Starting phenix.real_space_refine
on Wed Feb  4 20:31:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dvl_47210/02_2026/9dvl_47210_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dvl_47210/02_2026/9dvl_47210.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dvl_47210/02_2026/9dvl_47210.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dvl_47210/02_2026/9dvl_47210.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dvl_47210/02_2026/9dvl_47210_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dvl_47210/02_2026/9dvl_47210_trim.cif"
  }
  resolution = 2.97
  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=   0.032
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: 6
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     S      32      5.16       5
     C    4382      2.51       5
     N    1008      2.21       5
     O    1060      1.98       5
     H    6284      0.53       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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12774
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 378, 6292
          Classifications: {'peptide': 378}
          Link IDs: {'PTRANS': 13, 'TRANS': 364}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 6292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 378, 6292
          Classifications: {'peptide': 378}
          Link IDs: {'PTRANS': 13, 'TRANS': 364}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 95
          Unusual residues: {'CLR': 1, 'CPL': 1, 'PO4': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 95
          Unusual residues: {'CLR': 1, 'CPL': 1, 'PO4': 3}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 2.06, per 1000 atoms: 0.16
  Number of scatterers: 12774
  At special positions: 0
  Unit cell: (73.4695, 78.4225, 126.302, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      32     16.00
     P       8     15.00
     O    1060      8.00
     N    1008      7.00
     C    4382      6.00
     H    6284      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " 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: 1.09
  Conformation dependent library (CDL) restraints added in 323.6 milliseconds
  

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1436

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 0 sheets defined
      81.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 258
    Processing helix  chain 'A' and resid 267 through 296
      removed outlier: 4.320A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
    Processing helix  chain 'A' and resid 312 through 337
    Processing helix  chain 'A' and resid 345 through 360
      removed outlier: 3.836A  pdb=" N   LEU A 349 " --> pdb=" O   TYR A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 390 through 402
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 4.099A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 445 through 453
      removed outlier: 3.655A  pdb=" N   ALA A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 471
    Processing helix  chain 'A' and resid 472 through 502
      removed outlier: 3.935A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
    Processing helix  chain 'A' and resid 555 through 582
      removed outlier: 3.919A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   THR A 582 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 618
      Proline residue:  A 598  - end of helix
    Processing helix  chain 'B' and resid 230 through 258
    Processing helix  chain 'B' and resid 267 through 296
      removed outlier: 4.332A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 312 through 337
    Processing helix  chain 'B' and resid 345 through 360
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'B' and resid 390 through 403
    Processing helix  chain 'B' and resid 403 through 420
      removed outlier: 3.948A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 438 through 443
    Processing helix  chain 'B' and resid 445 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 472 through 502
      removed outlier: 4.113A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
    Processing helix  chain 'B' and resid 555 through 582
      removed outlier: 4.013A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   THR B 582 " --> pdb=" O   SER B 578 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 618
      removed outlier: 4.742A  pdb=" N   ILE B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix

    467 hydrogen bonds defined for protein.
    1401 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: 2.80

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 6268
        1.03 -     1.23: 53
        1.23 -     1.43: 2919
        1.43 -     1.62: 3696
        1.62 -     1.82: 48
  Bond restraints: 12984
  Sorted by residual:
  bond pdb=" O3P CPL B 805 "
       pdb=" P   CPL B 805 "
    ideal  model  delta    sigma   weight residual
    1.633  1.740 -0.107 2.00e-02 2.50e+03 2.89e+01
  bond pdb=" O3P CPL A 805 "
       pdb=" P   CPL A 805 "
    ideal  model  delta    sigma   weight residual
    1.633  1.740 -0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" O4  PO4 B 802 "
       pdb=" P   PO4 B 802 "
    ideal  model  delta    sigma   weight residual
    1.568  1.501  0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" O4P CPL B 805 "
       pdb=" P   CPL B 805 "
    ideal  model  delta    sigma   weight residual
    1.648  1.713 -0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" O4P CPL A 805 "
       pdb=" P   CPL A 805 "
    ideal  model  delta    sigma   weight residual
    1.648  1.713 -0.065 2.00e-02 2.50e+03 1.07e+01
  ... (remaining 12979 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.05: 23185
        3.05 -     6.10: 67
        6.10 -     9.15: 11
        9.15 -    12.19: 3
       12.19 -    15.24: 2
  Bond angle restraints: 23268
  Sorted by residual:
  angle pdb=" O1P CPL B 805 "
        pdb=" P   CPL B 805 "
        pdb=" O2P CPL B 805 "
      ideal   model   delta    sigma   weight residual
     119.55  134.79  -15.24 3.00e+00 1.11e-01 2.58e+01
  angle pdb=" O1P CPL A 805 "
        pdb=" P   CPL A 805 "
        pdb=" O2P CPL A 805 "
      ideal   model   delta    sigma   weight residual
     119.55  134.76  -15.21 3.00e+00 1.11e-01 2.57e+01
  angle pdb=" N   CPL A 805 "
        pdb=" C5  CPL A 805 "
        pdb=" C4  CPL A 805 "
      ideal   model   delta    sigma   weight residual
     117.50  107.92    9.58 3.00e+00 1.11e-01 1.02e+01
  angle pdb=" N   CPL B 805 "
        pdb=" C5  CPL B 805 "
        pdb=" C4  CPL B 805 "
      ideal   model   delta    sigma   weight residual
     117.50  108.04    9.46 3.00e+00 1.11e-01 9.94e+00
  angle pdb=" CB  MET B 508 "
        pdb=" CG  MET B 508 "
        pdb=" SD  MET B 508 "
      ideal   model   delta    sigma   weight residual
     112.70  121.89   -9.19 3.00e+00 1.11e-01 9.38e+00
  ... (remaining 23263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.54: 6013
       31.54 -    63.09: 244
       63.09 -    94.63: 13
       94.63 -   126.18: 4
      126.18 -   157.72: 2
  Dihedral angle restraints: 6276
    sinusoidal: 3276
      harmonic: 3000
  Sorted by residual:
  dihedral pdb=" C3  CPL A 805 "
           pdb=" C1  CPL A 805 "
           pdb=" C2  CPL A 805 "
           pdb=" O3P CPL A 805 "
      ideal   model   delta sinusoidal    sigma   weight residual
      72.09  -85.63  157.72     1      3.00e+01 1.11e-03 2.05e+01
  dihedral pdb=" O2  CPL A 805 "
           pdb=" C1  CPL A 805 "
           pdb=" C2  CPL A 805 "
           pdb=" O3P CPL A 805 "
      ideal   model   delta sinusoidal    sigma   weight residual
     309.18  153.73  155.45     1      3.00e+01 1.11e-03 2.04e+01
  dihedral pdb=" C33 CPL B 805 "
           pdb=" C31 CPL B 805 "
           pdb=" C32 CPL B 805 "
           pdb=" O2  CPL B 805 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.65   49.00  122.65     1      3.00e+01 1.11e-03 1.64e+01
  ... (remaining 6273 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 900
       0.072 -    0.143: 78
       0.143 -    0.215: 0
       0.215 -    0.286: 2
       0.286 -    0.357: 8
  Chirality restraints: 988
  Sorted by residual:
  chirality pdb=" C17 CLR B 804 "
            pdb=" C13 CLR B 804 "
            pdb=" C16 CLR B 804 "
            pdb=" C20 CLR B 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.91   -0.36 2.00e-01 2.50e+01 3.20e+00
  chirality pdb=" C17 CLR A 804 "
            pdb=" C13 CLR A 804 "
            pdb=" C16 CLR A 804 "
            pdb=" C20 CLR A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.91   -0.36 2.00e-01 2.50e+01 3.18e+00
  chirality pdb=" C13 CLR A 804 "
            pdb=" C12 CLR A 804 "
            pdb=" C14 CLR A 804 "
            pdb=" C17 CLR A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -3.27    0.34 2.00e-01 2.50e+01 2.83e+00
  ... (remaining 985 not shown)

  Planarity restraints: 1806
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 565 "    0.012 2.00e-02 2.50e+03   2.30e-02 5.31e+00
        pdb=" N   ASP B 566 "   -0.040 2.00e-02 2.50e+03
        pdb=" CA  ASP B 566 "    0.010 2.00e-02 2.50e+03
        pdb=" H   ASP B 566 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 496 "    0.013 2.00e-02 2.50e+03   1.03e-02 3.19e+00
        pdb=" CG  TYR A 496 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 496 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 496 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 496 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 496 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 496 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 496 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 496 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 496 "   -0.002 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 496 "    0.003 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 496 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 565 "    0.007 2.00e-02 2.50e+03   1.42e-02 2.01e+00
        pdb=" C   GLU B 565 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   GLU B 565 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASP B 566 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1803 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 893
        2.21 -     2.81: 26209
        2.81 -     3.40: 38040
        3.40 -     4.00: 48100
        4.00 -     4.60: 74022
  Nonbonded interactions: 187264
  Sorted by model distance:
  nonbonded pdb="HH22 ARG B 270 "
            pdb=" O3  PO4 B 803 "
     model   vdw
     1.610 2.450
  nonbonded pdb=" HH  TYR B 559 "
            pdb=" OE2 GLU B 613 "
     model   vdw
     1.613 2.450
  nonbonded pdb=" OD2 ASP B 529 "
            pdb=" HE  ARG B 570 "
     model   vdw
     1.620 2.450
  nonbonded pdb=" O   ILE A 271 "
            pdb=" HH  TYR A 352 "
     model   vdw
     1.626 2.450
  nonbonded pdb=" O   ILE B 271 "
            pdb=" HH  TYR B 352 "
     model   vdw
     1.658 2.450
  ... (remaining 187259 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:             5.000
  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:             0.070
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.950
  Find NCS groups from input model:        0.130
  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:9.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
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      :  0.005   0.107   6702  Z= 0.229
  Angle     :  0.671  15.242   9112  Z= 0.296
  Chirality :  0.047   0.357    988
  Planarity :  0.003   0.037   1082
  Dihedral  : 17.605 157.720   2452
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 17.96 %
    Favored  : 81.14 %
  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:  3.62 (0.30), residues: 744
  helix:  3.45 (0.21), residues: 570
  sheet:  None (None), residues: 0
  loop : -1.58 (0.36), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 270 
 TYR   0.030   0.001   TYR A 496 
 PHE   0.013   0.001   PHE A 610 
 TRP   0.008   0.001   TRP B 327 
 HIS   0.005   0.001   HIS A 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 6700)
  covalent geometry    : angle       0.67063 ( 9108)
  SS BOND              : bond        0.00223 (    2)
  SS BOND              : angle       0.58588 (    4)
  hydrogen bonds       : bond        0.09493 (  467)
  hydrogen bonds       : angle       4.65677 ( 1401)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.6862 (p90)
REVERT: A  609 PHE cc_start: 0.7589 (OUTLIER) cc_final: 0.6778 (t80)
REVERT: B  591 ILE cc_start: 0.7322 (mm) cc_final: 0.7071 (mt)
  outliers start: 6
  outliers final: 1
  residues processed: 85
  average time/residue: 0.7441
  time to fit residues: 68.0030
Evaluate side-chains
  64 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  609 PHE
Chi-restraints excluded: chain B residue  609 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
B 401 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.161396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.123981 restraints weight = 18694.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.94
r_work: 0.3130 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6702  Z= 0.203
  Angle     :  0.556   4.590   9112  Z= 0.302
  Chirality :  0.038   0.132    988
  Planarity :  0.005   0.064   1082
  Dihedral  : 13.333 141.129   1054
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.62 %
    Favored  : 81.59 %
  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:  2.99 (0.30), residues: 744
  helix:  2.93 (0.20), residues: 580
  sheet:  None (None), residues: 0
  loop : -1.81 (0.38), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 604 
 TYR   0.021   0.002   TYR A 496 
 PHE   0.030   0.002   PHE B 605 
 TRP   0.011   0.002   TRP A 395 
 HIS   0.004   0.001   HIS A 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 6700)
  covalent geometry    : angle       0.55549 ( 9108)
  SS BOND              : bond        0.00486 (    2)
  SS BOND              : angle       1.43872 (    4)
  hydrogen bonds       : bond        0.06040 (  467)
  hydrogen bonds       : angle       4.43806 ( 1401)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A  304 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7695 (mt-10)
REVERT: A  472 ARG cc_start: 0.7338 (mtt180) cc_final: 0.6990 (mmm160)
REVERT: B  386 PHE cc_start: 0.7628 (m-10) cc_final: 0.7400 (m-10)
REVERT: B  445 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6624 (p90)
REVERT: B  591 ILE cc_start: 0.7028 (mm) cc_final: 0.6781 (mt)
  outliers start: 12
  outliers final: 3
  residues processed: 79
  average time/residue: 0.8533
  time to fit residues: 72.2790
Evaluate side-chains
  68 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain B residue  445 TYR
Chi-restraints excluded: chain B residue  565 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   chunk 28 optimal weight:    0.2980
   chunk 59 optimal weight:    1.9990
   chunk 43 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 504 HIS
B 401 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.158693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.122195 restraints weight = 18845.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 1.87
r_work: 0.3093 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2945 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6702  Z= 0.155
  Angle     :  0.497   4.215   9112  Z= 0.270
  Chirality :  0.035   0.132    988
  Planarity :  0.004   0.053   1082
  Dihedral  : 11.703 111.931   1050
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.62 %
    Favored  : 81.29 %
  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:  2.87 (0.30), residues: 744
  helix:  2.78 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.92 (0.40), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 448 
 TYR   0.009   0.001   TYR B 352 
 PHE   0.026   0.002   PHE B 605 
 TRP   0.009   0.001   TRP A 573 
 HIS   0.010   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6700)
  covalent geometry    : angle       0.49577 ( 9108)
  SS BOND              : bond        0.00440 (    2)
  SS BOND              : angle       1.40594 (    4)
  hydrogen bonds       : bond        0.05976 (  467)
  hydrogen bonds       : angle       4.23750 ( 1401)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  472 ARG cc_start: 0.7571 (mtt180) cc_final: 0.7277 (mmm160)
REVERT: B  386 PHE cc_start: 0.7721 (m-10) cc_final: 0.7508 (m-10)
REVERT: B  591 ILE cc_start: 0.7285 (mm) cc_final: 0.7007 (mt)
  outliers start: 14
  outliers final: 5
  residues processed: 85
  average time/residue: 0.7290
  time to fit residues: 66.7740
Evaluate side-chains
  72 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  471 LYS
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.9780

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

Flipped N/Q/H residues before XYZ refinement:
A 618 ASN
B 401 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.150086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.112454 restraints weight = 18989.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 1.94
r_work: 0.2979 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6702  Z= 0.206
  Angle     :  0.538   4.385   9112  Z= 0.297
  Chirality :  0.038   0.135    988
  Planarity :  0.004   0.054   1082
  Dihedral  : 11.289 112.866   1050
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.57 %
    Favored  : 82.19 %
  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:  2.48 (0.30), residues: 744
  helix:  2.51 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.10 (0.40), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 604 
 TYR   0.023   0.002   TYR A 496 
 PHE   0.032   0.002   PHE B 605 
 TRP   0.010   0.002   TRP A 573 
 HIS   0.006   0.002   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 6700)
  covalent geometry    : angle       0.53689 ( 9108)
  SS BOND              : bond        0.00537 (    2)
  SS BOND              : angle       1.68178 (    4)
  hydrogen bonds       : bond        0.06806 (  467)
  hydrogen bonds       : angle       4.36158 ( 1401)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  442 LYS cc_start: 0.7969 (tttt) cc_final: 0.7416 (mttm)
REVERT: A  472 ARG cc_start: 0.7684 (mtt180) cc_final: 0.7469 (mmm160)
REVERT: A  622 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7856 (mt-10)
REVERT: B  445 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.7074 (p90)
REVERT: B  591 ILE cc_start: 0.7481 (mm) cc_final: 0.7195 (mt)
  outliers start: 15
  outliers final: 9
  residues processed: 81
  average time/residue: 0.7172
  time to fit residues: 62.3382
Evaluate side-chains
  75 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  496 TYR
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  445 TYR
Chi-restraints excluded: chain B residue  505 SER
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0570
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9990
   chunk 46 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 30 optimal weight:    0.1980
   overall best weight:    0.4698

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
A 576 GLN
B 401 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.152845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.115400 restraints weight = 18726.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3177 rms_B_bonded: 1.95
r_work: 0.3021 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   6702  Z= 0.135
  Angle     :  0.486   5.137   9112  Z= 0.273
  Chirality :  0.037   0.323    988
  Planarity :  0.004   0.052   1082
  Dihedral  : 10.971 109.124   1050
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 16.02 %
    Favored  : 81.59 %
  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:  2.70 (0.30), residues: 744
  helix:  2.66 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.02 (0.41), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 604 
 TYR   0.089   0.002   TYR A 496 
 PHE   0.024   0.001   PHE B 605 
 TRP   0.009   0.001   TRP A 573 
 HIS   0.005   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6700)
  covalent geometry    : angle       0.48503 ( 9108)
  SS BOND              : bond        0.00445 (    2)
  SS BOND              : angle       1.47295 (    4)
  hydrogen bonds       : bond        0.05967 (  467)
  hydrogen bonds       : angle       4.25970 ( 1401)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  442 LYS cc_start: 0.7958 (tttt) cc_final: 0.7445 (mttm)
REVERT: A  472 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7455 (mmm160)
REVERT: A  575 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7165 (mt)
REVERT: B  591 ILE cc_start: 0.7432 (mm) cc_final: 0.7155 (mt)
  outliers start: 16
  outliers final: 7
  residues processed: 85
  average time/residue: 0.7832
  time to fit residues: 71.5848
Evaluate side-chains
  74 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  496 TYR
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 401 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.149533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.112121 restraints weight = 18797.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3108 rms_B_bonded: 1.94
r_work: 0.2950 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6702  Z= 0.191
  Angle     :  0.532   6.312   9112  Z= 0.294
  Chirality :  0.038   0.173    988
  Planarity :  0.004   0.053   1082
  Dihedral  : 11.046 106.243   1050
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.72 %
    Favored  : 82.19 %
  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:  2.39 (0.30), residues: 744
  helix:  2.44 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.13 (0.41), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 604 
 TYR   0.077   0.002   TYR A 496 
 PHE   0.030   0.002   PHE B 605 
 TRP   0.010   0.001   TRP A 573 
 HIS   0.006   0.002   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 6700)
  covalent geometry    : angle       0.53113 ( 9108)
  SS BOND              : bond        0.00482 (    2)
  SS BOND              : angle       1.52496 (    4)
  hydrogen bonds       : bond        0.06754 (  467)
  hydrogen bonds       : angle       4.33816 ( 1401)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
REVERT: A  442 LYS cc_start: 0.7994 (tttt) cc_final: 0.7482 (mttm)
REVERT: A  472 ARG cc_start: 0.7852 (mtt180) cc_final: 0.7503 (mtm110)
REVERT: A  575 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7272 (mt)
REVERT: B  591 ILE cc_start: 0.7448 (mm) cc_final: 0.7156 (mt)
  outliers start: 14
  outliers final: 7
  residues processed: 76
  average time/residue: 0.7860
  time to fit residues: 63.8250
Evaluate side-chains
  70 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  496 TYR
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0670
   chunk 33 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
A 576 GLN
B 401 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.155178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.118836 restraints weight = 18603.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 1.91
r_work: 0.2987 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6702  Z= 0.144
  Angle     :  0.491   7.912   9112  Z= 0.273
  Chirality :  0.036   0.193    988
  Planarity :  0.004   0.047   1082
  Dihedral  : 10.814 105.561   1050
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 15.72 %
    Favored  : 82.04 %
  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 are not related in a simple way.
  whole:  2.56 (0.30), residues: 744
  helix:  2.57 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.09 (0.41), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 604 
 TYR   0.073   0.002   TYR A 496 
 PHE   0.024   0.001   PHE B 605 
 TRP   0.010   0.001   TRP A 573 
 HIS   0.006   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6700)
  covalent geometry    : angle       0.49049 ( 9108)
  SS BOND              : bond        0.00433 (    2)
  SS BOND              : angle       1.48008 (    4)
  hydrogen bonds       : bond        0.06054 (  467)
  hydrogen bonds       : angle       4.24817 ( 1401)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  442 LYS cc_start: 0.7949 (tttt) cc_final: 0.7442 (mttm)
REVERT: A  472 ARG cc_start: 0.7850 (mtt180) cc_final: 0.7533 (mtp85)
REVERT: A  575 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7167 (mt)
REVERT: B  591 ILE cc_start: 0.7425 (mm) cc_final: 0.7127 (mt)
  outliers start: 15
  outliers final: 8
  residues processed: 84
  average time/residue: 0.8110
  time to fit residues: 73.0357
Evaluate side-chains
  77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  496 TYR
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9990
   chunk 37 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 401 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.149942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.112749 restraints weight = 18553.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.3104 rms_B_bonded: 1.92
r_work: 0.2944 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6702  Z= 0.172
  Angle     :  0.520   8.600   9112  Z= 0.287
  Chirality :  0.037   0.154    988
  Planarity :  0.004   0.047   1082
  Dihedral  : 10.811 105.040   1050
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.17 %
    Favored  : 82.04 %
  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 are not related in a simple way.
  whole:  2.42 (0.30), residues: 744
  helix:  2.47 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.11 (0.41), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 604 
 TYR   0.061   0.002   TYR A 496 
 PHE   0.029   0.002   PHE B 605 
 TRP   0.009   0.001   TRP B 514 
 HIS   0.006   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6700)
  covalent geometry    : angle       0.51938 ( 9108)
  SS BOND              : bond        0.00494 (    2)
  SS BOND              : angle       1.54567 (    4)
  hydrogen bonds       : bond        0.06462 (  467)
  hydrogen bonds       : angle       4.29847 ( 1401)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A  442 LYS cc_start: 0.7959 (tttt) cc_final: 0.7452 (mttm)
REVERT: A  472 ARG cc_start: 0.7977 (mtt180) cc_final: 0.7626 (mtp85)
REVERT: A  575 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7193 (mt)
REVERT: B  591 ILE cc_start: 0.7489 (mm) cc_final: 0.7182 (mt)
  outliers start: 12
  outliers final: 7
  residues processed: 78
  average time/residue: 0.7922
  time to fit residues: 66.1070
Evaluate side-chains
  72 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  496 TYR
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 40 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9980
   chunk 33 optimal weight:    0.1980
   chunk 63 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 248 ASN
B 401 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.152483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.115363 restraints weight = 18701.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 1.94
r_work: 0.2992 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6702  Z= 0.134
  Angle     :  0.481   9.442   9112  Z= 0.267
  Chirality :  0.035   0.140    988
  Planarity :  0.004   0.050   1082
  Dihedral  : 10.482 102.128   1050
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 16.02 %
    Favored  : 82.04 %
  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 are not related in a simple way.
  whole:  2.69 (0.30), residues: 744
  helix:  2.66 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.03 (0.42), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 604 
 TYR   0.044   0.002   TYR A 496 
 PHE   0.022   0.001   PHE B 605 
 TRP   0.010   0.001   TRP A 573 
 HIS   0.005   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6700)
  covalent geometry    : angle       0.48034 ( 9108)
  SS BOND              : bond        0.00411 (    2)
  SS BOND              : angle       1.46517 (    4)
  hydrogen bonds       : bond        0.05749 (  467)
  hydrogen bonds       : angle       4.19672 ( 1401)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: A  442 LYS cc_start: 0.7960 (tttt) cc_final: 0.7467 (mttm)
REVERT: A  472 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7616 (mtp85)
REVERT: A  575 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7190 (mt)
REVERT: B  394 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8420 (t80)
REVERT: B  591 ILE cc_start: 0.7466 (mm) cc_final: 0.7153 (mt)
  outliers start: 13
  outliers final: 6
  residues processed: 78
  average time/residue: 0.8275
  time to fit residues: 69.1920
Evaluate side-chains
  73 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 22 optimal weight:    0.4980
   chunk 36 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   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 576 GLN
B 401 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.150106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.112934 restraints weight = 18773.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 1.94
r_work: 0.2946 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6702  Z= 0.165
  Angle     :  0.497   4.597   9112  Z= 0.274
  Chirality :  0.037   0.162    988
  Planarity :  0.004   0.048   1082
  Dihedral  : 10.557 104.213   1050
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.32 %
    Favored  : 82.04 %
  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 are not related in a simple way.
  whole:  2.54 (0.30), residues: 744
  helix:  2.51 (0.20), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.97 (0.42), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 604 
 TYR   0.022   0.002   TYR A 496 
 PHE   0.028   0.002   PHE B 605 
 TRP   0.009   0.001   TRP A 573 
 HIS   0.006   0.001   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6700)
  covalent geometry    : angle       0.49589 ( 9108)
  SS BOND              : bond        0.00465 (    2)
  SS BOND              : angle       1.50303 (    4)
  hydrogen bonds       : bond        0.06267 (  467)
  hydrogen bonds       : angle       4.25659 ( 1401)

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

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

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1488 Ramachandran restraints generated.
    744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  442 LYS cc_start: 0.7954 (tttt) cc_final: 0.7451 (mttm)
REVERT: A  472 ARG cc_start: 0.7918 (mtt180) cc_final: 0.7557 (mtp85)
REVERT: A  575 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7249 (mt)
REVERT: B  394 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8492 (t80)
REVERT: B  591 ILE cc_start: 0.7473 (mm) cc_final: 0.7155 (mt)
  outliers start: 11
  outliers final: 6
  residues processed: 76
  average time/residue: 0.9256
  time to fit residues: 75.2176
Evaluate side-chains
  74 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  544 ASN
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain B residue  394 PHE
Chi-restraints excluded: chain B residue  565 GLU
Chi-restraints excluded: chain B residue  567 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 74
   random chunks:
   chunk 56 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0970
   chunk 66 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0670
   chunk 2 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   overall best weight:    0.5716

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

Flipped N/Q/H residues before XYZ refinement:
A 576 GLN
B 401 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.149555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.112731 restraints weight = 18840.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 1.92
r_work: 0.2962 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2816 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   6702  Z= 0.140
  Angle     :  0.476   4.464   9112  Z= 0.263
  Chirality :  0.035   0.134    988
  Planarity :  0.004   0.044   1082
  Dihedral  : 10.438 102.599   1050
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 16.17 %
    Favored  : 82.19 %
  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:  2.66 (0.30), residues: 744
  helix:  2.63 (0.20), residues: 592
  sheet:  None (None), residues: 0
  loop : -2.01 (0.43), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 604 
 TYR   0.020   0.001   TYR A 496 
 PHE   0.024   0.001   PHE B 605 
 TRP   0.010   0.001   TRP A 573 
 HIS   0.005   0.001   HIS B 441 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6700)
  covalent geometry    : angle       0.47476 ( 9108)
  SS BOND              : bond        0.00435 (    2)
  SS BOND              : angle       1.47431 (    4)
  hydrogen bonds       : bond        0.05914 (  467)
  hydrogen bonds       : angle       4.21853 ( 1401)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3705.42 seconds
wall clock time: 63 minutes 30.68 seconds (3810.68 seconds total)