Starting phenix.real_space_refine
on Fri Aug 22 13:14:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8qrs_18625/08_2025/8qrs_18625.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8qrs_18625/08_2025/8qrs_18625.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8qrs_18625/08_2025/8qrs_18625.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8qrs_18625/08_2025/8qrs_18625.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8qrs_18625/08_2025/8qrs_18625.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8qrs_18625/08_2025/8qrs_18625.cif"
  }
  resolution = 2.86
  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 2 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: 1.04, per 1000 atoms: 0.34
  Number of scatterers: 3093
  At special positions: 0
  Unit cell: (60.192, 69.388, 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: 0.28
  Conformation dependent library (CDL) restraints added in 122.5 milliseconds
  
  Enol-peptide restraints added in 238.4 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:
      18 helices and 1 sheets defined
      86.5% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'B' and resid 49 through 74
      removed outlier: 3.591A  pdb=" N   VAL B  55 " --> pdb=" O   ALA B  51 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   VAL B  62 " --> pdb=" O   THR B  58 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   VAL B  63 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 118
      Proline residue:  B  83  - end of helix
      removed outlier: 3.589A  pdb=" N   ALA B  88 " --> pdb=" O   GLU B  84 " (cutoff:3.500A)
      Proline residue:  B  92  - end of helix
      removed outlier: 3.501A  pdb=" N   ILE B 104 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
      removed outlier: 4.351A  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 154
    Processing helix  chain 'B' and resid 155 through 158
      removed outlier: 4.320A  pdb=" N   ALA B 158 " --> pdb=" O   PRO B 155 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 155 through 158'
    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: 3.606A  pdb=" N   GLY B 249 " --> pdb=" O   LEU B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 291
      removed outlier: 3.677A  pdb=" N   TRP B 275 " --> pdb=" O   SER B 271 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   TYR B 276 " --> pdb=" O   TRP B 272 " (cutoff:3.500A)
      Proline residue:  B 278  - end of helix
    Processing helix  chain 'B' and resid 294 through 319
      removed outlier: 5.478A  pdb=" N   LYS B 304 " --> pdb=" O   ALA B 300 " (cutoff:3.500A)
      removed outlier: 5.550A  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 340
      removed outlier: 3.747A  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
      removed outlier: 3.594A  pdb=" N   THR B 356 " --> pdb=" O   SER B 352 " (cutoff:3.500A)
      Proline residue:  B 358  - end of helix
    Processing helix  chain 'B' and resid 371 through 386
      removed outlier: 3.501A  pdb=" N   PHE B 377 " --> pdb=" O   HIS B 373 " (cutoff:3.500A)
      Proline residue:  B 380  - end of helix
      removed outlier: 3.909A  pdb=" N   THR B 384 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 405
    Processing helix  chain 'B' and resid 410 through 428
    Processing helix  chain 'B' and resid 438 through 446
      removed outlier: 3.849A  pdb=" N   ILE B 442 " --> pdb=" O   THR B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 487
      removed outlier: 3.824A  pdb=" N   ILE B 456 " --> pdb=" O   HIS B 452 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ALA B 458 " --> pdb=" O   SER B 454 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL B 459 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   TRP B 461 " --> pdb=" O   LEU B 457 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   LEU B 462 " --> pdb=" O   ALA B 458 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG B 465 " --> pdb=" O   TRP B 461 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 202 through 209

    256 hydrogen bonds defined for protein.
    765 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: 0.49

  Time building geometry restraints manager: 0.37 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: 649
        1.46 -     1.58: 1497
        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  1.490 -0.032 1.90e-02 2.77e+03 2.92e+00
  bond pdb=" N   LEU B  49 "
       pdb=" CA  LEU B  49 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.89e+00
  bond pdb=" C   LEU B 105 "
       pdb=" O   LEU B 105 "
    ideal  model  delta    sigma   weight residual
    1.238  1.245 -0.008 1.28e-02 6.10e+03 3.58e-01
  bond pdb=" CA  GLN B 154 "
       pdb=" C   GLN B 154 "
    ideal  model  delta    sigma   weight residual
    1.524  1.531 -0.008 1.26e-02 6.30e+03 3.56e-01
  bond pdb=" C   LEU B 379 "
       pdb=" O   LEU B 379 "
    ideal  model  delta    sigma   weight residual
    1.244  1.238  0.006 1.00e-02 1.00e+04 3.46e-01
  ... (remaining 3143 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.90: 4028
        0.90 -     1.80: 193
        1.80 -     2.70: 44
        2.70 -     3.59: 13
        3.59 -     4.49: 10
  Bond angle restraints: 4288
  Sorted by residual:
  angle pdb=" C   VAL B 222 "
        pdb=" N   GLY B 223 "
        pdb=" CA  GLY B 223 "
      ideal   model   delta    sigma   weight residual
     122.66  120.59    2.07 9.80e-01 1.04e+00 4.48e+00
  angle pdb=" N   VAL B  72 "
        pdb=" CA  VAL B  72 "
        pdb=" C   VAL B  72 "
      ideal   model   delta    sigma   weight residual
     111.00  109.08    1.92 1.09e+00 8.42e-01 3.10e+00
  angle pdb=" N   GLY B 223 "
        pdb=" CA  GLY B 223 "
        pdb=" C   GLY B 223 "
      ideal   model   delta    sigma   weight residual
     111.12  114.01   -2.89 1.89e+00 2.80e-01 2.34e+00
  angle pdb=" N   VAL B 450 "
        pdb=" CA  VAL B 450 "
        pdb=" CB  VAL B 450 "
      ideal   model   delta    sigma   weight residual
     112.07  109.81    2.26 1.52e+00 4.33e-01 2.21e+00
  angle pdb=" C   ASP B 294 "
        pdb=" N   VAL B 295 "
        pdb=" CA  VAL B 295 "
      ideal   model   delta    sigma   weight residual
     120.56  122.41   -1.85 1.26e+00 6.30e-01 2.17e+00
  ... (remaining 4283 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.25: 1624
       13.25 -    26.50: 158
       26.50 -    39.74: 41
       39.74 -    52.99: 16
       52.99 -    66.24: 6
  Dihedral angle restraints: 1845
    sinusoidal: 674
      harmonic: 1171
  Sorted by residual:
  dihedral pdb=" CA  SER B  73 "
           pdb=" C   SER B  73 "
           pdb=" N   GLY B  74 "
           pdb=" CA  GLY B  74 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.40   16.60     0      5.00e+00 4.00e-02 1.10e+01
  dihedral pdb=" CA  ASP B 388 "
           pdb=" CB  ASP B 388 "
           pdb=" CG  ASP B 388 "
           pdb=" OD1 ASP B 388 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.01   55.01     1      2.00e+01 2.50e-03 1.02e+01
  dihedral pdb=" CA  GLU B 225 "
           pdb=" CB  GLU B 225 "
           pdb=" CG  GLU B 225 "
           pdb=" CD  GLU B 225 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.31   58.31     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 1842 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 361
       0.026 -    0.053: 96
       0.053 -    0.079: 59
       0.079 -    0.106: 18
       0.106 -    0.132: 4
  Chirality restraints: 538
  Sorted by residual:
  chirality pdb=" CA  ILE B 431 "
            pdb=" N   ILE B 431 "
            pdb=" C   ILE B 431 "
            pdb=" CB  ILE B 431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  chirality pdb=" CA  VAL B 222 "
            pdb=" N   VAL B 222 "
            pdb=" C   VAL B 222 "
            pdb=" CB  VAL B 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.30e-01
  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    2.55   -0.11 2.00e-01 2.50e+01 3.21e-01
  ... (remaining 535 not shown)

  Planarity restraints: 530
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 342 "   -0.039 5.00e-02 4.00e+02   5.93e-02 5.62e+00
        pdb=" N   PRO B 343 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B 343 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B 343 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 126 "   -0.175 9.50e-02 1.11e+02   7.85e-02 3.99e+00
        pdb=" NE  ARG B 126 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 126 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 126 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 126 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 335 "   -0.137 9.50e-02 1.11e+02   6.18e-02 2.66e+00
        pdb=" NE  ARG B 335 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 335 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 335 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 335 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 527 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 395
        2.75 -     3.28: 3293
        3.28 -     3.82: 5498
        3.82 -     4.36: 6072
        4.36 -     4.90: 10911
  Nonbonded interactions: 26169
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 394 "
            pdb=" OG  SER B 424 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   THR B 350 "
            pdb=" OG  SER B 351 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   LEU B 318 "
            pdb=" OH  TYR B 334 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" CD2 LEU B 284 "
            pdb=" CE  LYS B 288 "
     model   vdw
     2.317 3.860
  nonbonded pdb=" O   THR B 416 "
            pdb=" OG1 THR B 420 "
     model   vdw
     2.369 3.040
  ... (remaining 26164 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:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.020
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
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   0.032   3148  Z= 0.134
  Angle     :  0.531   4.493   4288  Z= 0.299
  Chirality :  0.035   0.132    538
  Planarity :  0.006   0.078    530
  Dihedral  : 12.975  66.238   1093
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 11.62 %
    Favored  : 88.07 %
  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:  1.87 (0.43), residues: 409
  helix:  1.59 (0.29), residues: 340
  sheet: -1.52 (1.31), residues: 20
  loop :  0.37 (0.94), residues: 49

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 335 
 TYR   0.007   0.001   TYR B 208 
 PHE   0.009   0.001   PHE B 299 
 TRP   0.005   0.001   TRP B 275 
 HIS   0.002   0.001   HIS B 373 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 3148)
  covalent geometry    : angle       0.53125 ( 4288)
  hydrogen bonds       : bond        0.11412 (  256)
  hydrogen bonds       : angle       6.28012 (  765)

*********************** 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
  50 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.112 
Fit side-chains
REVERT: B   85 ARG cc_start: 0.7368 (mtt180) cc_final: 0.5853 (tmt170)
REVERT: B  247 LYS cc_start: 0.7660 (mttt) cc_final: 0.7204 (mtpm)
REVERT: B  301 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7130 (ttt180)
REVERT: B  362 LYS cc_start: 0.7990 (tttt) cc_final: 0.7669 (tttp)
REVERT: B  407 GLN cc_start: 0.8182 (mt0) cc_final: 0.7976 (mp10)
  outliers start: 1
  outliers final: 1
  residues processed: 49
  average time/residue: 0.5473
  time to fit residues: 27.5768
Evaluate side-chains
  46 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  284 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0060
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.8400

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

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 447 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.129212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.095495 restraints weight = 4128.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3084 rms_B_bonded: 2.05
r_work: 0.2960 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.1122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3148  Z= 0.152
  Angle     :  0.553   6.752   4288  Z= 0.274
  Chirality :  0.038   0.140    538
  Planarity :  0.005   0.042    530
  Dihedral  :  4.148  40.074    437
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 10.09 %
    Favored  : 86.54 %
  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:  2.51 (0.42), residues: 409
  helix:  2.16 (0.28), residues: 339
  sheet: -1.84 (1.27), residues: 20
  loop : -0.15 (0.95), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 126 
 TYR   0.006   0.001   TYR B 276 
 PHE   0.011   0.001   PHE B 336 
 TRP   0.004   0.001   TRP B 461 
 HIS   0.002   0.001   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 3148)
  covalent geometry    : angle       0.55267 ( 4288)
  hydrogen bonds       : bond        0.04452 (  256)
  hydrogen bonds       : angle       4.69741 (  765)

*********************** 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
  53 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.123 
Fit side-chains
REVERT: B   85 ARG cc_start: 0.7402 (mtt180) cc_final: 0.5732 (tmt170)
REVERT: B  247 LYS cc_start: 0.7799 (mttt) cc_final: 0.7391 (mtpm)
REVERT: B  301 ARG cc_start: 0.8014 (ttm110) cc_final: 0.7129 (ttt180)
REVERT: B  362 LYS cc_start: 0.8048 (tttt) cc_final: 0.7717 (tttp)
REVERT: B  387 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7375 (mtt)
REVERT: B  407 GLN cc_start: 0.8169 (mt0) cc_final: 0.7866 (mp10)
  outliers start: 11
  outliers final: 2
  residues processed: 46
  average time/residue: 0.5702
  time to fit residues: 27.0335
Evaluate side-chains
  42 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  224 GLN
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  387 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0770
   chunk 28 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 447 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.130883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.097369 restraints weight = 4109.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 2.07
r_work: 0.3000 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1471

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= 0.129
  Angle     :  0.525   6.835   4288  Z= 0.255
  Chirality :  0.037   0.141    538
  Planarity :  0.004   0.035    530
  Dihedral  :  4.165  43.534    437
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 11.31 %
    Favored  : 85.02 %
  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:  2.98 (0.43), residues: 409
  helix:  2.43 (0.28), residues: 336
  sheet: -1.78 (1.24), residues: 20
  loop :  0.60 (1.01), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 335 
 TYR   0.005   0.001   TYR B 276 
 PHE   0.009   0.001   PHE B 237 
 TRP   0.004   0.001   TRP B 461 
 HIS   0.001   0.001   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3148)
  covalent geometry    : angle       0.52507 ( 4288)
  hydrogen bonds       : bond        0.03961 (  256)
  hydrogen bonds       : angle       4.48685 (  765)

*********************** 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
  58 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
REVERT: B   85 ARG cc_start: 0.7377 (mtt180) cc_final: 0.5720 (tmt170)
REVERT: B  247 LYS cc_start: 0.7759 (mttt) cc_final: 0.7348 (mtpm)
REVERT: B  301 ARG cc_start: 0.8020 (ttm110) cc_final: 0.7140 (ttt180)
REVERT: B  387 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7278 (mtt)
REVERT: B  407 GLN cc_start: 0.8168 (mt0) cc_final: 0.7870 (mt0)
  outliers start: 12
  outliers final: 4
  residues processed: 51
  average time/residue: 0.5267
  time to fit residues: 27.7097
Evaluate side-chains
  45 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 40
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  387 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    0.0980
   chunk 29 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9990
   chunk 35 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0040
   chunk 13 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   overall best weight:    0.4392

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

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
** B 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 447 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.132429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.099303 restraints weight = 4058.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.3147 rms_B_bonded: 2.06
r_work: 0.3028 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2904 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1857

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= 0.115
  Angle     :  0.500   7.001   4288  Z= 0.241
  Chirality :  0.036   0.140    538
  Planarity :  0.004   0.034    530
  Dihedral  :  4.149  48.545    437
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 13.46 %
    Favored  : 82.87 %
  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:  3.22 (0.42), residues: 409
  helix:  2.49 (0.28), residues: 341
  sheet: -1.64 (1.26), residues: 20
  loop :  1.33 (0.97), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 335 
 TYR   0.005   0.001   TYR B 208 
 PHE   0.008   0.001   PHE B 237 
 TRP   0.003   0.001   TRP B 338 
 HIS   0.001   0.000   HIS B 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 3148)
  covalent geometry    : angle       0.50008 ( 4288)
  hydrogen bonds       : bond        0.03607 (  256)
  hydrogen bonds       : angle       4.28099 (  765)

*********************** 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
  59 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 47
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
REVERT: B   85 ARG cc_start: 0.7336 (mtt180) cc_final: 0.5588 (tmt170)
REVERT: B  247 LYS cc_start: 0.7674 (mttt) cc_final: 0.7262 (mtpm)
REVERT: B  301 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7091 (ttt180)
REVERT: B  362 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7686 (tttp)
REVERT: B  387 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7222 (mtt)
REVERT: B  407 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7894 (mt0)
REVERT: B  446 VAL cc_start: 0.7419 (OUTLIER) cc_final: 0.7163 (m)
  outliers start: 12
  outliers final: 3
  residues processed: 52
  average time/residue: 0.5106
  time to fit residues: 27.4043
Evaluate side-chains
  49 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 42
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  224 GLN
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  407 GLN
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  482 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
B 403 GLN
B 447 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.130711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.097224 restraints weight = 4087.915|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 2.07
r_work: 0.2999 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.1830

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= 0.135
  Angle     :  0.519   7.970   4288  Z= 0.249
  Chirality :  0.037   0.144    538
  Planarity :  0.004   0.035    530
  Dihedral  :  4.407  57.027    437
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 14.68 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.07 (0.42), residues: 409
  helix:  2.49 (0.28), residues: 338
  sheet: -1.66 (1.23), residues: 20
  loop :  0.51 (0.90), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 335 
 TYR   0.006   0.001   TYR B 334 
 PHE   0.010   0.001   PHE B 237 
 TRP   0.004   0.001   TRP B 275 
 HIS   0.002   0.001   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 3148)
  covalent geometry    : angle       0.51859 ( 4288)
  hydrogen bonds       : bond        0.03802 (  256)
  hydrogen bonds       : angle       4.32758 (  765)

*********************** 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
  54 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
REVERT: B  247 LYS cc_start: 0.7754 (mttt) cc_final: 0.7339 (mtpm)
REVERT: B  267 MET cc_start: 0.8183 (mmm) cc_final: 0.7945 (mtt)
REVERT: B  301 ARG cc_start: 0.7976 (ttm110) cc_final: 0.7160 (ttt180)
REVERT: B  362 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7704 (tttp)
REVERT: B  387 MET cc_start: 0.8733 (OUTLIER) cc_final: 0.7288 (mtt)
REVERT: B  407 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7937 (mt0)
REVERT: B  446 VAL cc_start: 0.7446 (OUTLIER) cc_final: 0.7186 (m)
  outliers start: 14
  outliers final: 6
  residues processed: 45
  average time/residue: 0.4545
  time to fit residues: 21.1278
Evaluate side-chains
  50 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  407 GLN
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  482 LEU
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:    3.9990
   chunk 8 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   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 224 GLN
B 447 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.130825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.097601 restraints weight = 4054.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 2.04
r_work: 0.3001 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2878 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2878
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.1917

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= 0.128
  Angle     :  0.513   8.026   4288  Z= 0.246
  Chirality :  0.037   0.144    538
  Planarity :  0.004   0.035    530
  Dihedral  :  4.403  57.947    437
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 15.29 %
    Favored  : 80.73 %
  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:  3.05 (0.42), residues: 409
  helix:  2.49 (0.28), residues: 338
  sheet: -1.66 (1.24), residues: 20
  loop :  0.34 (0.87), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 335 
 TYR   0.007   0.001   TYR B 334 
 PHE   0.009   0.001   PHE B 237 
 TRP   0.004   0.001   TRP B 275 
 HIS   0.001   0.001   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3148)
  covalent geometry    : angle       0.51287 ( 4288)
  hydrogen bonds       : bond        0.03740 (  256)
  hydrogen bonds       : angle       4.30990 (  765)

*********************** 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
  54 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.074 
Fit side-chains
   revert: symmetry clash
REVERT: B  247 LYS cc_start: 0.7798 (mttt) cc_final: 0.7392 (mtpm)
REVERT: B  292 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6992 (ptp)
REVERT: B  301 ARG cc_start: 0.7995 (ttm110) cc_final: 0.7199 (ttt180)
REVERT: B  362 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7725 (tttp)
REVERT: B  387 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.7304 (mtt)
REVERT: B  407 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7957 (mt0)
REVERT: B  446 VAL cc_start: 0.7471 (OUTLIER) cc_final: 0.7197 (m)
  outliers start: 13
  outliers final: 4
  residues processed: 45
  average time/residue: 0.5118
  time to fit residues: 23.7238
Evaluate side-chains
  50 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  224 GLN
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  407 GLN
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  482 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
B 447 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.130352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.096843 restraints weight = 4118.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3109 rms_B_bonded: 2.07
r_work: 0.2985 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.1910

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     :  0.520   8.084   4288  Z= 0.249
  Chirality :  0.037   0.148    538
  Planarity :  0.004   0.035    530
  Dihedral  :  4.276  53.025    437
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.60 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.06 (0.42), residues: 409
  helix:  2.50 (0.28), residues: 338
  sheet: -1.69 (1.22), residues: 20
  loop :  0.33 (0.86), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 335 
 TYR   0.008   0.001   TYR B 334 
 PHE   0.010   0.001   PHE B 237 
 TRP   0.004   0.001   TRP B 275 
 HIS   0.002   0.001   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3148)
  covalent geometry    : angle       0.51972 ( 4288)
  hydrogen bonds       : bond        0.03815 (  256)
  hydrogen bonds       : angle       4.30038 (  765)

*********************** 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
  53 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: B  247 LYS cc_start: 0.7804 (mttt) cc_final: 0.7404 (mtpm)
REVERT: B  292 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.7014 (ptp)
REVERT: B  301 ARG cc_start: 0.7971 (ttm170) cc_final: 0.7186 (ttt180)
REVERT: B  362 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7684 (tttp)
REVERT: B  387 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7300 (mtt)
REVERT: B  407 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7947 (mt0)
REVERT: B  446 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7181 (m)
REVERT: B  454 SER cc_start: 0.8351 (m) cc_final: 0.8049 (p)
  outliers start: 11
  outliers final: 4
  residues processed: 45
  average time/residue: 0.4828
  time to fit residues: 22.3841
Evaluate side-chains
  51 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  224 GLN
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  407 GLN
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  482 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 37 optimal weight:    0.2980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
B 447 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.130953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.097418 restraints weight = 4186.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 2.10
r_work: 0.2992 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1969

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= 0.131
  Angle     :  0.519   8.212   4288  Z= 0.248
  Chirality :  0.037   0.144    538
  Planarity :  0.004   0.034    530
  Dihedral  :  3.443  11.709    435
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.90 %
    Favored  : 80.73 %
  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:  3.07 (0.42), residues: 409
  helix:  2.50 (0.28), residues: 338
  sheet: -1.60 (1.24), residues: 20
  loop :  0.31 (0.86), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 335 
 TYR   0.007   0.001   TYR B 334 
 PHE   0.009   0.001   PHE B 237 
 TRP   0.005   0.001   TRP B 275 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3148)
  covalent geometry    : angle       0.51878 ( 4288)
  hydrogen bonds       : bond        0.03738 (  256)
  hydrogen bonds       : angle       4.29156 (  765)

*********************** 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
  52 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: B  247 LYS cc_start: 0.7786 (mttt) cc_final: 0.7384 (mtpm)
REVERT: B  292 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.7031 (ptp)
REVERT: B  301 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7190 (ttt180)
REVERT: B  362 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7667 (tttp)
REVERT: B  387 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.7361 (mtt)
REVERT: B  407 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7961 (mt0)
REVERT: B  446 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7191 (m)
  outliers start: 11
  outliers final: 4
  residues processed: 45
  average time/residue: 0.4672
  time to fit residues: 21.6263
Evaluate side-chains
  49 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  224 GLN
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  407 GLN
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  482 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 29 optimal weight:    0.0070
   chunk 11 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
B 447 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.131489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.098111 restraints weight = 4133.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 2.08
r_work: 0.3001 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.2006

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= 0.123
  Angle     :  0.514   8.320   4288  Z= 0.244
  Chirality :  0.037   0.144    538
  Planarity :  0.004   0.035    530
  Dihedral  :  3.416  11.527    435
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 15.29 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.12 (0.42), residues: 409
  helix:  2.55 (0.28), residues: 338
  sheet: -1.67 (1.25), residues: 20
  loop :  0.33 (0.87), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 335 
 TYR   0.007   0.001   TYR B 334 
 PHE   0.009   0.001   PHE B 237 
 TRP   0.005   0.001   TRP B 275 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3148)
  covalent geometry    : angle       0.51425 ( 4288)
  hydrogen bonds       : bond        0.03653 (  256)
  hydrogen bonds       : angle       4.25281 (  765)

*********************** 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
  52 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.080 
Fit side-chains
   revert: symmetry clash
REVERT: B  247 LYS cc_start: 0.7779 (mttt) cc_final: 0.7377 (mtpm)
REVERT: B  292 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.6984 (ptp)
REVERT: B  301 ARG cc_start: 0.7966 (ttm170) cc_final: 0.7185 (ttt180)
REVERT: B  362 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7667 (tttp)
REVERT: B  387 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7318 (mtt)
REVERT: B  407 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7952 (mt0)
REVERT: B  446 VAL cc_start: 0.7392 (OUTLIER) cc_final: 0.7107 (m)
  outliers start: 12
  outliers final: 6
  residues processed: 44
  average time/residue: 0.5226
  time to fit residues: 23.6532
Evaluate side-chains
  51 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   79 LEU
Chi-restraints excluded: chain B residue  224 GLN
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  407 GLN
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  482 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 25 optimal weight:    0.1980
   chunk 28 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0470
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
B 447 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.128890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.094628 restraints weight = 4085.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.13
r_work: 0.2955 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2831 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2085

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= 0.116
  Angle     :  0.511   8.119   4288  Z= 0.243
  Chirality :  0.036   0.141    538
  Planarity :  0.004   0.035    530
  Dihedral  :  3.400  11.571    435
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.51 %
    Favored  : 80.73 %
  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:  3.22 (0.42), residues: 409
  helix:  2.54 (0.28), residues: 341
  sheet: -1.59 (1.26), residues: 20
  loop :  0.80 (0.86), residues: 48

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 335 
 TYR   0.006   0.001   TYR B 334 
 PHE   0.008   0.001   PHE B 237 
 TRP   0.004   0.001   TRP B 275 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 3148)
  covalent geometry    : angle       0.51139 ( 4288)
  hydrogen bonds       : bond        0.03549 (  256)
  hydrogen bonds       : angle       4.23217 (  765)

********************** 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
  49 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.068 
Fit side-chains
   revert: symmetry clash
REVERT: B  247 LYS cc_start: 0.7600 (mttt) cc_final: 0.7200 (mtpm)
REVERT: B  292 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6922 (ptp)
REVERT: B  301 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7102 (ttt180)
REVERT: B  362 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7510 (tttp)
REVERT: B  387 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7170 (mtt)
REVERT: B  407 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7907 (mt0)
REVERT: B  446 VAL cc_start: 0.7266 (OUTLIER) cc_final: 0.6978 (m)
  outliers start: 9
  outliers final: 4
  residues processed: 44
  average time/residue: 0.4635
  time to fit residues: 20.9984
Evaluate side-chains
  48 residues out of total 327 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  356 THR
Chi-restraints excluded: chain B residue  362 LYS
Chi-restraints excluded: chain B residue  387 MET
Chi-restraints excluded: chain B residue  407 GLN
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  450 VAL
Chi-restraints excluded: chain B residue  482 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    0.2980
   chunk 4 optimal weight:    0.6980
   chunk 14 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 224 GLN
B 447 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.129180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.094848 restraints weight = 4067.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 2.12
r_work: 0.2954 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2123

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= 0.118
  Angle     :  0.510   8.107   4288  Z= 0.242
  Chirality :  0.036   0.141    538
  Planarity :  0.004   0.035    530
  Dihedral  :  3.386  11.560    435
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.60 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.26 (0.41), residues: 409
  helix:  2.55 (0.27), residues: 342
  sheet: -1.61 (1.24), residues: 20
  loop :  0.95 (0.85), residues: 47

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 335 
 TYR   0.006   0.001   TYR B 334 
 PHE   0.008   0.001   PHE B 237 
 TRP   0.003   0.001   TRP B 338 
 HIS   0.001   0.000   HIS B 316 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3148)
  covalent geometry    : angle       0.51019 ( 4288)
  hydrogen bonds       : bond        0.03530 (  256)
  hydrogen bonds       : angle       4.20393 (  765)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1255.45 seconds
wall clock time: 22 minutes 6.37 seconds (1326.37 seconds total)