Starting phenix.real_space_refine
on Tue Mar  3 13:15:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nu4_49796/03_2026/9nu4_49796.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nu4_49796/03_2026/9nu4_49796.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nu4_49796/03_2026/9nu4_49796.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nu4_49796/03_2026/9nu4_49796.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nu4_49796/03_2026/9nu4_49796.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nu4_49796/03_2026/9nu4_49796.map"
  }
  resolution = 3.6
  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=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    3183      2.51       5
     N     788      2.21       5
     O     829      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4824
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4598
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4598
          Classifications: {'peptide': 602}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 573}
    Chain: "B"
      Number of atoms: 226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 226
          Classifications: {'peptide': 29}
          Link IDs: {'PTRANS': 1, 'TRANS': 27}
  Time building chain proxies: 1.16, per 1000 atoms: 0.24
  Number of scatterers: 4824
  At special positions: 0
  Unit cell: (72.15, 80.6, 91.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O     829      8.00
     N     788      7.00
     C    3183      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: 0.33
  Conformation dependent library (CDL) restraints added in 304.5 milliseconds
  

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1180

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      91.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid -101 through -83
    Processing helix  chain 'A' and resid -81 through -60
      removed outlier: 3.624A  pdb=" N   VAL A -77 " --> pdb=" O   ASN A -81 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   LYS A -61 " --> pdb=" O   LEU A -65 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ALA A -60 " --> pdb=" O   ASP A -64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -58 through -54
    Processing helix  chain 'A' and resid -48 through -23
      removed outlier: 3.730A  pdb=" N   LEU A -25 " --> pdb=" O   ASP A -29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid -20 through -1
      removed outlier: 4.257A  pdb=" N   GLN A -10 " --> pdb=" O   ALA A -14 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   LEU A  -9 " --> pdb=" O   ALA A -13 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS A  -8 " --> pdb=" O   ALA A -12 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ALA A  -3 " --> pdb=" O   THR A  -7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 0 through 32
    Processing helix  chain 'A' and resid 35 through 56
      Proline residue:  A  48  - end of helix
      removed outlier: 3.535A  pdb=" N   LEU A  51 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ARG A  53 " --> pdb=" O   ASN A  49 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   ILE A  54 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 75
      Proline residue:  A  66  - end of helix
    Processing helix  chain 'A' and resid 78 through 105
    Processing helix  chain 'A' and resid 105 through 114
    Processing helix  chain 'A' and resid 114 through 120
      removed outlier: 4.032A  pdb=" N   THR A 120 " --> pdb=" O   GLY A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 135
    Processing helix  chain 'A' and resid 136 through 154
      removed outlier: 3.531A  pdb=" N   TRP A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 177
      removed outlier: 3.740A  pdb=" N   ALA A 161 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
      Proline residue:  A 164  - end of helix
      removed outlier: 3.874A  pdb=" N   LEU A 167 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ASN A 168 " --> pdb=" O   PRO A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 182
    Processing helix  chain 'A' and resid 186 through 212
      removed outlier: 3.784A  pdb=" N   ALA A 190 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
    Processing helix  chain 'A' and resid 223 through 257
      removed outlier: 3.638A  pdb=" N   GLY A 234 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
      removed outlier: 3.544A  pdb=" N   LEU A 257 " --> pdb=" O   PHE A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 297
      removed outlier: 3.853A  pdb=" N   PHE A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      Proline residue:  A 275  - end of helix
      removed outlier: 3.910A  pdb=" N   ALA A 282 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
      Proline residue:  A 289  - end of helix
      removed outlier: 3.619A  pdb=" N   SER A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 328
      removed outlier: 3.634A  pdb=" N   LEU A 319 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
      Proline residue:  A 320  - end of helix
    Processing helix  chain 'A' and resid 328 through 337
    Processing helix  chain 'A' and resid 343 through 376
      removed outlier: 4.005A  pdb=" N   ALA A 356 " --> pdb=" O   ARG A 352 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ILE A 362 " --> pdb=" O   SER A 358 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   GLY A 363 " --> pdb=" O   VAL A 359 " (cutoff:3.500A)
      Proline residue:  A 372  - end of helix
    Processing helix  chain 'A' and resid 380 through 402
    Processing helix  chain 'A' and resid 406 through 432
      removed outlier: 3.520A  pdb=" N   LEU A 410 " --> pdb=" O   LYS A 406 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER A 411 " --> pdb=" O   HIS A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 466
    Processing helix  chain 'A' and resid 473 through 499
    Processing helix  chain 'B' and resid 3 through 17
    Processing helix  chain 'B' and resid 17 through 28
      removed outlier: 3.527A  pdb=" N   ARG B  23 " --> pdb=" O   SER B  19 " (cutoff:3.500A)

    414 hydrogen bonds defined for protein.
    1230 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: 0.78

  Time building geometry restraints manager: 0.46 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: 1484
        1.34 -     1.46: 757
        1.46 -     1.57: 2645
        1.57 -     1.69: 0
        1.69 -     1.81: 45
  Bond restraints: 4931
  Sorted by residual:
  bond pdb=" CB  PRO A 383 "
       pdb=" CG  PRO A 383 "
    ideal  model  delta    sigma   weight residual
    1.492  1.422  0.070 5.00e-02 4.00e+02 1.98e+00
  bond pdb=" C   PHE A 135 "
       pdb=" N   PRO A 136 "
    ideal  model  delta    sigma   weight residual
    1.335  1.349 -0.015 1.19e-02 7.06e+03 1.53e+00
  bond pdb=" CG  LEU A 313 "
       pdb=" CD2 LEU A 313 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.26e+00
  bond pdb=" CB  ILE A 138 "
       pdb=" CG2 ILE A 138 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.17e+00
  bond pdb=" CG  LEU A 391 "
       pdb=" CD1 LEU A 391 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.14e+00
  ... (remaining 4926 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 6574
        2.08 -     4.15: 108
        4.15 -     6.23: 24
        6.23 -     8.30: 1
        8.30 -    10.38: 1
  Bond angle restraints: 6708
  Sorted by residual:
  angle pdb=" C   LYS A -52 "
        pdb=" N   SER A -51 "
        pdb=" CA  SER A -51 "
      ideal   model   delta    sigma   weight residual
     120.49  130.87  -10.38 1.42e+00 4.96e-01 5.34e+01
  angle pdb=" CB  ARG A 480 "
        pdb=" CG  ARG A 480 "
        pdb=" CD  ARG A 480 "
      ideal   model   delta    sigma   weight residual
     111.30  105.82    5.48 2.30e+00 1.89e-01 5.67e+00
  angle pdb=" CA  ARG A 480 "
        pdb=" CB  ARG A 480 "
        pdb=" CG  ARG A 480 "
      ideal   model   delta    sigma   weight residual
     114.10  118.85   -4.75 2.00e+00 2.50e-01 5.63e+00
  angle pdb=" C   LEU A 446 "
        pdb=" N   ARG A 447 "
        pdb=" CA  ARG A 447 "
      ideal   model   delta    sigma   weight residual
     120.31  117.05    3.26 1.52e+00 4.33e-01 4.61e+00
  angle pdb=" C   SER A 358 "
        pdb=" N   VAL A 359 "
        pdb=" CA  VAL A 359 "
      ideal   model   delta    sigma   weight residual
     120.64  117.19    3.45 1.66e+00 3.63e-01 4.32e+00
  ... (remaining 6703 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 2681
       17.40 -    34.81: 203
       34.81 -    52.21: 29
       52.21 -    69.62: 13
       69.62 -    87.02: 4
  Dihedral angle restraints: 2930
    sinusoidal: 1103
      harmonic: 1827
  Sorted by residual:
  dihedral pdb=" CA  LEU A 471 "
           pdb=" C   LEU A 471 "
           pdb=" N   GLY A 472 "
           pdb=" CA  GLY A 472 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.39   16.61     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CG  ARG A 447 "
           pdb=" CD  ARG A 447 "
           pdb=" NE  ARG A 447 "
           pdb=" CZ  ARG A 447 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -139.22  -40.78     2      1.50e+01 4.44e-03 9.10e+00
  dihedral pdb=" CB  MET A 349 "
           pdb=" CG  MET A 349 "
           pdb=" SD  MET A 349 "
           pdb=" CE  MET A 349 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  130.08   49.92     3      1.50e+01 4.44e-03 8.84e+00
  ... (remaining 2927 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 452
       0.033 -    0.066: 240
       0.066 -    0.098: 82
       0.098 -    0.131: 29
       0.131 -    0.163: 2
  Chirality restraints: 805
  Sorted by residual:
  chirality pdb=" CB  VAL A 359 "
            pdb=" CA  VAL A 359 "
            pdb=" CG1 VAL A 359 "
            pdb=" CG2 VAL A 359 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.68e-01
  chirality pdb=" CA  PRO A 235 "
            pdb=" N   PRO A 235 "
            pdb=" C   PRO A 235 "
            pdb=" CB  PRO A 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  PHE A 135 "
            pdb=" N   PHE A 135 "
            pdb=" C   PHE A 135 "
            pdb=" CB  PHE A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 802 not shown)

  Planarity restraints: 827
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 183 "    0.028 5.00e-02 4.00e+02   4.16e-02 2.77e+00
        pdb=" N   PRO A 184 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 184 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 184 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 135 "   -0.025 5.00e-02 4.00e+02   3.78e-02 2.29e+00
        pdb=" N   PRO A 136 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 136 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 136 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A -96 "    0.016 2.00e-02 2.50e+03   9.54e-03 2.27e+00
        pdb=" CG  TRP A -96 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TRP A -96 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP A -96 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A -96 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A -96 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A -96 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A -96 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A -96 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A -96 "    0.001 2.00e-02 2.50e+03
  ... (remaining 824 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 92
        2.69 -     3.24: 5250
        3.24 -     3.79: 8075
        3.79 -     4.35: 10240
        4.35 -     4.90: 16764
  Nonbonded interactions: 40421
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 469 "
            pdb=" NH1 ARG A 477 "
     model   vdw
     2.137 3.120
  nonbonded pdb=" O   ILE A 355 "
            pdb=" OG  SER A 358 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   ILE A -86 "
            pdb=" NE2 GLN A -15 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" NE2 GLN A -62 "
            pdb=" OD1 ASP A -37 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" OD1 ASP A 308 "
            pdb=" NE1 TRP A 441 "
     model   vdw
     2.308 3.120
  ... (remaining 40416 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             10.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.140
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
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      :  0.006   0.070   4931  Z= 0.261
  Angle     :  0.718  10.376   6708  Z= 0.383
  Chirality :  0.044   0.163    805
  Planarity :  0.006   0.042    827
  Dihedral  : 13.357  87.019   1750
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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: -1.51 (0.28), residues: 627
  helix: -1.15 (0.17), residues: 528
  sheet:  None (None), residues: 0
  loop :  1.24 (0.73), residues: 99

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A -69 
 TYR   0.023   0.002   TYR A  71 
 PHE   0.016   0.002   PHE A  41 
 TRP   0.024   0.002   TRP A -96 
 HIS   0.004   0.002   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00625 ( 4931)
  covalent geometry    : angle       0.71811 ( 6708)
  hydrogen bonds       : bond        0.12375 (  414)
  hydrogen bonds       : angle       5.47064 ( 1230)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  -59 THR cc_start: 0.8809 (m) cc_final: 0.8371 (p)
REVERT: A  -43 ASP cc_start: 0.7429 (t70) cc_final: 0.6442 (m-30)
REVERT: A   70 GLU cc_start: 0.8489 (tm-30) cc_final: 0.7936 (tt0)
REVERT: A  272 MET cc_start: 0.8505 (tpt) cc_final: 0.8120 (tpt)
REVERT: A  339 TYR cc_start: 0.6205 (m-80) cc_final: 0.5600 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0749
  time to fit residues: 12.6235
Evaluate side-chains
  79 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 61 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0970
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.0970
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
** A -78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.139266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.112004 restraints weight = 6962.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.114637 restraints weight = 4407.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.116674 restraints weight = 3378.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.117708 restraints weight = 2858.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.118500 restraints weight = 2594.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.2095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4931  Z= 0.148
  Angle     :  0.595   7.228   6708  Z= 0.301
  Chirality :  0.039   0.134    805
  Planarity :  0.005   0.037    827
  Dihedral  :  3.795  12.763    669
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  :  9.50 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  1.21 (0.32), residues: 627
  helix:  0.93 (0.21), residues: 539
  sheet:  None (None), residues: 0
  loop :  0.65 (0.74), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A -69 
 TYR   0.011   0.002   TYR A 339 
 PHE   0.022   0.002   PHE A 342 
 TRP   0.011   0.001   TRP A -96 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 4931)
  covalent geometry    : angle       0.59453 ( 6708)
  hydrogen bonds       : bond        0.04862 (  414)
  hydrogen bonds       : angle       4.20737 ( 1230)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A  -59 THR cc_start: 0.8762 (m) cc_final: 0.8398 (p)
REVERT: A  -45 MET cc_start: 0.8057 (tpp) cc_final: 0.7849 (mmt)
REVERT: A   70 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8121 (tm-30)
REVERT: A  111 MET cc_start: 0.8123 (tpp) cc_final: 0.7892 (tpt)
REVERT: A  177 PHE cc_start: 0.8399 (m-80) cc_final: 0.8009 (m-10)
REVERT: A  227 MET cc_start: 0.7260 (tpp) cc_final: 0.6919 (ttt)
REVERT: A  272 MET cc_start: 0.8434 (tpt) cc_final: 0.8065 (tpt)
REVERT: A  482 MET cc_start: 0.7821 (tpt) cc_final: 0.7620 (tpt)
REVERT: B   19 SER cc_start: 0.9342 (t) cc_final: 0.9131 (t)
  outliers start: 14
  outliers final: 8
  residues processed: 107
  average time/residue: 0.0690
  time to fit residues: 9.6639
Evaluate side-chains
  90 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -86 ILE
Chi-restraints excluded: chain A residue  -27 LEU
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  486 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 55 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A -90 ASN
A -78 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.137152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.109831 restraints weight = 7006.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.112663 restraints weight = 4476.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.114509 restraints weight = 3412.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.115571 restraints weight = 2897.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.115571 restraints weight = 2625.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.2408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   4931  Z= 0.157
  Angle     :  0.566   6.536   6708  Z= 0.282
  Chirality :  0.039   0.142    805
  Planarity :  0.004   0.035    827
  Dihedral  :  3.668  13.405    669
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 12.08 %
    Favored  : 84.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.07 (0.33), residues: 627
  helix:  1.54 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop :  0.72 (0.77), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 480 
 TYR   0.013   0.002   TYR A 339 
 PHE   0.020   0.001   PHE A 342 
 TRP   0.017   0.001   TRP A 264 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4931)
  covalent geometry    : angle       0.56563 ( 6708)
  hydrogen bonds       : bond        0.04523 (  414)
  hydrogen bonds       : angle       3.99134 ( 1230)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A  -59 THR cc_start: 0.8774 (m) cc_final: 0.8384 (p)
REVERT: A  -17 GLU cc_start: 0.7300 (mp0) cc_final: 0.6905 (tt0)
REVERT: A  227 MET cc_start: 0.7279 (tpp) cc_final: 0.6955 (ttt)
REVERT: A  272 MET cc_start: 0.8436 (tpt) cc_final: 0.8059 (tpt)
REVERT: A  349 MET cc_start: 0.7919 (mmp) cc_final: 0.7220 (mmp)
REVERT: A  482 MET cc_start: 0.7798 (tpt) cc_final: 0.7582 (tpt)
  outliers start: 15
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0625
  time to fit residues: 7.9868
Evaluate side-chains
  95 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -86 ILE
Chi-restraints excluded: chain A residue  -27 LEU
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  279 LEU
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  499 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9980
   chunk 1 optimal weight:    3.9990
   chunk 21 optimal weight:    0.2980
   chunk 32 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0980
   chunk 0 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A -90 ASN
A -78 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.134612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.107052 restraints weight = 7015.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.109689 restraints weight = 4597.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.111177 restraints weight = 3567.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.112417 restraints weight = 3085.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.112650 restraints weight = 2807.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4931  Z= 0.137
  Angle     :  0.546   8.135   6708  Z= 0.269
  Chirality :  0.038   0.146    805
  Planarity :  0.004   0.032    827
  Dihedral  :  3.620  13.356    669
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 13.27 %
    Favored  : 82.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.53 (0.34), residues: 627
  helix:  1.88 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop :  0.68 (0.77), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 305 
 TYR   0.012   0.002   TYR A 375 
 PHE   0.018   0.001   PHE A 342 
 TRP   0.022   0.001   TRP A 264 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4931)
  covalent geometry    : angle       0.54607 ( 6708)
  hydrogen bonds       : bond        0.04206 (  414)
  hydrogen bonds       : angle       3.83785 ( 1230)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A  -90 ASN cc_start: 0.8023 (m-40) cc_final: 0.7794 (m-40)
REVERT: A  -59 THR cc_start: 0.8432 (m) cc_final: 0.7873 (p)
REVERT: A  420 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8286 (tt)
  outliers start: 19
  outliers final: 10
  residues processed: 102
  average time/residue: 0.0632
  time to fit residues: 8.6186
Evaluate side-chains
  95 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -86 ILE
Chi-restraints excluded: chain A residue  -27 LEU
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   28 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 43 optimal weight:    0.1980
   chunk 40 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.137632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.110674 restraints weight = 7024.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.113390 restraints weight = 4512.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.115126 restraints weight = 3474.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.115767 restraints weight = 2967.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.116744 restraints weight = 2752.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.2950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4931  Z= 0.139
  Angle     :  0.552   6.629   6708  Z= 0.268
  Chirality :  0.038   0.145    805
  Planarity :  0.004   0.032    827
  Dihedral  :  3.569  13.404    669
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 16.04 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.68 (0.34), residues: 627
  helix:  2.01 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop :  0.45 (0.75), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 305 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.015   0.001   PHE A 342 
 TRP   0.013   0.001   TRP A 264 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4931)
  covalent geometry    : angle       0.55186 ( 6708)
  hydrogen bonds       : bond        0.04123 (  414)
  hydrogen bonds       : angle       3.80451 ( 1230)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  -59 THR cc_start: 0.8399 (m) cc_final: 0.7829 (p)
REVERT: A  174 PHE cc_start: 0.8880 (OUTLIER) cc_final: 0.7820 (t80)
REVERT: A  227 MET cc_start: 0.7259 (tpp) cc_final: 0.6777 (ttt)
  outliers start: 13
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0638
  time to fit residues: 8.0916
Evaluate side-chains
  95 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -86 ILE
Chi-restraints excluded: chain A residue  -27 LEU
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  499 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0570
   chunk 43 optimal weight:    0.2980
   chunk 41 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.4298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.145759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.119052 restraints weight = 6853.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.121878 restraints weight = 4249.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.123980 restraints weight = 3210.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.125058 restraints weight = 2688.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.125290 restraints weight = 2424.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4931  Z= 0.125
  Angle     :  0.545   7.615   6708  Z= 0.263
  Chirality :  0.038   0.145    805
  Planarity :  0.004   0.032    827
  Dihedral  :  3.550  13.329    669
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 17.62 %
    Favored  : 79.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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 (0.34), residues: 627
  helix:  2.17 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop :  0.32 (0.73), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 305 
 TYR   0.009   0.001   TYR A 492 
 PHE   0.015   0.001   PHE A 342 
 TRP   0.010   0.001   TRP A 264 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4931)
  covalent geometry    : angle       0.54481 ( 6708)
  hydrogen bonds       : bond        0.03955 (  414)
  hydrogen bonds       : angle       3.71847 ( 1230)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  -59 THR cc_start: 0.8381 (m) cc_final: 0.7795 (p)
REVERT: A  -56 LYS cc_start: 0.7785 (mptt) cc_final: 0.7452 (mtpp)
REVERT: A  227 MET cc_start: 0.7381 (tpp) cc_final: 0.6744 (ttt)
REVERT: A  307 MET cc_start: 0.8045 (tpp) cc_final: 0.7750 (tpp)
  outliers start: 15
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0671
  time to fit residues: 8.5717
Evaluate side-chains
  99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -86 ILE
Chi-restraints excluded: chain A residue  -27 LEU
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   28 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 36 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A -78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.143378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.116424 restraints weight = 6840.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.119411 restraints weight = 4304.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.121330 restraints weight = 3242.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.122254 restraints weight = 2735.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.122977 restraints weight = 2494.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4931  Z= 0.162
  Angle     :  0.573   6.986   6708  Z= 0.278
  Chirality :  0.039   0.163    805
  Planarity :  0.004   0.033    827
  Dihedral  :  3.544  13.723    669
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.01 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.85 (0.33), residues: 627
  helix:  2.14 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop :  0.38 (0.73), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A -69 
 TYR   0.011   0.002   TYR A 375 
 PHE   0.014   0.001   PHE A 342 
 TRP   0.009   0.001   TRP A -96 
 HIS   0.002   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 4931)
  covalent geometry    : angle       0.57283 ( 6708)
  hydrogen bonds       : bond        0.04110 (  414)
  hydrogen bonds       : angle       3.79378 ( 1230)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A  -59 THR cc_start: 0.8412 (m) cc_final: 0.7796 (p)
REVERT: A  174 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.7849 (t80)
REVERT: A  227 MET cc_start: 0.7297 (tpp) cc_final: 0.6755 (ttt)
REVERT: A  307 MET cc_start: 0.7925 (tpp) cc_final: 0.7686 (tpp)
  outliers start: 14
  outliers final: 12
  residues processed: 93
  average time/residue: 0.0654
  time to fit residues: 8.0255
Evaluate side-chains
  98 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -27 LEU
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   28 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 47 optimal weight:    0.2980
   chunk 48 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A -78 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.142220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.115190 restraints weight = 6952.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.118107 restraints weight = 4372.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.119958 restraints weight = 3311.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.120977 restraints weight = 2810.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.121254 restraints weight = 2550.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4931  Z= 0.137
  Angle     :  0.554   6.601   6708  Z= 0.270
  Chirality :  0.038   0.162    805
  Planarity :  0.004   0.033    827
  Dihedral  :  3.534  13.702    669
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 19.21 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.93 (0.34), residues: 627
  helix:  2.21 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop :  0.32 (0.72), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A -69 
 TYR   0.015   0.001   TYR A 375 
 PHE   0.014   0.001   PHE A 342 
 TRP   0.010   0.001   TRP A -96 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4931)
  covalent geometry    : angle       0.55447 ( 6708)
  hydrogen bonds       : bond        0.03950 (  414)
  hydrogen bonds       : angle       3.73056 ( 1230)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A  -59 THR cc_start: 0.8382 (m) cc_final: 0.7750 (p)
REVERT: A  210 LYS cc_start: 0.8336 (mttm) cc_final: 0.7862 (ttmm)
REVERT: A  227 MET cc_start: 0.7257 (tpp) cc_final: 0.6991 (tpt)
REVERT: A  307 MET cc_start: 0.7907 (tpp) cc_final: 0.7675 (tpp)
  outliers start: 13
  outliers final: 13
  residues processed: 96
  average time/residue: 0.0636
  time to fit residues: 8.1060
Evaluate side-chains
  97 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -27 LEU
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   28 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.140315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.112970 restraints weight = 6923.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.115852 restraints weight = 4421.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.117673 restraints weight = 3365.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.118801 restraints weight = 2857.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.118814 restraints weight = 2599.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4931  Z= 0.171
  Angle     :  0.596   6.795   6708  Z= 0.291
  Chirality :  0.039   0.167    805
  Planarity :  0.004   0.033    827
  Dihedral  :  3.593  14.253    669
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.80 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.86 (0.34), residues: 627
  helix:  2.14 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop :  0.45 (0.74), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 480 
 TYR   0.018   0.002   TYR A 375 
 PHE   0.014   0.001   PHE A 342 
 TRP   0.011   0.001   TRP A -96 
 HIS   0.002   0.001   HIS A 300 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 4931)
  covalent geometry    : angle       0.59586 ( 6708)
  hydrogen bonds       : bond        0.04125 (  414)
  hydrogen bonds       : angle       3.81838 ( 1230)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.173 
Fit side-chains
REVERT: A  -59 THR cc_start: 0.8417 (m) cc_final: 0.7784 (p)
REVERT: A  210 LYS cc_start: 0.8350 (mttm) cc_final: 0.7868 (ttmm)
REVERT: A  227 MET cc_start: 0.7299 (tpp) cc_final: 0.7042 (tpt)
REVERT: A  307 MET cc_start: 0.7932 (tpp) cc_final: 0.7697 (tpp)
  outliers start: 14
  outliers final: 14
  residues processed: 93
  average time/residue: 0.0647
  time to fit residues: 7.9829
Evaluate side-chains
  97 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -27 LEU
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   28 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 56 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0470
   chunk 44 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.5278

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.145073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.118419 restraints weight = 6804.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.121431 restraints weight = 4224.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.123092 restraints weight = 3181.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.124454 restraints weight = 2706.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.125092 restraints weight = 2429.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4931  Z= 0.134
  Angle     :  0.564   6.757   6708  Z= 0.278
  Chirality :  0.038   0.165    805
  Planarity :  0.004   0.033    827
  Dihedral  :  3.578  13.849    669
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.20 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  2.96 (0.34), residues: 627
  helix:  2.24 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop :  0.26 (0.72), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 477 
 TYR   0.016   0.001   TYR A 375 
 PHE   0.018   0.001   PHE A 342 
 TRP   0.011   0.001   TRP A -96 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4931)
  covalent geometry    : angle       0.56357 ( 6708)
  hydrogen bonds       : bond        0.03934 (  414)
  hydrogen bonds       : angle       3.74331 ( 1230)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.147 
Fit side-chains
REVERT: A  -59 THR cc_start: 0.8369 (m) cc_final: 0.7702 (p)
REVERT: A  210 LYS cc_start: 0.8343 (mttm) cc_final: 0.7864 (ttmm)
REVERT: A  227 MET cc_start: 0.7293 (tpp) cc_final: 0.7029 (tpt)
REVERT: A  307 MET cc_start: 0.7951 (tpp) cc_final: 0.7701 (tpp)
  outliers start: 14
  outliers final: 14
  residues processed: 93
  average time/residue: 0.0613
  time to fit residues: 7.4768
Evaluate side-chains
  99 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  -27 LEU
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   73 SER
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  128 SER
Chi-restraints excluded: chain A residue  135 PHE
Chi-restraints excluded: chain A residue  278 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  442 MET
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain B residue   28 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 62
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 14 optimal weight:    0.1980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0870
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.5358

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.144021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.117128 restraints weight = 6888.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.120051 restraints weight = 4306.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.121900 restraints weight = 3259.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.122930 restraints weight = 2763.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.123264 restraints weight = 2510.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.3509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4931  Z= 0.134
  Angle     :  0.572   8.283   6708  Z= 0.279
  Chirality :  0.038   0.164    805
  Planarity :  0.004   0.033    827
  Dihedral  :  3.549  13.817    669
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 19.60 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    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:  3.01 (0.34), residues: 627
  helix:  2.28 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop :  0.22 (0.72), residues: 88

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 477 
 TYR   0.017   0.001   TYR A 375 
 PHE   0.018   0.001   PHE A 342 
 TRP   0.011   0.001   TRP A -96 
 HIS   0.002   0.001   HIS A 207 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4931)
  covalent geometry    : angle       0.57179 ( 6708)
  hydrogen bonds       : bond        0.03887 (  414)
  hydrogen bonds       : angle       3.72289 ( 1230)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1046.92 seconds
wall clock time: 18 minutes 43.45 seconds (1123.45 seconds total)