Starting phenix.real_space_refine
on Tue Mar  3 12:59:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uwl_20923/03_2026/6uwl_20923.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uwl_20923/03_2026/6uwl_20923.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uwl_20923/03_2026/6uwl_20923.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uwl_20923/03_2026/6uwl_20923.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uwl_20923/03_2026/6uwl_20923.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uwl_20923/03_2026/6uwl_20923.map"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1634 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      18      5.16       5
     C    1998      2.51       5
     N     479      2.21       5
     O     533      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.00s

  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: 3029
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 402, 2990
          Classifications: {'peptide': 402}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 384}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 39
          Unusual residues: {'6OU': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 10
  Time building chain proxies: 0.92, per 1000 atoms: 0.30
  Number of scatterers: 3029
  At special positions: 0
  Unit cell: (67.84, 67.84, 77.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P       1     15.00
     O     533      8.00
     N     479      7.00
     C    1998      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.33
  Conformation dependent library (CDL) restraints added in 129.4 milliseconds
  

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  724

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 0 sheets defined
      84.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 8
      removed outlier: 3.820A  pdb=" N   LYS A   6 " --> pdb=" O   GLY A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 11 through 14
      removed outlier: 3.518A  pdb=" N   GLN A  14 " --> pdb=" O   PRO A  11 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 11 through 14'
    Processing helix  chain 'A' and resid 15 through 32
      removed outlier: 3.931A  pdb=" N   VAL A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 35 through 43
    Processing helix  chain 'A' and resid 43 through 57
      removed outlier: 3.971A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 70
      removed outlier: 3.590A  pdb=" N   PHE A  63 " --> pdb=" O   MET A  59 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   SER A  65 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LEU A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 103
      removed outlier: 3.755A  pdb=" N   TYR A  88 " --> pdb=" O   LYS A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 136
    Processing helix  chain 'A' and resid 143 through 148
    Processing helix  chain 'A' and resid 150 through 169
    Processing helix  chain 'A' and resid 173 through 220
      removed outlier: 3.901A  pdb=" N   TYR A 195 " --> pdb=" O   ALA A 191 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS A 196 " --> pdb=" O   GLU A 192 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TYR A 204 " --> pdb=" O   GLY A 200 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
      removed outlier: 3.732A  pdb=" N   GLN A 220 " --> pdb=" O   VAL A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 224
      removed outlier: 3.826A  pdb=" N   VAL A 224 " --> pdb=" O   GLY A 221 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 221 through 224'
    Processing helix  chain 'A' and resid 228 through 254
      removed outlier: 3.884A  pdb=" N   THR A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   PHE A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 4.807A  pdb=" N   VAL A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   TYR A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 276
      removed outlier: 6.153A  pdb=" N   ASP A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ALA A 268 " --> pdb=" O   HIS A 264 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG A 276 " --> pdb=" O   ALA A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 293
    Processing helix  chain 'A' and resid 295 through 300
    Processing helix  chain 'A' and resid 301 through 310
      removed outlier: 4.050A  pdb=" N   THR A 308 " --> pdb=" O   PRO A 304 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASN A 310 " --> pdb=" O   GLY A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 327
      removed outlier: 4.012A  pdb=" N   GLY A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   VAL A 320 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 351
      removed outlier: 3.678A  pdb=" N   ILE A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 371
      removed outlier: 3.705A  pdb=" N   MET A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 415
      removed outlier: 4.016A  pdb=" N   MET A 385 " --> pdb=" O   ALA A 381 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ILE A 386 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   ALA A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 5.841A  pdb=" N   ILE A 392 " --> pdb=" O   GLY A 388 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU A 393 " --> pdb=" O   ILE A 389 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   MET A 395 " --> pdb=" O   ALA A 391 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   GLY A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)

    221 hydrogen bonds defined for protein.
    663 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: 0.37

  Time building geometry restraints manager: 0.39 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 467
        1.31 -     1.43: 749
        1.43 -     1.56: 1819
        1.56 -     1.68: 13
        1.68 -     1.81: 35
  Bond restraints: 3083
  Sorted by residual:
  bond pdb=" C16 6OU A 502 "
       pdb=" O18 6OU A 502 "
    ideal  model  delta    sigma   weight residual
    1.327  1.413 -0.086 2.00e-02 2.50e+03 1.83e+01
  bond pdb=" C31 6OU A 502 "
       pdb=" O30 6OU A 502 "
    ideal  model  delta    sigma   weight residual
    1.331  1.403 -0.072 2.00e-02 2.50e+03 1.30e+01
  bond pdb=" C39 6OU A 502 "
       pdb=" C40 6OU A 502 "
    ideal  model  delta    sigma   weight residual
    1.497  1.565 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" C15 6OU A 502 "
       pdb=" C16 6OU A 502 "
    ideal  model  delta    sigma   weight residual
    1.501  1.558 -0.057 2.00e-02 2.50e+03 8.21e+00
  bond pdb=" SD  FME A   1 "
       pdb=" CE  FME A   1 "
    ideal  model  delta    sigma   weight residual
    1.805  1.751  0.054 2.00e-02 2.50e+03 7.33e+00
  ... (remaining 3078 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.26: 4095
        3.26 -     6.51: 77
        6.51 -     9.77: 14
        9.77 -    13.02: 2
       13.02 -    16.28: 2
  Bond angle restraints: 4190
  Sorted by residual:
  angle pdb=" N   ALA A 205 "
        pdb=" CA  ALA A 205 "
        pdb=" C   ALA A 205 "
      ideal   model   delta    sigma   weight residual
     109.81  120.81  -11.00 2.21e+00 2.05e-01 2.48e+01
  angle pdb=" CA  LEU A 228 "
        pdb=" CB  LEU A 228 "
        pdb=" CG  LEU A 228 "
      ideal   model   delta    sigma   weight residual
     116.30  132.58  -16.28 3.50e+00 8.16e-02 2.16e+01
  angle pdb=" O22 6OU A 502 "
        pdb=" P23 6OU A 502 "
        pdb=" O26 6OU A 502 "
      ideal   model   delta    sigma   weight residual
      93.95  107.46  -13.51 3.00e+00 1.11e-01 2.03e+01
  angle pdb=" C   ILE A 294 "
        pdb=" N   SER A 295 "
        pdb=" CA  SER A 295 "
      ideal   model   delta    sigma   weight residual
     121.54  129.72   -8.18 1.91e+00 2.74e-01 1.83e+01
  angle pdb=" CA  TYR A 299 "
        pdb=" CB  TYR A 299 "
        pdb=" CG  TYR A 299 "
      ideal   model   delta    sigma   weight residual
     113.90  121.13   -7.23 1.80e+00 3.09e-01 1.61e+01
  ... (remaining 4185 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.45: 1708
       25.45 -    50.91: 100
       50.91 -    76.36: 14
       76.36 -   101.81: 0
      101.81 -   127.26: 3
  Dihedral angle restraints: 1825
    sinusoidal: 684
      harmonic: 1141
  Sorted by residual:
  dihedral pdb=" CA  ILE A 294 "
           pdb=" C   ILE A 294 "
           pdb=" N   SER A 295 "
           pdb=" CA  SER A 295 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.05   36.95     0      5.00e+00 4.00e-02 5.46e+01
  dihedral pdb=" CA  PRO A  75 "
           pdb=" C   PRO A  75 "
           pdb=" N   ALA A  76 "
           pdb=" CA  ALA A  76 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.43  -26.57     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CA  SER A  72 "
           pdb=" C   SER A  72 "
           pdb=" N   ILE A  73 "
           pdb=" CA  ILE A  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.02   20.98     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 1822 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 357
       0.052 -    0.105: 112
       0.105 -    0.157: 45
       0.157 -    0.209: 9
       0.209 -    0.262: 1
  Chirality restraints: 524
  Sorted by residual:
  chirality pdb=" CB  ILE A  73 "
            pdb=" CA  ILE A  73 "
            pdb=" CG1 ILE A  73 "
            pdb=" CG2 ILE A  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CB  VAL A  62 "
            pdb=" CA  VAL A  62 "
            pdb=" CG1 VAL A  62 "
            pdb=" CG2 VAL A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  ALA A 205 "
            pdb=" N   ALA A 205 "
            pdb=" C   ALA A 205 "
            pdb=" CB  ALA A 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.29    0.20 2.00e-01 2.50e+01 9.51e-01
  ... (remaining 521 not shown)

  Planarity restraints: 510
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 355 "    0.042 5.00e-02 4.00e+02   6.40e-02 6.56e+00
        pdb=" N   PRO A 356 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A 356 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 356 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  44 "   -0.041 5.00e-02 4.00e+02   6.14e-02 6.03e+00
        pdb=" N   PRO A  45 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A  45 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  45 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 243 "   -0.011 2.00e-02 2.50e+03   2.19e-02 4.81e+00
        pdb=" C   ILE A 243 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ILE A 243 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A 244 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 507 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 926
        2.82 -     3.34: 2992
        3.34 -     3.86: 5003
        3.86 -     4.38: 5617
        4.38 -     4.90: 9689
  Nonbonded interactions: 24227
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 247 "
            pdb=" OD2 ASP A 312 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OH  TYR A 236 "
            pdb=" O   ILE A 392 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" O   THR A 403 "
            pdb=" OG1 THR A 407 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   ILE A  61 "
            pdb=" OG  SER A  65 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" O   MET A 311 "
            pdb=" OG  SER A 349 "
     model   vdw
     2.349 3.040
  ... (remaining 24222 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.080
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
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      :  0.008   0.086   3084  Z= 0.356
  Angle     :  1.158  16.279   4190  Z= 0.567
  Chirality :  0.060   0.262    524
  Planarity :  0.009   0.064    510
  Dihedral  : 16.853 127.264   1101
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.58 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.01 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -4.71 (0.31), residues: 396
  helix: -2.71 (0.20), residues: 321
  sheet:  None (None), residues: 0
  loop : -3.85 (0.67), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 397 
 TYR   0.028   0.002   TYR A 299 
 PHE   0.017   0.002   PHE A 248 
 HIS   0.005   0.002   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00808 ( 3083)
  covalent geometry    : angle       1.15805 ( 4190)
  hydrogen bonds       : bond        0.10267 (  221)
  hydrogen bonds       : angle       6.21565 (  663)
  Misc. bond           : bond        0.00007 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 TYR cc_start: 0.8103 (m-80) cc_final: 0.7888 (m-80)
REVERT: A  337 GLN cc_start: 0.7419 (mm-40) cc_final: 0.5816 (tt0)
REVERT: A  362 MET cc_start: 0.8500 (mmm) cc_final: 0.8280 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0641
  time to fit residues: 7.0838
Evaluate side-chains
  70 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0050
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
A  14 GLN
A  40 HIS
A 173 ASN
A 199 ASN
** A 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.131139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.105134 restraints weight = 5825.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.107483 restraints weight = 3319.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.108986 restraints weight = 2389.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.109465 restraints weight = 1976.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.110260 restraints weight = 1827.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3084  Z= 0.152
  Angle     :  0.689  10.027   4190  Z= 0.350
  Chirality :  0.042   0.135    524
  Planarity :  0.006   0.054    510
  Dihedral  : 11.613  88.974    463
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.06 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.11 %
    Favored  : 78.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -2.03 (0.40), residues: 396
  helix: -0.75 (0.26), residues: 321
  sheet:  None (None), residues: 0
  loop : -3.44 (0.72), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 105 
 TYR   0.025   0.001   TYR A 299 
 PHE   0.014   0.001   PHE A 324 
 HIS   0.003   0.001   HIS A 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3083)
  covalent geometry    : angle       0.68860 ( 4190)
  hydrogen bonds       : bond        0.04238 (  221)
  hydrogen bonds       : angle       4.75758 (  663)
  Misc. bond           : bond        0.00009 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 TYR cc_start: 0.8062 (m-80) cc_final: 0.7860 (m-80)
REVERT: A  102 ILE cc_start: 0.8412 (mt) cc_final: 0.8185 (mt)
REVERT: A  227 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7293 (tm-30)
REVERT: A  247 TYR cc_start: 0.7927 (m-80) cc_final: 0.7680 (m-80)
REVERT: A  337 GLN cc_start: 0.7523 (mm-40) cc_final: 0.6431 (tt0)
REVERT: A  406 LEU cc_start: 0.8976 (mm) cc_final: 0.8622 (mp)
  outliers start: 9
  outliers final: 6
  residues processed: 90
  average time/residue: 0.0566
  time to fit residues: 6.3570
Evaluate side-chains
  83 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 77
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  355 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    0.1980
   chunk 6 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 35 optimal weight:    0.3980
   chunk 25 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 318 GLN
A 332 HIS

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 = 0.131303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.105605 restraints weight = 5863.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.107932 restraints weight = 3319.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.109452 restraints weight = 2393.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.110291 restraints weight = 1984.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.110925 restraints weight = 1788.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3084  Z= 0.142
  Angle     :  0.669  10.290   4190  Z= 0.334
  Chirality :  0.042   0.134    524
  Planarity :  0.005   0.051    510
  Dihedral  :  9.957  85.254    463
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.31 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 21.97 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -0.98 (0.42), residues: 396
  helix:  0.02 (0.28), residues: 324
  sheet:  None (None), residues: 0
  loop : -3.41 (0.73), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 397 
 TYR   0.024   0.001   TYR A 299 
 PHE   0.009   0.001   PHE A 324 
 HIS   0.003   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3083)
  covalent geometry    : angle       0.66934 ( 4190)
  hydrogen bonds       : bond        0.04062 (  221)
  hydrogen bonds       : angle       4.61473 (  663)
  Misc. bond           : bond        0.00002 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A   86 VAL cc_start: 0.9302 (t) cc_final: 0.9072 (m)
REVERT: A  286 MET cc_start: 0.8701 (mtp) cc_final: 0.8333 (mtp)
REVERT: A  337 GLN cc_start: 0.7442 (mm-40) cc_final: 0.6109 (tt0)
REVERT: A  390 ASP cc_start: 0.8103 (t0) cc_final: 0.7896 (t0)
REVERT: A  406 LEU cc_start: 0.8908 (mm) cc_final: 0.8561 (mt)
  outliers start: 10
  outliers final: 5
  residues processed: 89
  average time/residue: 0.0504
  time to fit residues: 5.6533
Evaluate side-chains
  79 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 74
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  355 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 1 optimal weight:    0.3980
   chunk 21 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS
A 318 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.130214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.104117 restraints weight = 5820.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.106501 restraints weight = 3314.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.107995 restraints weight = 2379.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.108794 restraints weight = 1970.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.108797 restraints weight = 1778.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3084  Z= 0.164
  Angle     :  0.692  10.453   4190  Z= 0.342
  Chirality :  0.043   0.148    524
  Planarity :  0.005   0.054    510
  Dihedral  :  9.103  85.874    463
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.57 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 26.11 %
    Favored  : 69.75 %
  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: -0.54 (0.43), residues: 396
  helix:  0.35 (0.29), residues: 323
  sheet:  None (None), residues: 0
  loop : -3.35 (0.72), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 105 
 TYR   0.024   0.001   TYR A 299 
 PHE   0.008   0.001   PHE A 324 
 HIS   0.007   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 3083)
  covalent geometry    : angle       0.69171 ( 4190)
  hydrogen bonds       : bond        0.04215 (  221)
  hydrogen bonds       : angle       4.64478 (  663)
  Misc. bond           : bond        0.00010 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8489 (m) cc_final: 0.8184 (m)
REVERT: A   86 VAL cc_start: 0.9262 (t) cc_final: 0.9061 (m)
REVERT: A  247 TYR cc_start: 0.7817 (m-80) cc_final: 0.7616 (m-80)
REVERT: A  337 GLN cc_start: 0.7517 (mm-40) cc_final: 0.6150 (tt0)
REVERT: A  397 ARG cc_start: 0.7162 (ttm110) cc_final: 0.6817 (ttm110)
REVERT: A  406 LEU cc_start: 0.8985 (mm) cc_final: 0.8641 (mt)
  outliers start: 13
  outliers final: 11
  residues processed: 83
  average time/residue: 0.0541
  time to fit residues: 5.6876
Evaluate side-chains
  86 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  138 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  398 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0980
   chunk 15 optimal weight:    0.3980
   chunk 11 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 8 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   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  37 HIS
A 318 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.129176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.101456 restraints weight = 5817.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.103825 restraints weight = 3165.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.105204 restraints weight = 2249.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.106122 restraints weight = 1878.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.106626 restraints weight = 1689.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3084  Z= 0.142
  Angle     :  0.684  10.285   4190  Z= 0.336
  Chirality :  0.043   0.139    524
  Planarity :  0.005   0.054    510
  Dihedral  :  8.597  80.024    463
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.81 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 28.34 %
    Favored  : 68.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -0.26 (0.43), residues: 396
  helix:  0.57 (0.29), residues: 324
  sheet:  None (None), residues: 0
  loop : -3.45 (0.71), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 105 
 TYR   0.021   0.001   TYR A 299 
 PHE   0.008   0.001   PHE A 324 
 HIS   0.007   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 3083)
  covalent geometry    : angle       0.68431 ( 4190)
  hydrogen bonds       : bond        0.03956 (  221)
  hydrogen bonds       : angle       4.55737 (  663)
  Misc. bond           : bond        0.00019 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.7091 (t80)
REVERT: A   83 VAL cc_start: 0.8417 (m) cc_final: 0.8107 (m)
REVERT: A   86 VAL cc_start: 0.9248 (t) cc_final: 0.9016 (m)
REVERT: A  247 TYR cc_start: 0.7848 (m-80) cc_final: 0.7639 (m-80)
REVERT: A  286 MET cc_start: 0.8591 (mtp) cc_final: 0.8244 (mtp)
REVERT: A  337 GLN cc_start: 0.7595 (mm-40) cc_final: 0.6348 (tt0)
REVERT: A  397 ARG cc_start: 0.7167 (ttm110) cc_final: 0.6907 (ttm110)
REVERT: A  406 LEU cc_start: 0.8908 (mm) cc_final: 0.8516 (mt)
  outliers start: 9
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0570
  time to fit residues: 5.9505
Evaluate side-chains
  84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 76
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 0 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0980
   chunk 35 optimal weight:    6.9990
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS
A 264 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.128664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.102766 restraints weight = 5840.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.105093 restraints weight = 3277.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.106519 restraints weight = 2366.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.107373 restraints weight = 1967.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.107643 restraints weight = 1776.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3084  Z= 0.198
  Angle     :  0.732  10.591   4190  Z= 0.359
  Chirality :  0.045   0.166    524
  Planarity :  0.005   0.056    510
  Dihedral  :  9.051  91.325    463
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 15.05
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.81 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 25.16 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -0.27 (0.43), residues: 396
  helix:  0.53 (0.29), residues: 325
  sheet:  None (None), residues: 0
  loop : -3.34 (0.72), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 105 
 TYR   0.021   0.001   TYR A 299 
 PHE   0.006   0.001   PHE A 324 
 HIS   0.006   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 3083)
  covalent geometry    : angle       0.73232 ( 4190)
  hydrogen bonds       : bond        0.04331 (  221)
  hydrogen bonds       : angle       4.68458 (  663)
  Misc. bond           : bond        0.00001 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 VAL cc_start: 0.8514 (m) cc_final: 0.8197 (m)
REVERT: A   86 VAL cc_start: 0.9245 (t) cc_final: 0.9036 (m)
REVERT: A  136 ASP cc_start: 0.8193 (t0) cc_final: 0.7978 (t0)
REVERT: A  337 GLN cc_start: 0.7534 (mm-40) cc_final: 0.6286 (tt0)
  outliers start: 17
  outliers final: 11
  residues processed: 86
  average time/residue: 0.0517
  time to fit residues: 5.6199
Evaluate side-chains
  80 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0070
   chunk 2 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS
A 264 HIS
A 318 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.127548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.099515 restraints weight = 6003.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.101962 restraints weight = 3241.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.103513 restraints weight = 2291.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.104192 restraints weight = 1887.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.104903 restraints weight = 1721.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   3084  Z= 0.147
  Angle     :  0.710  11.387   4190  Z= 0.342
  Chirality :  0.043   0.149    524
  Planarity :  0.005   0.058    510
  Dihedral  :  8.540  83.346    463
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 14.57
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.56 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 25.80 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -0.16 (0.43), residues: 396
  helix:  0.59 (0.29), residues: 330
  sheet:  None (None), residues: 0
  loop : -3.51 (0.73), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 105 
 TYR   0.021   0.001   TYR A 299 
 PHE   0.007   0.001   PHE A 324 
 HIS   0.007   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3083)
  covalent geometry    : angle       0.71014 ( 4190)
  hydrogen bonds       : bond        0.04015 (  221)
  hydrogen bonds       : angle       4.59114 (  663)
  Misc. bond           : bond        0.00019 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.7042 (t80)
REVERT: A   83 VAL cc_start: 0.8414 (m) cc_final: 0.8098 (m)
REVERT: A   86 VAL cc_start: 0.9219 (t) cc_final: 0.8982 (m)
REVERT: A  136 ASP cc_start: 0.8235 (t0) cc_final: 0.8014 (t0)
REVERT: A  286 MET cc_start: 0.8617 (mtp) cc_final: 0.8295 (mtp)
REVERT: A  337 GLN cc_start: 0.7493 (mm-40) cc_final: 0.6305 (tt0)
REVERT: A  406 LEU cc_start: 0.8967 (mm) cc_final: 0.8574 (mt)
  outliers start: 13
  outliers final: 11
  residues processed: 83
  average time/residue: 0.0481
  time to fit residues: 5.0031
Evaluate side-chains
  84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   73 ILE
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 6 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 12 optimal weight:    0.0980
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.125479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.096765 restraints weight = 6018.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.098985 restraints weight = 3430.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.100394 restraints weight = 2515.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.100981 restraints weight = 2116.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.101649 restraints weight = 1948.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3084  Z= 0.147
  Angle     :  0.711  12.141   4190  Z= 0.341
  Chirality :  0.042   0.148    524
  Planarity :  0.005   0.053    510
  Dihedral  :  8.455  81.618    463
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 14.89
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.30 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 26.11 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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: -0.05 (0.43), residues: 396
  helix:  0.69 (0.29), residues: 329
  sheet:  None (None), residues: 0
  loop : -3.52 (0.71), residues: 67

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 397 
 TYR   0.023   0.001   TYR A 299 
 PHE   0.007   0.001   PHE A 324 
 HIS   0.007   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 3083)
  covalent geometry    : angle       0.71134 ( 4190)
  hydrogen bonds       : bond        0.03973 (  221)
  hydrogen bonds       : angle       4.52579 (  663)
  Misc. bond           : bond        0.00017 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 73
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A   10 TYR cc_start: 0.7640 (OUTLIER) cc_final: 0.7068 (t80)
REVERT: A   83 VAL cc_start: 0.8447 (m) cc_final: 0.8122 (m)
REVERT: A   86 VAL cc_start: 0.9248 (t) cc_final: 0.9015 (m)
REVERT: A  136 ASP cc_start: 0.8251 (t0) cc_final: 0.8037 (t0)
REVERT: A  286 MET cc_start: 0.8700 (mtp) cc_final: 0.8359 (mtp)
REVERT: A  337 GLN cc_start: 0.7408 (mm-40) cc_final: 0.6336 (tt0)
REVERT: A  406 LEU cc_start: 0.8982 (mm) cc_final: 0.8589 (mt)
  outliers start: 15
  outliers final: 12
  residues processed: 82
  average time/residue: 0.0426
  time to fit residues: 4.5596
Evaluate side-chains
  84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  341 ILE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 13 optimal weight:    0.0060
   chunk 10 optimal weight:    0.0270
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    0.1980
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.2854

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS
** A 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 318 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.131194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.103097 restraints weight = 6034.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.105533 restraints weight = 3295.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.107040 restraints weight = 2344.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.107838 restraints weight = 1937.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.107972 restraints weight = 1752.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3084  Z= 0.129
  Angle     :  0.723  13.124   4190  Z= 0.341
  Chirality :  0.042   0.145    524
  Planarity :  0.005   0.057    510
  Dihedral  :  8.131  72.701    463
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.56 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 26.43 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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:  0.11 (0.43), residues: 396
  helix:  0.83 (0.29), residues: 332
  sheet:  None (None), residues: 0
  loop : -3.83 (0.70), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 397 
 TYR   0.021   0.001   TYR A 299 
 PHE   0.007   0.001   PHE A 324 
 HIS   0.008   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3083)
  covalent geometry    : angle       0.72261 ( 4190)
  hydrogen bonds       : bond        0.03816 (  221)
  hydrogen bonds       : angle       4.45690 (  663)
  Misc. bond           : bond        0.00028 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   10 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7067 (t80)
REVERT: A   83 VAL cc_start: 0.8292 (m) cc_final: 0.7948 (m)
REVERT: A   86 VAL cc_start: 0.9227 (t) cc_final: 0.9001 (m)
REVERT: A  136 ASP cc_start: 0.8256 (t0) cc_final: 0.8033 (t0)
REVERT: A  286 MET cc_start: 0.8671 (mtp) cc_final: 0.8335 (mtp)
REVERT: A  337 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6407 (tt0)
REVERT: A  406 LEU cc_start: 0.8935 (mm) cc_final: 0.8541 (mt)
  outliers start: 14
  outliers final: 10
  residues processed: 86
  average time/residue: 0.0448
  time to fit residues: 4.9834
Evaluate side-chains
  84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  366 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0270
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0970
   chunk 14 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.3036

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS
A 318 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.131429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.103538 restraints weight = 5941.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.105934 restraints weight = 3233.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.107397 restraints weight = 2289.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.108224 restraints weight = 1884.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.108346 restraints weight = 1697.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3084  Z= 0.129
  Angle     :  0.727  13.157   4190  Z= 0.342
  Chirality :  0.042   0.150    524
  Planarity :  0.005   0.059    510
  Dihedral  :  7.995  66.764    463
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  6.06 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 28.98 %
    Favored  : 67.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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:  0.11 (0.43), residues: 396
  helix:  0.80 (0.29), residues: 333
  sheet:  None (None), residues: 0
  loop : -3.75 (0.70), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 397 
 TYR   0.021   0.001   TYR A 299 
 PHE   0.006   0.001   PHE A 324 
 HIS   0.008   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3083)
  covalent geometry    : angle       0.72745 ( 4190)
  hydrogen bonds       : bond        0.03801 (  221)
  hydrogen bonds       : angle       4.44477 (  663)
  Misc. bond           : bond        0.00023 (    1)

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

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

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  792 Ramachandran restraints generated.
    396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 73
  time to evaluate  : 0.104 
Fit side-chains
REVERT: A   10 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.7124 (t80)
REVERT: A   83 VAL cc_start: 0.8311 (m) cc_final: 0.7970 (m)
REVERT: A   86 VAL cc_start: 0.9219 (t) cc_final: 0.9002 (m)
REVERT: A  136 ASP cc_start: 0.8277 (t0) cc_final: 0.8043 (t0)
REVERT: A  286 MET cc_start: 0.8642 (mtp) cc_final: 0.8276 (mtp)
REVERT: A  337 GLN cc_start: 0.7312 (mm-40) cc_final: 0.6427 (tt0)
REVERT: A  406 LEU cc_start: 0.8934 (mm) cc_final: 0.8544 (mt)
  outliers start: 12
  outliers final: 10
  residues processed: 80
  average time/residue: 0.0434
  time to fit residues: 4.5173
Evaluate side-chains
  83 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 TYR
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  323 PHE
Chi-restraints excluded: chain A residue  355 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 6 optimal weight:    0.3980
   chunk 18 optimal weight:    0.3980
   chunk 29 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  37 HIS
A 318 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.129014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.100781 restraints weight = 6051.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.103056 restraints weight = 3386.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.104461 restraints weight = 2434.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.105262 restraints weight = 2021.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.105819 restraints weight = 1828.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.3296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3084  Z= 0.147
  Angle     :  0.738  13.135   4190  Z= 0.349
  Chirality :  0.043   0.144    524
  Planarity :  0.005   0.059    510
  Dihedral  :  8.177  72.802    463
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  5.56 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 28.66 %
    Favored  : 67.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

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:  0.06 (0.43), residues: 396
  helix:  0.81 (0.29), residues: 330
  sheet:  None (None), residues: 0
  loop : -3.83 (0.64), residues: 66

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 397 
 TYR   0.023   0.001   TYR A 299 
 PHE   0.006   0.001   PHE A  50 
 HIS   0.007   0.001   HIS A  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3083)
  covalent geometry    : angle       0.73811 ( 4190)
  hydrogen bonds       : bond        0.03991 (  221)
  hydrogen bonds       : angle       4.48479 (  663)
  Misc. bond           : bond        0.00015 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 717.31 seconds
wall clock time: 13 minutes 0.68 seconds (780.68 seconds total)