Starting phenix.real_space_refine
on Fri Aug 22 13:13:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qru_18626/08_2025/8qru_18626.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qru_18626/08_2025/8qru_18626.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qru_18626/08_2025/8qru_18626.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qru_18626/08_2025/8qru_18626.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qru_18626/08_2025/8qru_18626.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qru_18626/08_2025/8qru_18626.map"
  }
  resolution = 2.9
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2034      2.51       5
     N     504      2.21       5
     O     540      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3093
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3083
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 415, 3083
          Classifications: {'peptide': 415}
          Link IDs: {'PTRANS': 16, 'TRANS': 398}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 0.93, per 1000 atoms: 0.30
  Number of scatterers: 3093
  At special positions: 0
  Unit cell: (61.028, 67.716, 71.896, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O     540      8.00
     N     504      7.00
     C    2034      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: 0.20
  Conformation dependent library (CDL) restraints added in 148.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  752

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      86.5% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'B' and resid 49 through 75
    Processing helix  chain 'B' and resid 76 through 117
      removed outlier: 3.549A  pdb=" N   ALA B  80 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
      Proline residue:  B  83  - end of helix
      removed outlier: 3.756A  pdb=" N   ALA B  88 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      Proline residue:  B  92  - end of helix
      removed outlier: 4.364A  pdb=" N   LEU B 105 " --> pdb=" O   ARG B 101 " (cutoff:3.500A)
      Proline residue:  B 106  - end of helix
    Processing helix  chain 'B' and resid 120 through 125
    Processing helix  chain 'B' and resid 126 through 154
    Processing helix  chain 'B' and resid 179 through 192
    Processing helix  chain 'B' and resid 195 through 200
    Processing helix  chain 'B' and resid 230 through 249
      removed outlier: 3.711A  pdb=" N   GLY B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 292
      removed outlier: 3.704A  pdb=" N   TRP B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TYR B 276 " --> pdb=" O   TRP B 272 " (cutoff:3.500A)
      Proline residue:  B 278  - end of helix
      removed outlier: 3.844A  pdb=" N   MET B 292 " --> pdb=" O   LYS B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 319
      removed outlier: 3.713A  pdb=" N   ALA B 300 " --> pdb=" O   GLY B 296 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARG B 301 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   LYS B 304 " --> pdb=" O   ALA B 300 " (cutoff:3.500A)
      removed outlier: 5.178A  pdb=" N   TYR B 305 " --> pdb=" O   ARG B 301 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 329
    Processing helix  chain 'B' and resid 332 through 339
      removed outlier: 3.518A  pdb=" N   PHE B 336 " --> pdb=" O   ASN B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 351
    Processing helix  chain 'B' and resid 352 through 367
      Proline residue:  B 358  - end of helix
    Processing helix  chain 'B' and resid 371 through 386
      Proline residue:  B 380  - end of helix
      removed outlier: 4.124A  pdb=" N   THR B 384 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 401
    Processing helix  chain 'B' and resid 410 through 427
    Processing helix  chain 'B' and resid 433 through 446
      removed outlier: 3.743A  pdb=" N   LEU B 437 " --> pdb=" O   ALA B 433 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   THR B 438 " --> pdb=" O   GLY B 434 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ALA B 440 " --> pdb=" O   VAL B 436 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   ILE B 441 " --> pdb=" O   LEU B 437 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ILE B 442 " --> pdb=" O   THR B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 451
      No H-bonds generated for 'chain 'B' and resid 449 through 451'
    Processing helix  chain 'B' and resid 452 through 487
      removed outlier: 3.670A  pdb=" N   ILE B 456 " --> pdb=" O   HIS B 452 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL B 459 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   TRP B 461 " --> pdb=" O   LEU B 457 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   LEU B 462 " --> pdb=" O   ALA B 458 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL B 463 " --> pdb=" O   VAL B 459 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   ARG B 465 " --> pdb=" O   TRP B 461 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   SER B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 209

    250 hydrogen bonds defined for protein.
    747 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: 0.28 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 978
        1.34 -     1.46: 660
        1.46 -     1.58: 1486
        1.58 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 3148
  Sorted by residual:
  bond pdb=" N   GLN B 601 "
       pdb=" CA  GLN B 601 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.63e+00
  bond pdb=" CG  PRO B  83 "
       pdb=" CD  PRO B  83 "
    ideal  model  delta    sigma   weight residual
    1.503  1.544 -0.041 3.40e-02 8.65e+02 1.47e+00
  bond pdb=" CB  PRO B  83 "
       pdb=" CG  PRO B  83 "
    ideal  model  delta    sigma   weight residual
    1.492  1.552 -0.060 5.00e-02 4.00e+02 1.42e+00
  bond pdb=" C   LEU B 379 "
       pdb=" O   LEU B 379 "
    ideal  model  delta    sigma   weight residual
    1.244  1.237  0.007 1.00e-02 1.00e+04 5.13e-01
  bond pdb=" CB  PHE B 348 "
       pdb=" CG  PHE B 348 "
    ideal  model  delta    sigma   weight residual
    1.502  1.518 -0.016 2.30e-02 1.89e+03 4.93e-01
  ... (remaining 3143 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.85: 3996
        0.85 -     1.70: 219
        1.70 -     2.55: 44
        2.55 -     3.40: 17
        3.40 -     4.25: 12
  Bond angle restraints: 4288
  Sorted by residual:
  angle pdb=" N   VAL B 446 "
        pdb=" CA  VAL B 446 "
        pdb=" C   VAL B 446 "
      ideal   model   delta    sigma   weight residual
     112.17  109.18    2.99 9.50e-01 1.11e+00 9.88e+00
  angle pdb=" CA  PRO B  83 "
        pdb=" N   PRO B  83 "
        pdb=" CD  PRO B  83 "
      ideal   model   delta    sigma   weight residual
     112.00  107.75    4.25 1.40e+00 5.10e-01 9.23e+00
  angle pdb=" N   GLN B 403 "
        pdb=" CA  GLN B 403 "
        pdb=" C   GLN B 403 "
      ideal   model   delta    sigma   weight residual
     114.04  111.58    2.46 1.24e+00 6.50e-01 3.93e+00
  angle pdb=" CA  GLU B 210 "
        pdb=" C   GLU B 210 "
        pdb=" N   ARG B 211 "
      ideal   model   delta    sigma   weight residual
     114.76  116.86   -2.10 1.14e+00 7.69e-01 3.41e+00
  angle pdb=" CA  GLU B 210 "
        pdb=" C   GLU B 210 "
        pdb=" O   GLU B 210 "
      ideal   model   delta    sigma   weight residual
     122.64  120.55    2.09 1.25e+00 6.40e-01 2.80e+00
  ... (remaining 4283 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.41: 1657
       16.41 -    32.82: 150
       32.82 -    49.23: 25
       49.23 -    65.64: 11
       65.64 -    82.05: 2
  Dihedral angle restraints: 1845
    sinusoidal: 674
      harmonic: 1171
  Sorted by residual:
  dihedral pdb=" CA  PHE B 400 "
           pdb=" C   PHE B 400 "
           pdb=" N   ILE B 401 "
           pdb=" CA  ILE B 401 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.80   17.20     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CG  ARG B 376 "
           pdb=" CD  ARG B 376 "
           pdb=" NE  ARG B 376 "
           pdb=" CZ  ARG B 376 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.07  -43.93     2      1.50e+01 4.44e-03 1.03e+01
  dihedral pdb=" CA  ILE B 401 "
           pdb=" C   ILE B 401 "
           pdb=" N   ALA B 402 "
           pdb=" CA  ALA B 402 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.02  -15.98     0      5.00e+00 4.00e-02 1.02e+01
  ... (remaining 1842 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 354
       0.026 -    0.052: 93
       0.052 -    0.078: 62
       0.078 -    0.104: 25
       0.104 -    0.130: 4
  Chirality restraints: 538
  Sorted by residual:
  chirality pdb=" CA  VAL B 220 "
            pdb=" N   VAL B 220 "
            pdb=" C   VAL B 220 "
            pdb=" CB  VAL B 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.26e-01
  chirality pdb=" CA  PRO B 432 "
            pdb=" N   PRO B 432 "
            pdb=" C   PRO B 432 "
            pdb=" CB  PRO B 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.61    0.11 2.00e-01 2.50e+01 2.97e-01
  chirality pdb=" CA  ILE B 401 "
            pdb=" N   ILE B 401 "
            pdb=" C   ILE B 401 "
            pdb=" CB  ILE B 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 2.80e-01
  ... (remaining 535 not shown)

  Planarity restraints: 530
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  82 "    0.061 5.00e-02 4.00e+02   9.07e-02 1.32e+01
        pdb=" N   PRO B  83 "   -0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO B  83 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO B  83 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 342 "   -0.031 5.00e-02 4.00e+02   4.70e-02 3.54e+00
        pdb=" N   PRO B 343 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 343 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 343 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 431 "    0.020 5.00e-02 4.00e+02   2.99e-02 1.43e+00
        pdb=" N   PRO B 432 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B 432 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 432 "    0.017 5.00e-02 4.00e+02
  ... (remaining 527 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 708
        2.79 -     3.31: 3336
        3.31 -     3.84: 5327
        3.84 -     4.37: 6035
        4.37 -     4.90: 10768
  Nonbonded interactions: 26174
  Sorted by model distance:
  nonbonded pdb=" O   ARG B 126 "
            pdb=" CD1 TRP B 130 "
     model   vdw
     2.257 3.260
  nonbonded pdb=" OD1 ASP B 120 "
            pdb=" NH2 ARG B 246 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" NE1 TRP B 130 "
            pdb=" OH  TYR B 485 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" O   THR B 416 "
            pdb=" OG1 THR B 420 "
     model   vdw
     2.347 3.040
  nonbonded pdb=" O   GLN B 483 "
            pdb=" NE2 GLN B 483 "
     model   vdw
     2.431 3.120
  ... (remaining 26169 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.610
  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:7.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
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      :  0.003   0.060   3148  Z= 0.132
  Angle     :  0.521   4.252   4288  Z= 0.298
  Chirality :  0.036   0.130    538
  Planarity :  0.006   0.091    530
  Dihedral  : 13.619  82.049   1093
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 11.62 %
    Favored  : 87.77 %
  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:  1.76 (0.43), residues: 409
  helix:  1.69 (0.30), residues: 335
  sheet:  None (None), residues: 0
  loop : -1.17 (0.66), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 335 
 TYR   0.007   0.001   TYR B 485 
 PHE   0.007   0.001   PHE B 237 
 TRP   0.006   0.001   TRP B 275 
 HIS   0.002   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3148)
  covalent geometry    : angle       0.52106 ( 4288)
  hydrogen bonds       : bond        0.10256 (  250)
  hydrogen bonds       : angle       5.35300 (  747)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.089 
Fit side-chains
REVERT: B  182 ASP cc_start: 0.8289 (m-30) cc_final: 0.8086 (m-30)
REVERT: B  224 GLN cc_start: 0.7623 (mm110) cc_final: 0.7315 (pt0)
REVERT: B  229 MET cc_start: 0.9156 (ttm) cc_final: 0.8943 (ttm)
REVERT: B  483 GLN cc_start: 0.8782 (tp40) cc_final: 0.8385 (tp-100)
  outliers start: 2
  outliers final: 0
  residues processed: 55
  average time/residue: 0.3601
  time to fit residues: 20.5613
Evaluate side-chains
  50 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 2 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.1980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 452 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.151444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.106513 restraints weight = 3849.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 1.97
r_work: 0.3074 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3148  Z= 0.139
  Angle     :  0.566   5.573   4288  Z= 0.282
  Chirality :  0.038   0.125    538
  Planarity :  0.006   0.058    530
  Dihedral  :  4.215  27.333    435
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 11.62 %
    Favored  : 85.32 %
  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:  1.90 (0.41), residues: 409
  helix:  1.81 (0.28), residues: 336
  sheet:  None (None), residues: 0
  loop : -1.34 (0.61), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 335 
 TYR   0.006   0.001   TYR B 276 
 PHE   0.010   0.001   PHE B 237 
 TRP   0.005   0.001   TRP B 130 
 HIS   0.001   0.001   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3148)
  covalent geometry    : angle       0.56582 ( 4288)
  hydrogen bonds       : bond        0.04231 (  250)
  hydrogen bonds       : angle       4.66976 (  747)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.069 
Fit side-chains
REVERT: B  224 GLN cc_start: 0.7749 (mm110) cc_final: 0.7213 (pt0)
REVERT: B  229 MET cc_start: 0.9136 (ttm) cc_final: 0.8932 (ttm)
REVERT: B  444 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7399 (mt-10)
REVERT: B  483 GLN cc_start: 0.8620 (tp40) cc_final: 0.8396 (tp40)
  outliers start: 10
  outliers final: 4
  residues processed: 64
  average time/residue: 0.3246
  time to fit residues: 21.4591
Evaluate side-chains
  52 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  147 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0980
   chunk 9 optimal weight:    0.6980
   chunk 13 optimal weight:    0.0980
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.152234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.107607 restraints weight = 3830.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.89
r_work: 0.3092 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.1673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3148  Z= 0.130
  Angle     :  0.580   6.634   4288  Z= 0.283
  Chirality :  0.038   0.121    538
  Planarity :  0.005   0.055    530
  Dihedral  :  4.331  35.641    435
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 12.23 %
    Favored  : 84.10 %
  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:  2.00 (0.41), residues: 409
  helix:  1.86 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.31 (0.66), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 335 
 TYR   0.005   0.001   TYR B 276 
 PHE   0.015   0.001   PHE B 326 
 TRP   0.003   0.001   TRP B 130 
 HIS   0.001   0.000   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 3148)
  covalent geometry    : angle       0.58029 ( 4288)
  hydrogen bonds       : bond        0.03980 (  250)
  hydrogen bonds       : angle       4.53884 (  747)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.092 
Fit side-chains
REVERT: B  120 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6721 (m-30)
REVERT: B  224 GLN cc_start: 0.7803 (mm110) cc_final: 0.7254 (pt0)
REVERT: B  229 MET cc_start: 0.9127 (ttm) cc_final: 0.8850 (ttm)
REVERT: B  246 ARG cc_start: 0.8877 (tpt170) cc_final: 0.8545 (tpt90)
REVERT: B  444 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7298 (mt-10)
REVERT: B  483 GLN cc_start: 0.8736 (tp40) cc_final: 0.8352 (tp-100)
  outliers start: 12
  outliers final: 4
  residues processed: 59
  average time/residue: 0.3046
  time to fit residues: 18.6623
Evaluate side-chains
  54 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  329 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 394 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.151407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.106080 restraints weight = 3759.682|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 1.92
r_work: 0.3078 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3148  Z= 0.143
  Angle     :  0.558   5.706   4288  Z= 0.275
  Chirality :  0.038   0.128    538
  Planarity :  0.005   0.052    530
  Dihedral  :  4.462  40.699    435
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 14.37 %
    Favored  : 82.57 %
  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:  1.99 (0.41), residues: 409
  helix:  1.86 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.36 (0.65), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 335 
 TYR   0.009   0.002   TYR B 485 
 PHE   0.019   0.001   PHE B 348 
 TRP   0.005   0.001   TRP B 130 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 3148)
  covalent geometry    : angle       0.55850 ( 4288)
  hydrogen bonds       : bond        0.04050 (  250)
  hydrogen bonds       : angle       4.50672 (  747)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.085 
Fit side-chains
REVERT: B  120 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6687 (m-30)
REVERT: B  126 ARG cc_start: 0.7364 (mtm110) cc_final: 0.7014 (ptm-80)
REVERT: B  224 GLN cc_start: 0.7777 (mm110) cc_final: 0.7256 (pt0)
REVERT: B  229 MET cc_start: 0.9130 (ttm) cc_final: 0.8839 (ttm)
REVERT: B  246 ARG cc_start: 0.8876 (tpt170) cc_final: 0.8508 (tpt90)
REVERT: B  444 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7202 (mt-10)
REVERT: B  483 GLN cc_start: 0.8733 (tp40) cc_final: 0.8328 (tp-100)
REVERT: B  484 ASN cc_start: 0.8580 (t0) cc_final: 0.8379 (t0)
REVERT: B  601 GLN cc_start: 0.7793 (mm110) cc_final: 0.7584 (mm110)
  outliers start: 10
  outliers final: 7
  residues processed: 58
  average time/residue: 0.3794
  time to fit residues: 22.7278
Evaluate side-chains
  58 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 LEU
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  413 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    0.0670
   chunk 8 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 32 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 23 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    1.1122

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.148874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.103926 restraints weight = 3834.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 1.93
r_work: 0.3043 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.1978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3148  Z= 0.168
  Angle     :  0.573   6.252   4288  Z= 0.285
  Chirality :  0.038   0.130    538
  Planarity :  0.005   0.049    530
  Dihedral  :  4.517  41.780    435
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 14.68 %
    Favored  : 81.65 %
  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:  1.96 (0.41), residues: 409
  helix:  1.83 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.35 (0.66), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 335 
 TYR   0.009   0.002   TYR B 485 
 PHE   0.012   0.002   PHE B 326 
 TRP   0.005   0.001   TRP B 130 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 3148)
  covalent geometry    : angle       0.57318 ( 4288)
  hydrogen bonds       : bond        0.04243 (  250)
  hydrogen bonds       : angle       4.50911 (  747)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.090 
Fit side-chains
REVERT: B  126 ARG cc_start: 0.7397 (mtm110) cc_final: 0.6965 (ptt90)
REVERT: B  224 GLN cc_start: 0.7838 (mm110) cc_final: 0.7248 (pt0)
REVERT: B  229 MET cc_start: 0.9163 (ttm) cc_final: 0.8854 (ttm)
REVERT: B  376 ARG cc_start: 0.8321 (mtt90) cc_final: 0.8050 (mtt90)
REVERT: B  444 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7224 (mt-10)
REVERT: B  483 GLN cc_start: 0.8727 (tp40) cc_final: 0.8264 (tp-100)
REVERT: B  484 ASN cc_start: 0.8557 (t0) cc_final: 0.8347 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 62
  average time/residue: 0.3432
  time to fit residues: 21.9902
Evaluate side-chains
  58 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   56 LEU
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  120 ASP
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  384 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0870
   overall best weight:    0.6160

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.151003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.106455 restraints weight = 3801.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 1.91
r_work: 0.3083 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3148  Z= 0.130
  Angle     :  0.551   7.167   4288  Z= 0.272
  Chirality :  0.037   0.140    538
  Planarity :  0.005   0.046    530
  Dihedral  :  4.331  35.405    435
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.13 %
    Favored  : 79.82 %
  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:  2.09 (0.41), residues: 409
  helix:  1.94 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.41 (0.64), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 335 
 TYR   0.011   0.002   TYR B 485 
 PHE   0.010   0.001   PHE B 348 
 TRP   0.007   0.001   TRP B 130 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3148)
  covalent geometry    : angle       0.55063 ( 4288)
  hydrogen bonds       : bond        0.03872 (  250)
  hydrogen bonds       : angle       4.44226 (  747)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 55
  time to evaluate  : 0.067 
Fit side-chains
REVERT: B  126 ARG cc_start: 0.7399 (mtm110) cc_final: 0.6986 (ptt90)
REVERT: B  224 GLN cc_start: 0.7806 (mm110) cc_final: 0.7270 (pt0)
REVERT: B  229 MET cc_start: 0.9131 (ttm) cc_final: 0.8819 (ttm)
REVERT: B  246 ARG cc_start: 0.8882 (tpt170) cc_final: 0.8628 (tpt90)
REVERT: B  444 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7129 (mt-10)
REVERT: B  483 GLN cc_start: 0.8738 (tp40) cc_final: 0.8275 (tp-100)
REVERT: B  487 ASP cc_start: 0.5681 (m-30) cc_final: 0.5388 (m-30)
  outliers start: 10
  outliers final: 5
  residues processed: 62
  average time/residue: 0.3473
  time to fit residues: 22.3026
Evaluate side-chains
  56 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  384 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   chunk 21 optimal weight:    0.3980
   chunk 24 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 22 optimal weight:    0.5980
   chunk 32 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 484 ASN ** 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 = 0.3803 r_free = 0.3803 target = 0.152209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.106865 restraints weight = 3835.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.94
r_work: 0.3086 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3148  Z= 0.139
  Angle     :  0.564   7.753   4288  Z= 0.281
  Chirality :  0.037   0.127    538
  Planarity :  0.005   0.045    530
  Dihedral  :  4.302  35.156    435
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.96 %
    Favored  : 78.90 %
  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:  2.00 (0.41), residues: 409
  helix:  1.88 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.46 (0.63), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 335 
 TYR   0.012   0.002   TYR B 485 
 PHE   0.013   0.001   PHE B 326 
 TRP   0.012   0.001   TRP B 130 
 HIS   0.003   0.001   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3148)
  covalent geometry    : angle       0.56392 ( 4288)
  hydrogen bonds       : bond        0.04018 (  250)
  hydrogen bonds       : angle       4.48011 (  747)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.117 
Fit side-chains
REVERT: B  126 ARG cc_start: 0.7439 (mtm110) cc_final: 0.7009 (ptt90)
REVERT: B  224 GLN cc_start: 0.7766 (mm110) cc_final: 0.7256 (pt0)
REVERT: B  229 MET cc_start: 0.9139 (ttm) cc_final: 0.8808 (ttm)
REVERT: B  444 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7143 (mt-10)
REVERT: B  483 GLN cc_start: 0.8650 (tp40) cc_final: 0.8090 (tp-100)
REVERT: B  487 ASP cc_start: 0.5564 (m-30) cc_final: 0.5350 (m-30)
  outliers start: 7
  outliers final: 4
  residues processed: 65
  average time/residue: 0.3218
  time to fit residues: 21.5955
Evaluate side-chains
  55 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  384 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0270
   chunk 37 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
** B 471 ASN ** 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 = 0.3799 r_free = 0.3799 target = 0.152083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.106535 restraints weight = 3919.947|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.96
r_work: 0.3087 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3148  Z= 0.133
  Angle     :  0.568   8.663   4288  Z= 0.280
  Chirality :  0.038   0.125    538
  Planarity :  0.005   0.044    530
  Dihedral  :  4.211  31.367    435
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 19.88 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.41), residues: 409
  helix:  1.92 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.75 (0.62), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 335 
 TYR   0.010   0.002   TYR B 485 
 PHE   0.009   0.001   PHE B 237 
 TRP   0.011   0.001   TRP B 130 
 HIS   0.001   0.000   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3148)
  covalent geometry    : angle       0.56840 ( 4288)
  hydrogen bonds       : bond        0.03931 (  250)
  hydrogen bonds       : angle       4.40026 (  747)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.074 
Fit side-chains
REVERT: B  126 ARG cc_start: 0.7450 (mtm110) cc_final: 0.7246 (ptm-80)
REVERT: B  224 GLN cc_start: 0.7782 (mm110) cc_final: 0.7269 (pt0)
REVERT: B  229 MET cc_start: 0.9145 (ttm) cc_final: 0.8815 (ttm)
REVERT: B  376 ARG cc_start: 0.8212 (mtt90) cc_final: 0.7808 (mtm-85)
REVERT: B  483 GLN cc_start: 0.8730 (tp40) cc_final: 0.8114 (tp-100)
REVERT: B  487 ASP cc_start: 0.5833 (m-30) cc_final: 0.5623 (m-30)
  outliers start: 6
  outliers final: 6
  residues processed: 61
  average time/residue: 0.3841
  time to fit residues: 24.2191
Evaluate side-chains
  57 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  329 THR
Chi-restraints excluded: chain B residue  384 THR
Chi-restraints excluded: chain B residue  417 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 26 optimal weight:    0.4980
   chunk 31 optimal weight:    9.9990
   chunk 39 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 484 ASN ** 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 = 0.3806 r_free = 0.3806 target = 0.152678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.107697 restraints weight = 3882.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 1.93
r_work: 0.3092 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3148  Z= 0.134
  Angle     :  0.573   9.372   4288  Z= 0.282
  Chirality :  0.037   0.122    538
  Planarity :  0.005   0.043    530
  Dihedral  :  4.266  36.714    435
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 19.88 %
    Favored  : 78.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.41), residues: 409
  helix:  1.88 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.77 (0.62), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 335 
 TYR   0.008   0.002   TYR B 485 
 PHE   0.014   0.001   PHE B 326 
 TRP   0.016   0.001   TRP B 130 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 3148)
  covalent geometry    : angle       0.57309 ( 4288)
  hydrogen bonds       : bond        0.03929 (  250)
  hydrogen bonds       : angle       4.44902 (  747)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.095 
Fit side-chains
REVERT: B  126 ARG cc_start: 0.7426 (mtm110) cc_final: 0.7098 (ptt90)
REVERT: B  224 GLN cc_start: 0.7735 (mm110) cc_final: 0.7253 (pt0)
REVERT: B  229 MET cc_start: 0.9141 (ttm) cc_final: 0.8816 (ttm)
REVERT: B  464 ASP cc_start: 0.6920 (OUTLIER) cc_final: 0.6034 (m-30)
REVERT: B  483 GLN cc_start: 0.8693 (tp40) cc_final: 0.8056 (tp-100)
  outliers start: 6
  outliers final: 5
  residues processed: 55
  average time/residue: 0.3937
  time to fit residues: 22.3425
Evaluate side-chains
  54 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  384 THR
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  464 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 24 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 40 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0470
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** B 471 ASN ** 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 = 0.3803 r_free = 0.3803 target = 0.152247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.107089 restraints weight = 3823.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 1.92
r_work: 0.3091 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3148  Z= 0.134
  Angle     :  0.580  10.336   4288  Z= 0.283
  Chirality :  0.038   0.158    538
  Planarity :  0.005   0.043    530
  Dihedral  :  4.377  40.090    435
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 21.10 %
    Favored  : 77.06 %
  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:  1.94 (0.41), residues: 409
  helix:  1.89 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.79 (0.61), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 335 
 TYR   0.007   0.002   TYR B 204 
 PHE   0.009   0.001   PHE B 237 
 TRP   0.016   0.001   TRP B 130 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 3148)
  covalent geometry    : angle       0.57975 ( 4288)
  hydrogen bonds       : bond        0.03967 (  250)
  hydrogen bonds       : angle       4.39609 (  747)

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

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

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  818 Ramachandran restraints generated.
    409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.123 
Fit side-chains
REVERT: B  126 ARG cc_start: 0.7416 (mtm110) cc_final: 0.7092 (ptt90)
REVERT: B  224 GLN cc_start: 0.7756 (mm110) cc_final: 0.7272 (pt0)
REVERT: B  229 MET cc_start: 0.9150 (ttm) cc_final: 0.8825 (ttm)
REVERT: B  464 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.5979 (m-30)
REVERT: B  483 GLN cc_start: 0.8663 (tp40) cc_final: 0.8234 (tp-100)
  outliers start: 6
  outliers final: 5
  residues processed: 55
  average time/residue: 0.3843
  time to fit residues: 21.8330
Evaluate side-chains
  54 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  103 ILE
Chi-restraints excluded: chain B residue  104 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  384 THR
Chi-restraints excluded: chain B residue  417 ILE
Chi-restraints excluded: chain B residue  464 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 25 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    0.4980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 471 ASN ** 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 = 0.3803 r_free = 0.3803 target = 0.152211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.106795 restraints weight = 3806.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 1.94
r_work: 0.3083 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8463
moved from start:          0.2542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3148  Z= 0.140
  Angle     :  0.587  10.622   4288  Z= 0.287
  Chirality :  0.038   0.160    538
  Planarity :  0.006   0.067    530
  Dihedral  :  4.475  42.797    435
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 20.80 %
    Favored  : 77.06 %
  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:  1.89 (0.41), residues: 409
  helix:  1.85 (0.28), residues: 339
  sheet:  None (None), residues: 0
  loop : -1.79 (0.62), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 376 
 TYR   0.008   0.002   TYR B 485 
 PHE   0.012   0.001   PHE B 326 
 TRP   0.020   0.001   TRP B 130 
 HIS   0.001   0.000   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3148)
  covalent geometry    : angle       0.58738 ( 4288)
  hydrogen bonds       : bond        0.04023 (  250)
  hydrogen bonds       : angle       4.43731 (  747)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1089.43 seconds
wall clock time: 19 minutes 19.71 seconds (1159.71 seconds total)