residues: 878
  helix:  1.92 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.33 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 500 
 TYR   0.008   0.001   TYR A 231 
 PHE   0.026   0.001   PHE A 486 
 TRP   0.006   0.001   TRP B  89 
 HIS   0.004   0.001   HIS B 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.16 ( 7248)
  covalent geometry    : angle       0.52309 /  0.27 ( 9832)
  hydrogen bonds       : bond        0.04015 /  2.65 (  541)
  hydrogen bonds       : angle       4.08422 /  2.89 ( 1623)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.7406 (tpp80)
REVERT: A  101 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6960 (mt-10)
REVERT: A  174 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7159 (mtm-85)
REVERT: A  337 MET cc_start: 0.7887 (tpp) cc_final: 0.7502 (mmm)
REVERT: A  422 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7287 (pt0)
REVERT: A  569 MET cc_start: 0.8057 (mmp) cc_final: 0.6652 (tpt)
REVERT: B   94 ARG cc_start: 0.7648 (mmm-85) cc_final: 0.7351 (tpp80)
REVERT: B  174 ARG cc_start: 0.7613 (mtm180) cc_final: 0.7151 (mtm-85)
REVERT: B  240 THR cc_start: 0.8481 (m) cc_final: 0.7900 (p)
REVERT: B  306 GLN cc_start: 0.8203 (mm-40) cc_final: 0.7944 (mm-40)
REVERT: B  422 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7313 (pt0)
REVERT: B  565 TRP cc_start: 0.5711 (OUTLIER) cc_final: 0.4724 (p90)
REVERT: B  569 MET cc_start: 0.8099 (mmp) cc_final: 0.6728 (tpt)
  outliers start: 22
  outliers final: 16
  residues processed: 103
  average time/residue: 0.0971
  time to fit residues: 13.0305
Evaluate side-chains
  103 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 GLU
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain A residue  581 LEU
Chi-restraints excluded: chain B residue  176 VAL
Chi-restraints excluded: chain B residue  234 VAL
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  422 GLU
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  476 ILE
Chi-restraints excluded: chain B residue  479 ASN
Chi-restraints excluded: chain B residue  565 TRP
Chi-restraints excluded: chain B residue  577 TYR
Chi-restraints excluded: chain B residue  581 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 17 optimal weight:    0.2980
   chunk 81 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0010
   chunk 75 optimal weight:    0.0270
   chunk 13 optimal weight:    0.6980
   overall best weight:    0.3044

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 121 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.137185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.119757 restraints weight = 8234.048|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.76
r_work: 0.3174 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.4048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7248  Z= 0.114
  Angle     :  0.482   6.999   9832  Z= 0.254
  Chirality :  0.036   0.162   1142
  Planarity :  0.003   0.044   1200
  Dihedral  :  3.882  40.456    956
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 20.05 %
    Favored  : 77.54 %
  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 are not related in a simple way.
  whole:  2.32 (0.28), residues: 878
  helix:  2.18 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.25 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 500 
 TYR   0.006   0.001   TYR A 231 
 PHE   0.026   0.001   PHE A 486 
 TRP   0.008   0.001   TRP A 379 
 HIS   0.005   0.001   HIS B 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00242 /  0.11 ( 7248)
  covalent geometry    : angle       0.48231 /  0.25 ( 9832)
  hydrogen bonds       : bond        0.03720 /  2.45 (  541)
  hydrogen bonds       : angle       3.90686 /  2.77 ( 1623)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7358 (tpp80)
REVERT: A  174 ARG cc_start: 0.7556 (mtm180) cc_final: 0.6979 (mtm-85)
REVERT: A  240 THR cc_start: 0.8547 (m) cc_final: 0.8018 (p)
REVERT: A  337 MET cc_start: 0.7773 (tpp) cc_final: 0.7383 (mmm)
REVERT: A  422 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7232 (pt0)
REVERT: A  565 TRP cc_start: 0.5684 (OUTLIER) cc_final: 0.4735 (p90)
REVERT: A  569 MET cc_start: 0.7955 (mmp) cc_final: 0.6537 (tpt)
REVERT: B   94 ARG cc_start: 0.7603 (mmm-85) cc_final: 0.7284 (tpp80)
REVERT: B  121 HIS cc_start: 0.5564 (OUTLIER) cc_final: 0.5349 (t-170)
REVERT: B  174 ARG cc_start: 0.7553 (mtm180) cc_final: 0.6976 (mtm-85)
REVERT: B  240 THR cc_start: 0.8406 (m) cc_final: 0.7860 (p)
REVERT: B  306 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7929 (mm-40)
REVERT: B  422 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7234 (pt0)
REVERT: B  565 TRP cc_start: 0.5730 (OUTLIER) cc_final: 0.4734 (p90)
REVERT: B  569 MET cc_start: 0.7985 (mmp) cc_final: 0.6571 (tpt)
  outliers start: 18
  outliers final: 11
  residues processed: 104
  average time/residue: 0.0928
  time to fit residues: 12.5748
Evaluate side-chains
  102 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  479 ASN
Chi-restraints excluded: chain A residue  565 TRP
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain B residue  121 HIS
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  422 GLU
Chi-restraints excluded: chain B residue  476 ILE
Chi-restraints excluded: chain B residue  479 ASN
Chi-restraints excluded: chain B residue  565 TRP
Chi-restraints excluded: chain B residue  577 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 42 optimal weight:    6.9990
   chunk 83 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 43 optimal weight:    0.1980
   chunk 19 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0980
   overall best weight:    0.4180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.135263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.118431 restraints weight = 8304.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.71
r_work: 0.3168 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.4106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7248  Z= 0.123
  Angle     :  0.504   7.352   9832  Z= 0.262
  Chirality :  0.036   0.161   1142
  Planarity :  0.003   0.044   1200
  Dihedral  :  3.881  39.778    956
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 20.72 %
    Favored  : 77.54 %
  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 are not related in a simple way.
  whole:  2.31 (0.28), residues: 878
  helix:  2.17 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.26 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  97 
 TYR   0.006   0.001   TYR A 231 
 PHE   0.027   0.001   PHE A 486 
 TRP   0.007   0.001   TRP B  89 
 HIS   0.008   0.001   HIS B 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 ( 7248)
  covalent geometry    : angle       0.50356 /  0.26 ( 9832)
  hydrogen bonds       : bond        0.03800 /  2.51 (  541)
  hydrogen bonds       : angle       3.89607 /  2.77 ( 1623)

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

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

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1756 Ramachandran restraints generated.
    878 Oldfield, 0 Emsley, 878 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.7526 (mmm-85) cc_final: 0.7214 (tpp80)
REVERT: A  174 ARG cc_start: 0.7556 (mtm180) cc_final: 0.6960 (mtm-85)
REVERT: A  240 THR cc_start: 0.8480 (m) cc_final: 0.7890 (p)
REVERT: A  337 MET cc_start: 0.7763 (tpp) cc_final: 0.7348 (mmm)
REVERT: A  422 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7198 (pt0)
REVERT: A  565 TRP cc_start: 0.5716 (OUTLIER) cc_final: 0.4714 (p90)
REVERT: A  569 MET cc_start: 0.7929 (mmp) cc_final: 0.6527 (tpt)
REVERT: B   94 ARG cc_start: 0.7578 (mmm-85) cc_final: 0.7297 (tpp80)
REVERT: B  174 ARG cc_start: 0.7537 (mtm180) cc_final: 0.6939 (mtm-85)
REVERT: B  240 THR cc_start: 0.8361 (m) cc_final: 0.7806 (p)
REVERT: B  306 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7924 (mm-40)
REVERT: B  422 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7150 (pt0)
REVERT: B  565 TRP cc_start: 0.5712 (OUTLIER) cc_final: 0.4727 (p90)
REVERT: B  569 MET cc_start: 0.7966 (mmp) cc_final: 0.6552 (tpt)
  outliers start: 13
  outliers final: 8
  residues processed: 98
  average time/residue: 0.0951
  time to fit residues: 12.1267
Evaluate side-chains
  98 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain A residue  422 GLU
Chi-restraints excluded: chain A residue  565 TRP
Chi-restraints excluded: chain A residue  577 TYR
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  299 SER
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain B residue  422 GLU
Chi-restraints excluded: chain B residue  565 TRP
Chi-restraints excluded: chain B residue  577 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0770
   chunk 83 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.6738

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.132724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.115579 restraints weight = 8352.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.77
r_work: 0.3132 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.4128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7248  Z= 0.149
  Angle     :  0.526   7.506   9832  Z= 0.274
  Chirality :  0.038   0.162   1142
  Planarity :  0.003   0.044   1200
  Dihedral  :  3.927  38.925    956
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 20.59 %
    Favored  : 77.67 %
  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 are not related in a simple way.
  whole:  2.16 (0.28), residues: 878
  helix:  2.05 (0.19), residues: 706
  sheet:  None (None), residues: 0
  loop : -1.26 (0.49), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 500 
 TYR   0.008   0.001   TYR A 231 
 PHE   0.028   0.001   PHE A 486 
 TRP   0.006   0.001   TRP B  89 
 HIS   0.006   0.001   HIS B 121 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 ( 7248)
  covalent geometry    : angle       0.52619 /  0.27 ( 9832)
  hydrogen bonds       : bond        0.03976 /  2.63 (  541)
  hydrogen bonds       : angle       3.97962 /  2.82 ( 1623)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1622.43 seconds
wall clock time: 28 minutes 33.87 seconds (1713.87 seconds total)