Starting phenix.real_space_refine
on Wed Sep 17 03:44:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m0s_63562/09_2025/9m0s_63562.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m0s_63562/09_2025/9m0s_63562.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m0s_63562/09_2025/9m0s_63562.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m0s_63562/09_2025/9m0s_63562.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m0s_63562/09_2025/9m0s_63562.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m0s_63562/09_2025/9m0s_63562.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.046
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      13      5.16       5
     C    2288      2.51       5
     N     515      2.21       5
     O     594      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3413
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3362
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 424, 3362
          Classifications: {'peptide': 424}
          Link IDs: {'PTRANS': 22, 'TRANS': 401}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 51
          Unusual residues: {'ACO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.93, per 1000 atoms: 0.27
  Number of scatterers: 3413
  At special positions: 0
  Unit cell: (73.87, 68.06, 77.19, 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      13     16.00
     P       3     15.00
     O     594      8.00
     N     515      7.00
     C    2288      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: 0.28
  Conformation dependent library (CDL) restraints added in 133.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 0 sheets defined
      86.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 71 through 102
      removed outlier: 4.471A  pdb=" N   LEU A  77 " --> pdb=" O   SER A  73 " (cutoff:3.500A)
      Proline residue:  A  88  - end of helix
      Proline residue:  A  96  - end of helix
    Processing helix  chain 'A' and resid 105 through 113
    Processing helix  chain 'A' and resid 116 through 121
      removed outlier: 3.972A  pdb=" N   SER A 120 " --> pdb=" O   PHE A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 124
      No H-bonds generated for 'chain 'A' and resid 122 through 124'
    Processing helix  chain 'A' and resid 125 through 131
    Processing helix  chain 'A' and resid 144 through 166
      removed outlier: 4.718A  pdb=" N   ASP A 163 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   ARG A 164 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   LEU A 166 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 205
      removed outlier: 4.283A  pdb=" N   LEU A 202 " --> pdb=" O   ASP A 198 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   THR A 203 " --> pdb=" O   GLY A 199 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU A 205 " --> pdb=" O   ALA A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 230
      removed outlier: 3.556A  pdb=" N   SER A 214 " --> pdb=" O   VAL A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 235
    Processing helix  chain 'A' and resid 237 through 244
      removed outlier: 3.679A  pdb=" N   CYS A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 278
    Processing helix  chain 'A' and resid 295 through 307
    Processing helix  chain 'A' and resid 307 through 321
      removed outlier: 4.366A  pdb=" N   LYS A 321 " --> pdb=" O   ILE A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 339
      removed outlier: 4.060A  pdb=" N   ALA A 326 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   ALA A 327 " --> pdb=" O   GLY A 323 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   GLY A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   LEU A 333 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   VAL A 336 " --> pdb=" O   GLY A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 348
    Processing helix  chain 'A' and resid 351 through 363
      removed outlier: 4.153A  pdb=" N   LEU A 355 " --> pdb=" O   PRO A 351 " (cutoff:3.500A)
      Proline residue:  A 360  - end of helix
    Processing helix  chain 'A' and resid 363 through 369
    Processing helix  chain 'A' and resid 373 through 397
      Proline residue:  A 381  - end of helix
    Processing helix  chain 'A' and resid 398 through 400
      No H-bonds generated for 'chain 'A' and resid 398 through 400'
    Processing helix  chain 'A' and resid 407 through 440
      removed outlier: 3.752A  pdb=" N   TYR A 411 " --> pdb=" O   PRO A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 470
      removed outlier: 4.710A  pdb=" N   THR A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      Proline residue:  A 463  - end of helix
    Processing helix  chain 'A' and resid 471 through 475
      removed outlier: 3.511A  pdb=" N   THR A 475 " --> pdb=" O   ASP A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 535
      removed outlier: 4.078A  pdb=" N   VAL A 512 " --> pdb=" O   ASP A 508 " (cutoff:3.500A)
      Proline residue:  A 530  - end of helix

    239 hydrogen bonds defined for protein.
    714 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: 0.48

  Time building geometry restraints manager: 0.30 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: 505
        1.31 -     1.44: 1009
        1.44 -     1.57: 1969
        1.57 -     1.70: 7
        1.70 -     1.83: 22
  Bond restraints: 3512
  Sorted by residual:
  bond pdb=" C6A ACO A 601 "
       pdb=" N6A ACO A 601 "
    ideal  model  delta    sigma   weight residual
    1.337  1.478 -0.141 1.00e-02 1.00e+04 1.98e+02
  bond pdb=" C5P ACO A 601 "
       pdb=" N4P ACO A 601 "
    ideal  model  delta    sigma   weight residual
    1.331  1.474 -0.143 1.20e-02 6.94e+03 1.42e+02
  bond pdb=" C9P ACO A 601 "
       pdb=" N8P ACO A 601 "
    ideal  model  delta    sigma   weight residual
    1.333  1.480 -0.147 1.30e-02 5.92e+03 1.28e+02
  bond pdb=" C3B ACO A 601 "
       pdb=" O3B ACO A 601 "
    ideal  model  delta    sigma   weight residual
    1.444  1.338  0.106 1.20e-02 6.94e+03 7.75e+01
  bond pdb=" O5B ACO A 601 "
       pdb=" P1A ACO A 601 "
    ideal  model  delta    sigma   weight residual
    1.579  1.674 -0.095 1.50e-02 4.44e+03 4.01e+01
  ... (remaining 3507 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 4651
        2.76 -     5.52: 118
        5.52 -     8.28: 31
        8.28 -    11.05: 7
       11.05 -    13.81: 2
  Bond angle restraints: 4809
  Sorted by residual:
  angle pdb=" P1A ACO A 601 "
        pdb=" O3A ACO A 601 "
        pdb=" P2A ACO A 601 "
      ideal   model   delta    sigma   weight residual
     136.83  123.02   13.81 1.00e+00 1.00e+00 1.91e+02
  angle pdb=" N1A ACO A 601 "
        pdb=" C2A ACO A 601 "
        pdb=" N3A ACO A 601 "
      ideal   model   delta    sigma   weight residual
     128.69  119.81    8.88 1.00e+00 1.00e+00 7.89e+01
  angle pdb=" C5A ACO A 601 "
        pdb=" C4A ACO A 601 "
        pdb=" N3A ACO A 601 "
      ideal   model   delta    sigma   weight residual
     126.80  120.12    6.68 1.00e+00 1.00e+00 4.46e+01
  angle pdb=" C   ACO A 601 "
        pdb=" S1P ACO A 601 "
        pdb=" C2P ACO A 601 "
      ideal   model   delta    sigma   weight residual
     101.25  107.61   -6.36 1.00e+00 1.00e+00 4.05e+01
  angle pdb=" CH3 ACO A 601 "
        pdb=" C   ACO A 601 "
        pdb=" S1P ACO A 601 "
      ideal   model   delta    sigma   weight residual
     112.98  119.28   -6.30 1.00e+00 1.00e+00 3.97e+01
  ... (remaining 4804 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.87: 1877
       15.87 -    31.74: 96
       31.74 -    47.62: 44
       47.62 -    63.49: 15
       63.49 -    79.36: 3
  Dihedral angle restraints: 2035
    sinusoidal: 800
      harmonic: 1235
  Sorted by residual:
  dihedral pdb=" CA  GLU A 338 "
           pdb=" C   GLU A 338 "
           pdb=" N   GLY A 339 "
           pdb=" CA  GLY A 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.13   24.87     0      5.00e+00 4.00e-02 2.47e+01
  dihedral pdb=" CA  MET A 307 "
           pdb=" C   MET A 307 "
           pdb=" N   PRO A 308 "
           pdb=" CA  PRO A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.37  -18.63     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CA  ARG A 246 "
           pdb=" C   ARG A 246 "
           pdb=" N   PHE A 247 "
           pdb=" CA  PHE A 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.21   16.79     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 2032 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 346
       0.048 -    0.096: 136
       0.096 -    0.144: 58
       0.144 -    0.192: 19
       0.192 -    0.240: 6
  Chirality restraints: 565
  Sorted by residual:
  chirality pdb=" CB  VAL A 353 "
            pdb=" CA  VAL A 353 "
            pdb=" CG1 VAL A 353 "
            pdb=" CG2 VAL A 353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.44e+00
  chirality pdb=" CB  VAL A 350 "
            pdb=" CA  VAL A 350 "
            pdb=" CG1 VAL A 350 "
            pdb=" CG2 VAL A 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CB  ILE A 363 "
            pdb=" CA  ILE A 363 "
            pdb=" CG1 ILE A 363 "
            pdb=" CG2 ILE A 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 562 not shown)

  Planarity restraints: 574
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 186 "   -0.023 2.00e-02 2.50e+03   1.97e-02 6.81e+00
        pdb=" CG  PHE A 186 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 186 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 186 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 186 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 186 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 186 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 340 "   -0.039 5.00e-02 4.00e+02   5.93e-02 5.63e+00
        pdb=" N   PRO A 341 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 341 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 341 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 149 "    0.015 2.00e-02 2.50e+03   1.59e-02 5.07e+00
        pdb=" CG  TYR A 149 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 149 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 149 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 149 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 149 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 149 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 149 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 571 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 925
        2.80 -     3.33: 3322
        3.33 -     3.85: 5836
        3.85 -     4.38: 6658
        4.38 -     4.90: 11060
  Nonbonded interactions: 27801
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  82 "
            pdb=" OD1 ASP A 198 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" OH  TYR A 225 "
            pdb=" O9A ACO A 601 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" OE1 GLU A 389 "
            pdb=" OG  SER A 417 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" O   PHE A 268 "
            pdb=" OG1 THR A 272 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" OG1 THR A 331 "
            pdb=" OH  TYR A 510 "
     model   vdw
     2.328 3.040
  ... (remaining 27796 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:             1.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.640
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  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:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
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      :  0.010   0.147   3512  Z= 0.603
  Angle     :  1.184  13.807   4809  Z= 0.671
  Chirality :  0.065   0.240    565
  Planarity :  0.009   0.059    574
  Dihedral  : 13.207  79.361   1243
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.69 (0.31), residues: 418
  helix: -2.36 (0.21), residues: 316
  sheet:  None (None), residues: 0
  loop : -1.94 (0.55), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 246 
 TYR   0.039   0.003   TYR A 149 
 PHE   0.042   0.003   PHE A 186 
 TRP   0.030   0.003   TRP A 524 
 HIS   0.002   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00969 ( 3512)
  covalent geometry    : angle       1.18402 ( 4809)
  hydrogen bonds       : bond        0.09968 (  239)
  hydrogen bonds       : angle       5.98406 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  175 ASP cc_start: 0.8680 (t0) cc_final: 0.8091 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0634
  time to fit residues: 3.9724
Evaluate side-chains
  37 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 100 GLN
A 103 ASN
** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 242 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.158201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.126723 restraints weight = 3852.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.131494 restraints weight = 2018.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.134784 restraints weight = 1360.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.136802 restraints weight = 1057.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.138243 restraints weight = 904.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3512  Z= 0.163
  Angle     :  0.662   7.851   4809  Z= 0.335
  Chirality :  0.042   0.128    565
  Planarity :  0.005   0.041    574
  Dihedral  : 12.185  61.308    503
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.59 %
    Favored  : 89.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (0.38), residues: 418
  helix: -0.58 (0.27), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.13 (0.62), residues: 86

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 140 
 TYR   0.013   0.001   TYR A 149 
 PHE   0.025   0.002   PHE A 186 
 TRP   0.016   0.002   TRP A 143 
 HIS   0.002   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 3512)
  covalent geometry    : angle       0.66167 ( 4809)
  hydrogen bonds       : bond        0.04066 (  239)
  hydrogen bonds       : angle       4.67596 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 36
  time to evaluate  : 0.125 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 39
  average time/residue: 0.0700
  time to fit residues: 3.4384
Evaluate side-chains
  36 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  340 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0010
   chunk 11 optimal weight:    0.5980
   chunk 12 optimal weight:    0.6980
   chunk 37 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.158271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.127389 restraints weight = 3802.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.132137 restraints weight = 2011.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.135476 restraints weight = 1349.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.137612 restraints weight = 1047.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.138800 restraints weight = 887.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6973
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3512  Z= 0.144
  Angle     :  0.621   7.825   4809  Z= 0.313
  Chirality :  0.041   0.117    565
  Planarity :  0.005   0.037    574
  Dihedral  : 11.685  59.833    503
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 10.96 %
    Favored  : 86.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.01 (0.41), residues: 418
  helix:  0.23 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -0.43 (0.69), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 140 
 TYR   0.012   0.001   TYR A 149 
 PHE   0.022   0.001   PHE A 186 
 TRP   0.011   0.001   TRP A 143 
 HIS   0.001   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3512)
  covalent geometry    : angle       0.62101 ( 4809)
  hydrogen bonds       : bond        0.03724 (  239)
  hydrogen bonds       : angle       4.37403 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6150 (mp0)
  outliers start: 8
  outliers final: 5
  residues processed: 43
  average time/residue: 0.0731
  time to fit residues: 3.9213
Evaluate side-chains
  43 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  340 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0670
   chunk 11 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 27 optimal weight:   10.0000
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.157243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.125395 restraints weight = 3823.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.130110 restraints weight = 2062.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.133323 restraints weight = 1405.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.135386 restraints weight = 1100.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.136721 restraints weight = 939.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
moved from start:          0.1994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3512  Z= 0.150
  Angle     :  0.612   7.735   4809  Z= 0.308
  Chirality :  0.041   0.119    565
  Planarity :  0.004   0.035    574
  Dihedral  : 11.623  60.048    503
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.88 %
    Favored  : 84.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.42), residues: 418
  helix:  0.49 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -0.22 (0.71), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 246 
 TYR   0.009   0.001   TYR A 409 
 PHE   0.019   0.001   PHE A 186 
 TRP   0.009   0.001   TRP A 264 
 HIS   0.002   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3512)
  covalent geometry    : angle       0.61170 ( 4809)
  hydrogen bonds       : bond        0.03676 (  239)
  hydrogen bonds       : angle       4.32255 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  205 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7524 (pp)
REVERT: A  338 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6294 (mt-10)
  outliers start: 8
  outliers final: 5
  residues processed: 40
  average time/residue: 0.0679
  time to fit residues: 3.4392
Evaluate side-chains
  39 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  340 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 40 optimal weight:    0.6980
   chunk 12 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 37 optimal weight:    0.1980
   chunk 22 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 41 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.157536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.125135 restraints weight = 3880.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.129838 restraints weight = 2125.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.132981 restraints weight = 1453.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.135190 restraints weight = 1151.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.136481 restraints weight = 987.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7044
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3512  Z= 0.141
  Angle     :  0.604   7.807   4809  Z= 0.304
  Chirality :  0.042   0.129    565
  Planarity :  0.004   0.034    574
  Dihedral  : 11.524  59.789    503
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 13.42 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.42), residues: 418
  helix:  0.67 (0.29), residues: 334
  sheet:  None (None), residues: 0
  loop : -0.08 (0.73), residues: 84

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 246 
 TYR   0.009   0.001   TYR A 409 
 PHE   0.019   0.001   PHE A 186 
 TRP   0.008   0.001   TRP A 264 
 HIS   0.002   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3512)
  covalent geometry    : angle       0.60395 ( 4809)
  hydrogen bonds       : bond        0.03609 (  239)
  hydrogen bonds       : angle       4.30043 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 33
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A  205 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7515 (pp)
REVERT: A  338 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6418 (mt-10)
  outliers start: 10
  outliers final: 7
  residues processed: 41
  average time/residue: 0.0557
  time to fit residues: 3.0086
Evaluate side-chains
  42 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  340 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 27 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   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  85 GLN
** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.156212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.123266 restraints weight = 3826.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.128153 restraints weight = 2020.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.131590 restraints weight = 1358.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.133783 restraints weight = 1052.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.135111 restraints weight = 899.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7073
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3512  Z= 0.155
  Angle     :  0.610   7.838   4809  Z= 0.307
  Chirality :  0.042   0.126    565
  Planarity :  0.004   0.033    574
  Dihedral  : 11.497  59.583    503
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 13.97 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.42), residues: 418
  helix:  0.76 (0.29), residues: 335
  sheet:  None (None), residues: 0
  loop :  0.04 (0.73), residues: 83

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 246 
 TYR   0.009   0.001   TYR A 409 
 PHE   0.018   0.001   PHE A 186 
 TRP   0.009   0.001   TRP A 264 
 HIS   0.002   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 3512)
  covalent geometry    : angle       0.61012 ( 4809)
  hydrogen bonds       : bond        0.03619 (  239)
  hydrogen bonds       : angle       4.30598 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 33
  time to evaluate  : 0.074 
Fit side-chains
REVERT: A  205 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7529 (pp)
REVERT: A  254 ILE cc_start: 0.7917 (mm) cc_final: 0.7555 (mp)
REVERT: A  338 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6505 (mt-10)
  outliers start: 13
  outliers final: 9
  residues processed: 43
  average time/residue: 0.0462
  time to fit residues: 2.6654
Evaluate side-chains
  42 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  198 ASP
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  340 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0570
   chunk 17 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 38 optimal weight:    0.0980
   chunk 28 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.3298

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.158851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.125990 restraints weight = 3858.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.131088 restraints weight = 2010.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.134495 restraints weight = 1339.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.136885 restraints weight = 1037.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.138290 restraints weight = 872.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3512  Z= 0.128
  Angle     :  0.595   7.819   4809  Z= 0.298
  Chirality :  0.041   0.133    565
  Planarity :  0.004   0.033    574
  Dihedral  : 11.326  58.571    503
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.07 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.91 (0.43), residues: 418
  helix:  0.86 (0.29), residues: 336
  sheet:  None (None), residues: 0
  loop : -0.07 (0.74), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 246 
 TYR   0.009   0.001   TYR A 409 
 PHE   0.018   0.001   PHE A 186 
 TRP   0.007   0.001   TRP A 143 
 HIS   0.001   0.000   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3512)
  covalent geometry    : angle       0.59482 ( 4809)
  hydrogen bonds       : bond        0.03495 (  239)
  hydrogen bonds       : angle       4.24166 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.112 
Fit side-chains
REVERT: A  205 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7473 (pp)
REVERT: A  338 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6530 (mt-10)
  outliers start: 11
  outliers final: 7
  residues processed: 42
  average time/residue: 0.0492
  time to fit residues: 2.7050
Evaluate side-chains
  42 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  205 LEU
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  340 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 37 optimal weight:    0.1980
   chunk 32 optimal weight:    0.1980
   chunk 1 optimal weight:    0.0050
   chunk 26 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   overall best weight:    0.3794

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.159066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.126480 restraints weight = 3864.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.131607 restraints weight = 2000.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.135112 restraints weight = 1329.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.137358 restraints weight = 1027.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.138885 restraints weight = 868.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3512  Z= 0.129
  Angle     :  0.597   7.819   4809  Z= 0.298
  Chirality :  0.041   0.120    565
  Planarity :  0.004   0.033    574
  Dihedral  : 11.210  57.460    503
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.62 %
    Favored  : 81.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.01 (0.43), residues: 418
  helix:  0.91 (0.29), residues: 337
  sheet:  None (None), residues: 0
  loop :  0.05 (0.75), residues: 81

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 246 
 TYR   0.009   0.001   TYR A 409 
 PHE   0.017   0.001   PHE A 186 
 TRP   0.007   0.001   TRP A 264 
 HIS   0.001   0.000   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 3512)
  covalent geometry    : angle       0.59718 ( 4809)
  hydrogen bonds       : bond        0.03446 (  239)
  hydrogen bonds       : angle       4.21570 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 33
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  338 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.6512 (mt-10)
  outliers start: 11
  outliers final: 7
  residues processed: 41
  average time/residue: 0.0546
  time to fit residues: 2.9855
Evaluate side-chains
  41 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  340 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0170
   chunk 4 optimal weight:    0.5980
   chunk 35 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 41 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.157886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.125713 restraints weight = 3791.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.130701 restraints weight = 1982.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.134146 restraints weight = 1328.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.136329 restraints weight = 1029.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.137853 restraints weight = 871.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3512  Z= 0.143
  Angle     :  0.612   7.828   4809  Z= 0.303
  Chirality :  0.042   0.126    565
  Planarity :  0.004   0.034    574
  Dihedral  : 11.169  56.400    503
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.16 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.43), residues: 418
  helix:  0.92 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop :  0.13 (0.77), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 246 
 TYR   0.009   0.001   TYR A 409 
 PHE   0.015   0.001   PHE A 186 
 TRP   0.008   0.001   TRP A 264 
 HIS   0.001   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 3512)
  covalent geometry    : angle       0.61245 ( 4809)
  hydrogen bonds       : bond        0.03473 (  239)
  hydrogen bonds       : angle       4.22493 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A  254 ILE cc_start: 0.7927 (mm) cc_final: 0.7603 (mp)
REVERT: A  338 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6563 (mt-10)
  outliers start: 8
  outliers final: 7
  residues processed: 39
  average time/residue: 0.0548
  time to fit residues: 2.7996
Evaluate side-chains
  41 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  340 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:    0.1980
   chunk 24 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   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  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.157610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.125468 restraints weight = 3792.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.130321 restraints weight = 2069.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.133431 restraints weight = 1417.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.135672 restraints weight = 1120.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.137038 restraints weight = 957.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7033
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3512  Z= 0.145
  Angle     :  0.615   8.115   4809  Z= 0.304
  Chirality :  0.042   0.124    565
  Planarity :  0.004   0.034    574
  Dihedral  : 11.117  55.178    503
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 16.16 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.43), residues: 418
  helix:  0.93 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop :  0.17 (0.77), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 246 
 TYR   0.009   0.001   TYR A 409 
 PHE   0.016   0.001   PHE A 186 
 TRP   0.008   0.001   TRP A 143 
 HIS   0.002   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3512)
  covalent geometry    : angle       0.61501 ( 4809)
  hydrogen bonds       : bond        0.03484 (  239)
  hydrogen bonds       : angle       4.23330 (  714)

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

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

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  836 Ramachandran restraints generated.
    418 Oldfield, 0 Emsley, 418 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A  254 ILE cc_start: 0.7921 (mm) cc_final: 0.7576 (mp)
REVERT: A  338 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6591 (mt-10)
  outliers start: 8
  outliers final: 7
  residues processed: 39
  average time/residue: 0.0634
  time to fit residues: 3.2433
Evaluate side-chains
  41 residues out of total 365 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 33
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 GLN
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  318 LEU
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  340 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0970
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** A  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.156209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.124347 restraints weight = 3855.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.129137 restraints weight = 2130.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.132175 restraints weight = 1461.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.134441 restraints weight = 1162.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.135724 restraints weight = 989.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7049
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3512  Z= 0.154
  Angle     :  0.615   7.840   4809  Z= 0.306
  Chirality :  0.042   0.129    565
  Planarity :  0.004   0.034    574
  Dihedral  : 10.965  56.628    503
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 15.34 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.12 (0.43), residues: 418
  helix:  0.96 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop :  0.24 (0.77), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.010   0.001   TYR A 409 
 PHE   0.014   0.001   PHE A 186 
 TRP   0.010   0.001   TRP A 143 
 HIS   0.002   0.001   HIS A 402 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 3512)
  covalent geometry    : angle       0.61462 ( 4809)
  hydrogen bonds       : bond        0.03526 (  239)
  hydrogen bonds       : angle       4.22349 (  714)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 742.61 seconds
wall clock time: 13 minutes 27.49 seconds (807.49 seconds total)