Starting phenix.real_space_refine
on Tue Aug  4 14:29:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yr4_73359/08_2026/9yr4_73359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yr4_73359/08_2026/9yr4_73359.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yr4_73359/08_2026/9yr4_73359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yr4_73359/08_2026/9yr4_73359.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yr4_73359/08_2026/9yr4_73359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yr4_73359/08_2026/9yr4_73359.cif"
  }
  resolution = 3.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
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      26      5.16       5
     C    2406      2.51       5
     N     647      2.21       5
     O     740      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3819
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 475, 3785
          Classifications: {'peptide': 475}
          Link IDs: {'PTRANS': 13, 'TRANS': 461}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Classifications: {'peptide': 4}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 3}
  Time building chain proxies: 1.06, per 1000 atoms: 0.28
  Number of scatterers: 3819
  At special positions: 0
  Unit cell: (59.904, 69.056, 115.648, 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      26     16.00
     O     740      8.00
     N     647      7.00
     C    2406      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: 0.34
  Conformation dependent library (CDL) restraints added in 147.8 milliseconds
  

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  922

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 0 sheets defined
      84.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 110 through 128
      removed outlier: 3.750A  pdb=" N   ALA A 127 " --> pdb=" O   LYS A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 143
    Processing helix  chain 'A' and resid 150 through 165
    Processing helix  chain 'A' and resid 169 through 183
    Processing helix  chain 'A' and resid 187 through 200
    Processing helix  chain 'A' and resid 202 through 218
    Processing helix  chain 'A' and resid 221 through 245
      removed outlier: 3.719A  pdb=" N   LYS A 245 " --> pdb=" O   LYS A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 263
    Processing helix  chain 'A' and resid 296 through 308
    Processing helix  chain 'A' and resid 312 through 323
      removed outlier: 3.726A  pdb=" N   GLU A 316 " --> pdb=" O   LYS A 312 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ALA A 323 " --> pdb=" O   LYS A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 342
    Processing helix  chain 'A' and resid 348 through 358
    Processing helix  chain 'A' and resid 362 through 380
    Processing helix  chain 'A' and resid 382 through 397
      removed outlier: 4.185A  pdb=" N   SER A 386 " --> pdb=" O   GLN A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 414
      removed outlier: 3.805A  pdb=" N   TYR A 404 " --> pdb=" O   ASN A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 431
    Processing helix  chain 'A' and resid 435 through 453
    Processing helix  chain 'A' and resid 454 through 472
      removed outlier: 3.663A  pdb=" N   ILE A 458 " --> pdb=" O   ASN A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 489
      removed outlier: 3.521A  pdb=" N   TYR A 479 " --> pdb=" O   CYS A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 506
    Processing helix  chain 'A' and resid 509 through 524
      removed outlier: 3.809A  pdb=" N   TYR A 513 " --> pdb=" O   ASN A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 541
    Processing helix  chain 'A' and resid 544 through 559
      removed outlier: 3.701A  pdb=" N   TYR A 548 " --> pdb=" O   CYS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 573
      removed outlier: 3.760A  pdb=" N   ASN A 573 " --> pdb=" O   ASN A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 602

    294 hydrogen bonds defined for protein.
    882 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: 0.57

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1263
        1.34 -     1.46: 503
        1.46 -     1.58: 2073
        1.58 -     1.70: 0
        1.70 -     1.82: 40
  Bond restraints: 3879
  Sorted by residual:
  bond pdb=" C   GLN A 303 "
       pdb=" O   GLN A 303 "
    ideal  model  delta    sigma   weight residual
    1.237  1.217  0.019 1.19e-02 7.06e+03 2.60e+00
  bond pdb=" CA  LYS A 471 "
       pdb=" C   LYS A 471 "
    ideal  model  delta    sigma   weight residual
    1.524  1.506  0.018 1.24e-02 6.50e+03 2.14e+00
  bond pdb=" CA  GLU A 164 "
       pdb=" C   GLU A 164 "
    ideal  model  delta    sigma   weight residual
    1.524  1.509  0.015 1.27e-02 6.20e+03 1.39e+00
  bond pdb=" CB  GLN A 382 "
       pdb=" CG  GLN A 382 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.23e+00
  bond pdb=" CA  ASP A 589 "
       pdb=" C   ASP A 589 "
    ideal  model  delta    sigma   weight residual
    1.524  1.510  0.013 1.27e-02 6.20e+03 1.11e+00
  ... (remaining 3874 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 5057
        2.00 -     4.01: 126
        4.01 -     6.01: 21
        6.01 -     8.02: 5
        8.02 -    10.02: 3
  Bond angle restraints: 5212
  Sorted by residual:
  angle pdb=" CB  MET A 376 "
        pdb=" CG  MET A 376 "
        pdb=" SD  MET A 376 "
      ideal   model   delta    sigma   weight residual
     112.70  122.72  -10.02 3.00e+00 1.11e-01 1.12e+01
  angle pdb=" C   TYR A 186 "
        pdb=" N   VAL A 187 "
        pdb=" CA  VAL A 187 "
      ideal   model   delta    sigma   weight residual
     123.08  119.80    3.28 1.01e+00 9.80e-01 1.06e+01
  angle pdb=" CA  GLU A 306 "
        pdb=" CB  GLU A 306 "
        pdb=" CG  GLU A 306 "
      ideal   model   delta    sigma   weight residual
     114.10  120.32   -6.22 2.00e+00 2.50e-01 9.66e+00
  angle pdb=" N   TYR A 304 "
        pdb=" CA  TYR A 304 "
        pdb=" C   TYR A 304 "
      ideal   model   delta    sigma   weight residual
     111.36  108.18    3.18 1.09e+00 8.42e-01 8.50e+00
  angle pdb=" CB  MET A 462 "
        pdb=" CG  MET A 462 "
        pdb=" SD  MET A 462 "
      ideal   model   delta    sigma   weight residual
     112.70  103.98    8.72 3.00e+00 1.11e-01 8.45e+00
  ... (remaining 5207 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.36: 2064
       17.36 -    34.72: 243
       34.72 -    52.09: 87
       52.09 -    69.45: 10
       69.45 -    86.81: 10
  Dihedral angle restraints: 2414
    sinusoidal: 993
      harmonic: 1421
  Sorted by residual:
  dihedral pdb=" CA  ASP A 415 "
           pdb=" C   ASP A 415 "
           pdb=" N   GLN A 416 "
           pdb=" CA  GLN A 416 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.77   20.23     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  LYS A 168 "
           pdb=" C   LYS A 168 "
           pdb=" N   TRP A 169 "
           pdb=" CA  TRP A 169 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.77  -16.23     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CB  GLU A 320 "
           pdb=" CG  GLU A 320 "
           pdb=" CD  GLU A 320 "
           pdb=" OE1 GLU A 320 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.81  -86.81     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 2411 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 368
       0.034 -    0.068: 128
       0.068 -    0.102: 43
       0.102 -    0.136: 19
       0.136 -    0.170: 5
  Chirality restraints: 563
  Sorted by residual:
  chirality pdb=" CA  TYR A 339 "
            pdb=" N   TYR A 339 "
            pdb=" C   TYR A 339 "
            pdb=" CB  TYR A 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.25e-01
  chirality pdb=" CA  MET A 462 "
            pdb=" N   MET A 462 "
            pdb=" C   MET A 462 "
            pdb=" CB  MET A 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.40e-01
  chirality pdb=" CA  ASP A 415 "
            pdb=" N   ASP A 415 "
            pdb=" C   ASP A 415 "
            pdb=" CB  ASP A 415 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.38e-01
  ... (remaining 560 not shown)

  Planarity restraints: 683
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 373 "   -0.198 9.50e-02 1.11e+02   8.96e-02 6.51e+00
        pdb=" NE  ARG A 373 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 373 "   -0.020 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 373 "    0.009 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 373 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 397 "    0.039 5.00e-02 4.00e+02   6.00e-02 5.75e+00
        pdb=" N   PRO A 398 "   -0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 398 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 398 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 137 "   -0.010 2.00e-02 2.50e+03   1.22e-02 2.99e+00
        pdb=" CG  TYR A 137 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 137 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 137 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 137 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 137 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 137 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 137 "    0.000 2.00e-02 2.50e+03
  ... (remaining 680 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.86: 1373
        2.86 -     3.37: 4124
        3.37 -     3.88: 6146
        3.88 -     4.39: 6848
        4.39 -     4.90: 10970
  Nonbonded interactions: 29461
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 207 "
            pdb=" OG1 THR A 211 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" O   SER A 259 "
            pdb=" OG  SER A 262 "
     model   vdw
     2.367 3.040
  nonbonded pdb=" OD2 ASP A 266 "
            pdb=" ND2 ASN A 400 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" O   PRO A 398 "
            pdb=" OH  TYR A 404 "
     model   vdw
     2.393 3.040
  nonbonded pdb=" O   ASN A 509 "
            pdb=" OG1 THR A 512 "
     model   vdw
     2.400 3.040
  ... (remaining 29456 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.310
  Set stop_for_unknowns flag:              0.010
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.790
  Find NCS groups from input model:        0.020
  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:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
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      :  0.004   0.033   3879  Z= 0.196
  Angle     :  0.778  10.020   5212  Z= 0.435
  Chirality :  0.044   0.170    563
  Planarity :  0.006   0.090    683
  Dihedral  : 17.496  86.812   1492
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 22.72 %
    Favored  : 77.04 %
  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 are not related in a simple way.
  whole:  1.30 (0.39), residues: 473
  helix:  1.39 (0.26), residues: 400
  sheet:  None (None), residues: 0
  loop : -2.00 (0.64), residues: 73

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.002   ARG A 373 
 TYR   0.030   0.002   TYR A 137 
 PHE   0.014   0.002   PHE A 390 
 TRP   0.017   0.002   TRP A 523 
 HIS   0.007   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.20 ( 3879)
  covalent geometry    : angle       0.77799 /  0.43 ( 5212)
  hydrogen bonds       : bond        0.11375 /  7.46 (  294)
  hydrogen bonds       : angle       5.04586 /  3.64 (  882)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 GLN cc_start: 0.8817 (pt0) cc_final: 0.8501 (pt0)
REVERT: A  174 GLN cc_start: 0.8539 (mt0) cc_final: 0.8229 (pt0)
REVERT: A  178 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8324 (ttpt)
REVERT: A  181 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8301 (mt-10)
REVERT: A  195 LYS cc_start: 0.8736 (mmtp) cc_final: 0.8137 (mmtm)
REVERT: A  234 LEU cc_start: 0.8576 (mt) cc_final: 0.8323 (tt)
REVERT: A  248 GLU cc_start: 0.8462 (tp30) cc_final: 0.8218 (tp30)
REVERT: A  257 ILE cc_start: 0.8754 (mt) cc_final: 0.8440 (tp)
REVERT: A  267 ASP cc_start: 0.7142 (m-30) cc_final: 0.6660 (m-30)
REVERT: A  306 GLU cc_start: 0.8213 (tt0) cc_final: 0.7780 (tt0)
REVERT: A  354 LYS cc_start: 0.8946 (tptm) cc_final: 0.8602 (tppp)
REVERT: A  359 LYS cc_start: 0.8537 (mttt) cc_final: 0.8088 (mmtt)
REVERT: A  373 ARG cc_start: 0.7954 (ttt-90) cc_final: 0.7714 (ptm160)
REVERT: A  381 GLN cc_start: 0.8321 (mt0) cc_final: 0.8079 (mt0)
REVERT: A  390 PHE cc_start: 0.8645 (t80) cc_final: 0.8072 (t80)
REVERT: A  454 ASN cc_start: 0.7476 (t0) cc_final: 0.6938 (t0)
REVERT: A  462 MET cc_start: 0.7147 (ptm) cc_final: 0.6506 (ptm)
REVERT: A  466 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8289 (mt-10)
REVERT: A  529 ARG cc_start: 0.6892 (mmt180) cc_final: 0.5113 (tpp-160)
REVERT: A  544 CYS cc_start: 0.8325 (t) cc_final: 0.8016 (t)
REVERT: A  566 ASP cc_start: 0.7917 (m-30) cc_final: 0.7687 (t0)
REVERT: A  567 MET cc_start: 0.8214 (mmt) cc_final: 0.7888 (mmt)
REVERT: A  569 ASN cc_start: 0.8215 (t0) cc_final: 0.7958 (t0)
REVERT: A  570 LYS cc_start: 0.8327 (mttt) cc_final: 0.7994 (ttmm)
  outliers start: 1
  outliers final: 1
  residues processed: 169
  average time/residue: 0.0603
  time to fit residues: 12.0656
Evaluate side-chains
  167 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 166
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0980
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.3980
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 149 ASN
A 157 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.111558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.093488 restraints weight = 8769.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.097097 restraints weight = 4861.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.099572 restraints weight = 3098.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.101229 restraints weight = 2163.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.102466 restraints weight = 1629.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3879  Z= 0.136
  Angle     :  0.531   8.454   5212  Z= 0.290
  Chirality :  0.037   0.137    563
  Planarity :  0.004   0.055    683
  Dihedral  :  5.129  53.674    517
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 22.96 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.40), residues: 473
  helix:  2.30 (0.26), residues: 403
  sheet:  None (None), residues: 0
  loop : -2.12 (0.66), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 373 
 TYR   0.021   0.002   TYR A 137 
 PHE   0.010   0.001   PHE A 338 
 TRP   0.008   0.002   TRP A 523 
 HIS   0.006   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.14 ( 3879)
  covalent geometry    : angle       0.53140 /  0.29 ( 5212)
  hydrogen bonds       : bond        0.03628 /  2.42 (  294)
  hydrogen bonds       : angle       3.72570 /  2.72 (  882)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 158
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 TYR cc_start: 0.7711 (m-80) cc_final: 0.7160 (m-80)
REVERT: A  157 GLN cc_start: 0.8457 (pt0) cc_final: 0.7541 (pt0)
REVERT: A  174 GLN cc_start: 0.8398 (mt0) cc_final: 0.8120 (pt0)
REVERT: A  178 LYS cc_start: 0.8826 (ttpt) cc_final: 0.8129 (ttpt)
REVERT: A  181 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8020 (mt-10)
REVERT: A  182 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7914 (mm)
REVERT: A  192 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7408 (mtp85)
REVERT: A  195 LYS cc_start: 0.8709 (mmtp) cc_final: 0.8177 (mmtp)
REVERT: A  205 GLU cc_start: 0.7680 (mp0) cc_final: 0.7258 (mp0)
REVERT: A  234 LEU cc_start: 0.8562 (mt) cc_final: 0.8311 (tt)
REVERT: A  308 GLU cc_start: 0.6955 (mp0) cc_final: 0.6713 (mp0)
REVERT: A  342 ILE cc_start: 0.8223 (mt) cc_final: 0.8014 (tp)
REVERT: A  354 LYS cc_start: 0.8777 (tptm) cc_final: 0.8482 (tppp)
REVERT: A  364 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8627 (mmtt)
REVERT: A  366 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.7827 (mtm-85)
REVERT: A  370 LEU cc_start: 0.8848 (mt) cc_final: 0.8553 (mt)
REVERT: A  373 ARG cc_start: 0.8248 (ttt-90) cc_final: 0.7800 (ptm160)
REVERT: A  376 MET cc_start: 0.7947 (tmm) cc_final: 0.7736 (tmm)
REVERT: A  389 ASP cc_start: 0.7740 (t0) cc_final: 0.6952 (t0)
REVERT: A  390 PHE cc_start: 0.8548 (t80) cc_final: 0.8175 (t80)
REVERT: A  454 ASN cc_start: 0.7333 (t0) cc_final: 0.6966 (t0)
REVERT: A  462 MET cc_start: 0.6972 (ptm) cc_final: 0.6457 (ptm)
REVERT: A  466 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8204 (mt-10)
REVERT: A  498 MET cc_start: 0.7933 (mmt) cc_final: 0.7572 (mmt)
REVERT: A  506 GLU cc_start: 0.8448 (tp30) cc_final: 0.8223 (tp30)
REVERT: A  529 ARG cc_start: 0.6944 (mmt180) cc_final: 0.5127 (tpp-160)
REVERT: A  532 GLU cc_start: 0.7550 (pt0) cc_final: 0.7038 (pt0)
REVERT: A  544 CYS cc_start: 0.8402 (t) cc_final: 0.7938 (t)
REVERT: A  561 MET cc_start: 0.7987 (mmm) cc_final: 0.7684 (mmm)
REVERT: A  566 ASP cc_start: 0.7858 (m-30) cc_final: 0.7613 (t0)
REVERT: A  570 LYS cc_start: 0.8256 (mttt) cc_final: 0.7919 (ttmm)
REVERT: A  576 LYS cc_start: 0.8478 (mtmt) cc_final: 0.7941 (mtmt)
REVERT: A  594 GLN cc_start: 0.8599 (tp40) cc_final: 0.8338 (tt0)
  outliers start: 13
  outliers final: 5
  residues processed: 168
  average time/residue: 0.0596
  time to fit residues: 11.7950
Evaluate side-chains
  160 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 154
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  245 LYS
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  592 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.109883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.092320 restraints weight = 8609.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.095874 restraints weight = 4798.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.098320 restraints weight = 3052.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.100005 restraints weight = 2128.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.101196 restraints weight = 1589.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   3879  Z= 0.156
  Angle     :  0.539   6.269   5212  Z= 0.297
  Chirality :  0.037   0.133    563
  Planarity :  0.004   0.047    683
  Dihedral  :  5.204  55.939    517
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 23.70 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.79 (0.40), residues: 473
  helix:  2.54 (0.26), residues: 402
  sheet:  None (None), residues: 0
  loop : -2.56 (0.61), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 558 
 TYR   0.021   0.002   TYR A 304 
 PHE   0.012   0.001   PHE A 472 
 TRP   0.007   0.002   TRP A 523 
 HIS   0.006   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.16 ( 3879)
  covalent geometry    : angle       0.53948 /  0.30 ( 5212)
  hydrogen bonds       : bond        0.03655 /  2.45 (  294)
  hydrogen bonds       : angle       3.68491 /  2.69 (  882)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 173
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 TYR cc_start: 0.7743 (m-80) cc_final: 0.7182 (m-80)
REVERT: A  157 GLN cc_start: 0.8486 (pt0) cc_final: 0.8005 (pt0)
REVERT: A  159 ARG cc_start: 0.7362 (OUTLIER) cc_final: 0.6877 (ttt-90)
REVERT: A  170 LYS cc_start: 0.8693 (pttt) cc_final: 0.8007 (ptmt)
REVERT: A  174 GLN cc_start: 0.8451 (mt0) cc_final: 0.8136 (mt0)
REVERT: A  178 LYS cc_start: 0.8847 (ttpt) cc_final: 0.8603 (ttpt)
REVERT: A  181 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8075 (mt-10)
REVERT: A  211 THR cc_start: 0.8684 (m) cc_final: 0.8478 (p)
REVERT: A  229 ASP cc_start: 0.7511 (t0) cc_final: 0.7291 (t0)
REVERT: A  308 GLU cc_start: 0.6859 (mp0) cc_final: 0.6580 (mp0)
REVERT: A  354 LYS cc_start: 0.8776 (tptm) cc_final: 0.8533 (ttmm)
REVERT: A  366 ARG cc_start: 0.8325 (mtm-85) cc_final: 0.7828 (mtm-85)
REVERT: A  370 LEU cc_start: 0.8878 (mt) cc_final: 0.8658 (mt)
REVERT: A  373 ARG cc_start: 0.8346 (ttt-90) cc_final: 0.7779 (ttt90)
REVERT: A  389 ASP cc_start: 0.7692 (t0) cc_final: 0.7334 (t0)
REVERT: A  390 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.8204 (t80)
REVERT: A  404 TYR cc_start: 0.8407 (m-80) cc_final: 0.8062 (m-80)
REVERT: A  454 ASN cc_start: 0.7458 (t0) cc_final: 0.7159 (t0)
REVERT: A  459 GLN cc_start: 0.8608 (mm-40) cc_final: 0.8361 (mm-40)
REVERT: A  462 MET cc_start: 0.6941 (ptm) cc_final: 0.6434 (ptm)
REVERT: A  466 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8157 (mt-10)
REVERT: A  498 MET cc_start: 0.7949 (mmt) cc_final: 0.7597 (mmt)
REVERT: A  527 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8492 (tp)
REVERT: A  529 ARG cc_start: 0.6930 (mmt180) cc_final: 0.4997 (tpp-160)
REVERT: A  531 LEU cc_start: 0.8322 (mm) cc_final: 0.8116 (mm)
REVERT: A  532 GLU cc_start: 0.7539 (pt0) cc_final: 0.6914 (pt0)
REVERT: A  544 CYS cc_start: 0.8347 (t) cc_final: 0.7967 (t)
REVERT: A  570 LYS cc_start: 0.8224 (mttt) cc_final: 0.7877 (ttmm)
REVERT: A  576 LYS cc_start: 0.8485 (mtmt) cc_final: 0.7944 (mtmt)
  outliers start: 19
  outliers final: 9
  residues processed: 183
  average time/residue: 0.0604
  time to fit residues: 13.1074
Evaluate side-chains
  174 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 162
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 PHE
Chi-restraints excluded: chain A residue  159 ARG
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  245 LYS
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  592 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.109438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.091644 restraints weight = 8561.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.095167 restraints weight = 4803.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.097568 restraints weight = 3069.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.099281 restraints weight = 2153.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.100445 restraints weight = 1614.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3879  Z= 0.164
  Angle     :  0.539   5.954   5212  Z= 0.301
  Chirality :  0.037   0.133    563
  Planarity :  0.004   0.041    683
  Dihedral  :  5.197  58.135    517
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 24.20 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.84 (0.40), residues: 473
  helix:  2.62 (0.26), residues: 402
  sheet:  None (None), residues: 0
  loop : -2.85 (0.59), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 192 
 TYR   0.016   0.002   TYR A 304 
 PHE   0.008   0.001   PHE A 472 
 TRP   0.005   0.001   TRP A 523 
 HIS   0.005   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.16 ( 3879)
  covalent geometry    : angle       0.53882 /  0.30 ( 5212)
  hydrogen bonds       : bond        0.03690 /  2.46 (  294)
  hydrogen bonds       : angle       3.63222 /  2.65 (  882)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  137 TYR cc_start: 0.7796 (m-80) cc_final: 0.7193 (m-80)
REVERT: A  157 GLN cc_start: 0.8470 (pt0) cc_final: 0.7909 (pt0)
REVERT: A  159 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6940 (ttt-90)
REVERT: A  170 LYS cc_start: 0.8688 (pttt) cc_final: 0.7961 (ptmt)
REVERT: A  174 GLN cc_start: 0.8490 (mt0) cc_final: 0.8129 (mt0)
REVERT: A  178 LYS cc_start: 0.8935 (ttpt) cc_final: 0.8506 (ttpt)
REVERT: A  181 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8091 (mt-10)
REVERT: A  182 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8064 (mm)
REVERT: A  211 THR cc_start: 0.8713 (m) cc_final: 0.8494 (p)
REVERT: A  229 ASP cc_start: 0.7521 (t0) cc_final: 0.7290 (t0)
REVERT: A  308 GLU cc_start: 0.6769 (mp0) cc_final: 0.6447 (mp0)
REVERT: A  309 ASN cc_start: 0.8126 (m-40) cc_final: 0.7864 (t0)
REVERT: A  342 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.8010 (tp)
REVERT: A  344 ASN cc_start: 0.7258 (t0) cc_final: 0.7023 (t0)
REVERT: A  354 LYS cc_start: 0.8791 (tptm) cc_final: 0.8552 (ttmm)
REVERT: A  364 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8463 (mmtt)
REVERT: A  370 LEU cc_start: 0.8911 (mt) cc_final: 0.8663 (mt)
REVERT: A  373 ARG cc_start: 0.8419 (ttt-90) cc_final: 0.7930 (ttt90)
REVERT: A  376 MET cc_start: 0.7997 (tmm) cc_final: 0.7697 (tmm)
REVERT: A  382 GLN cc_start: 0.7425 (tm-30) cc_final: 0.6952 (tm-30)
REVERT: A  389 ASP cc_start: 0.7707 (t0) cc_final: 0.7400 (t0)
REVERT: A  390 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.8271 (t80)
REVERT: A  391 ASN cc_start: 0.8429 (t0) cc_final: 0.8165 (t0)
REVERT: A  407 ARG cc_start: 0.8132 (ttp-110) cc_final: 0.7446 (ttp-110)
REVERT: A  462 MET cc_start: 0.6946 (ptm) cc_final: 0.6423 (ptm)
REVERT: A  466 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8205 (mt-10)
REVERT: A  477 GLU cc_start: 0.7785 (mp0) cc_final: 0.7538 (mp0)
REVERT: A  498 MET cc_start: 0.7934 (mmt) cc_final: 0.7550 (mmt)
REVERT: A  527 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8506 (tp)
REVERT: A  529 ARG cc_start: 0.6973 (mmt180) cc_final: 0.4826 (tpp-160)
REVERT: A  531 LEU cc_start: 0.8281 (mm) cc_final: 0.8047 (mm)
REVERT: A  532 GLU cc_start: 0.7546 (pt0) cc_final: 0.6931 (pt0)
REVERT: A  544 CYS cc_start: 0.8317 (t) cc_final: 0.7952 (t)
REVERT: A  570 LYS cc_start: 0.8271 (mttt) cc_final: 0.7905 (ttmm)
REVERT: A  576 LYS cc_start: 0.8531 (mtmt) cc_final: 0.7990 (mtmt)
  outliers start: 26
  outliers final: 14
  residues processed: 180
  average time/residue: 0.0562
  time to fit residues: 12.0041
Evaluate side-chains
  183 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 164
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  150 VAL
Chi-restraints excluded: chain A residue  159 ARG
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  245 LYS
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  595 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 31 optimal weight:    0.8980
   chunk 13 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0980
   chunk 9 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 4 optimal weight:    0.2980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.111231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.092983 restraints weight = 8706.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096616 restraints weight = 4913.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.099093 restraints weight = 3162.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 17)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.100811 restraints weight = 2226.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.102126 restraints weight = 1686.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3879  Z= 0.121
  Angle     :  0.551   5.733   5212  Z= 0.294
  Chirality :  0.036   0.126    563
  Planarity :  0.004   0.039    683
  Dihedral  :  4.439  35.448    515
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 27.16 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.06 (0.40), residues: 473
  helix:  2.78 (0.26), residues: 402
  sheet:  None (None), residues: 0
  loop : -2.87 (0.58), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 447 
 TYR   0.013   0.001   TYR A 446 
 PHE   0.018   0.001   PHE A 125 
 TRP   0.011   0.002   TRP A 169 
 HIS   0.005   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 3879)
  covalent geometry    : angle       0.55139 /  0.29 ( 5212)
  hydrogen bonds       : bond        0.03109 /  2.07 (  294)
  hydrogen bonds       : angle       3.45040 /  2.51 (  882)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 166
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 TYR cc_start: 0.8483 (m-80) cc_final: 0.7701 (m-80)
REVERT: A  137 TYR cc_start: 0.7809 (m-80) cc_final: 0.7208 (m-80)
REVERT: A  157 GLN cc_start: 0.8481 (pt0) cc_final: 0.7880 (pt0)
REVERT: A  159 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6904 (ttt-90)
REVERT: A  170 LYS cc_start: 0.8710 (pttt) cc_final: 0.8240 (ptpt)
REVERT: A  174 GLN cc_start: 0.8490 (mt0) cc_final: 0.8116 (mt0)
REVERT: A  178 LYS cc_start: 0.8928 (ttpt) cc_final: 0.8228 (ttpt)
REVERT: A  181 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8062 (mt-10)
REVERT: A  195 LYS cc_start: 0.8593 (mmtp) cc_final: 0.8039 (mttt)
REVERT: A  211 THR cc_start: 0.8692 (m) cc_final: 0.8453 (p)
REVERT: A  229 ASP cc_start: 0.7491 (t0) cc_final: 0.7233 (t0)
REVERT: A  247 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.7283 (ttp-110)
REVERT: A  308 GLU cc_start: 0.6731 (mp0) cc_final: 0.6267 (mp0)
REVERT: A  344 ASN cc_start: 0.7221 (t0) cc_final: 0.6996 (t0)
REVERT: A  354 LYS cc_start: 0.8730 (tptm) cc_final: 0.8438 (ttmm)
REVERT: A  366 ARG cc_start: 0.8336 (mtm-85) cc_final: 0.7824 (mtm-85)
REVERT: A  370 LEU cc_start: 0.8855 (mt) cc_final: 0.8645 (mt)
REVERT: A  373 ARG cc_start: 0.8408 (ttt-90) cc_final: 0.7895 (ttt90)
REVERT: A  376 MET cc_start: 0.8016 (tmm) cc_final: 0.7680 (tmm)
REVERT: A  389 ASP cc_start: 0.7692 (t0) cc_final: 0.7423 (t0)
REVERT: A  390 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.8305 (t80)
REVERT: A  404 TYR cc_start: 0.8350 (m-80) cc_final: 0.8140 (m-80)
REVERT: A  407 ARG cc_start: 0.8073 (ttp-110) cc_final: 0.7359 (ttp-110)
REVERT: A  462 MET cc_start: 0.6945 (ptm) cc_final: 0.6410 (ptm)
REVERT: A  466 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8203 (mt-10)
REVERT: A  477 GLU cc_start: 0.7765 (mp0) cc_final: 0.7474 (mp0)
REVERT: A  498 MET cc_start: 0.7882 (mmt) cc_final: 0.7496 (mmt)
REVERT: A  527 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8444 (tp)
REVERT: A  529 ARG cc_start: 0.6891 (mmt180) cc_final: 0.4787 (tpp-160)
REVERT: A  531 LEU cc_start: 0.8231 (mm) cc_final: 0.8006 (mm)
REVERT: A  532 GLU cc_start: 0.7467 (pt0) cc_final: 0.6848 (pt0)
REVERT: A  544 CYS cc_start: 0.8263 (t) cc_final: 0.7859 (t)
REVERT: A  561 MET cc_start: 0.7842 (mmm) cc_final: 0.7606 (mmm)
REVERT: A  570 LYS cc_start: 0.8261 (mttt) cc_final: 0.7839 (ttmm)
REVERT: A  576 LYS cc_start: 0.8523 (mtmt) cc_final: 0.8001 (mtmt)
REVERT: A  594 GLN cc_start: 0.8637 (tp40) cc_final: 0.8193 (tt0)
REVERT: A  600 LYS cc_start: 0.8528 (tttt) cc_final: 0.8017 (ttmm)
  outliers start: 14
  outliers final: 9
  residues processed: 173
  average time/residue: 0.0664
  time to fit residues: 13.6222
Evaluate side-chains
  178 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 166
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ARG
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  592 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0070
   overall best weight:    0.7398

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.109685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.091531 restraints weight = 8738.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.095052 restraints weight = 4891.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.097526 restraints weight = 3151.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.099231 restraints weight = 2213.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.100479 restraints weight = 1666.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3879  Z= 0.163
  Angle     :  0.576   5.990   5212  Z= 0.313
  Chirality :  0.037   0.132    563
  Planarity :  0.004   0.042    683
  Dihedral  :  4.428  35.508    515
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 26.67 %
    Favored  : 68.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.97 (0.40), residues: 473
  helix:  2.73 (0.26), residues: 402
  sheet:  None (None), residues: 0
  loop : -2.96 (0.57), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 558 
 TYR   0.014   0.002   TYR A 446 
 PHE   0.018   0.002   PHE A 338 
 TRP   0.010   0.002   TRP A 169 
 HIS   0.004   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.16 ( 3879)
  covalent geometry    : angle       0.57645 /  0.31 ( 5212)
  hydrogen bonds       : bond        0.03598 /  2.38 (  294)
  hydrogen bonds       : angle       3.57567 /  2.58 (  882)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 168
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 TYR cc_start: 0.8523 (m-80) cc_final: 0.7687 (m-80)
REVERT: A  137 TYR cc_start: 0.7848 (m-80) cc_final: 0.7249 (m-80)
REVERT: A  157 GLN cc_start: 0.8475 (pt0) cc_final: 0.7633 (pt0)
REVERT: A  159 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6966 (ttt-90)
REVERT: A  170 LYS cc_start: 0.8732 (pttt) cc_final: 0.8157 (ptmt)
REVERT: A  174 GLN cc_start: 0.8551 (mt0) cc_final: 0.8154 (mt0)
REVERT: A  178 LYS cc_start: 0.8938 (ttpt) cc_final: 0.8456 (ttpt)
REVERT: A  181 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8199 (mt-10)
REVERT: A  186 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7462 (t80)
REVERT: A  195 LYS cc_start: 0.8628 (mmtp) cc_final: 0.8079 (mttt)
REVERT: A  211 THR cc_start: 0.8707 (m) cc_final: 0.8484 (p)
REVERT: A  229 ASP cc_start: 0.7516 (t0) cc_final: 0.7255 (t0)
REVERT: A  247 ARG cc_start: 0.7640 (ttp-110) cc_final: 0.7255 (ttp-110)
REVERT: A  308 GLU cc_start: 0.6755 (mp0) cc_final: 0.6269 (mp0)
REVERT: A  354 LYS cc_start: 0.8778 (tptm) cc_final: 0.8483 (ttmm)
REVERT: A  366 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.7832 (mtm-85)
REVERT: A  370 LEU cc_start: 0.8906 (mt) cc_final: 0.8658 (mt)
REVERT: A  373 ARG cc_start: 0.8483 (ttt-90) cc_final: 0.7830 (ttt90)
REVERT: A  376 MET cc_start: 0.8007 (tmm) cc_final: 0.7540 (tmm)
REVERT: A  382 GLN cc_start: 0.7455 (tm-30) cc_final: 0.7022 (tm-30)
REVERT: A  389 ASP cc_start: 0.7619 (t0) cc_final: 0.7357 (t0)
REVERT: A  390 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.8263 (t80)
REVERT: A  407 ARG cc_start: 0.8139 (ttp-110) cc_final: 0.7485 (ttp-110)
REVERT: A  462 MET cc_start: 0.6940 (ptm) cc_final: 0.6365 (ptm)
REVERT: A  466 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8179 (mt-10)
REVERT: A  477 GLU cc_start: 0.7813 (mp0) cc_final: 0.7555 (mp0)
REVERT: A  486 LEU cc_start: 0.8363 (mt) cc_final: 0.7962 (mt)
REVERT: A  498 MET cc_start: 0.7884 (mmt) cc_final: 0.7489 (mmt)
REVERT: A  509 ASN cc_start: 0.8188 (t0) cc_final: 0.7687 (t0)
REVERT: A  529 ARG cc_start: 0.6826 (mmt180) cc_final: 0.4847 (tpp-160)
REVERT: A  531 LEU cc_start: 0.8274 (mm) cc_final: 0.8063 (mm)
REVERT: A  532 GLU cc_start: 0.7508 (pt0) cc_final: 0.6893 (pt0)
REVERT: A  544 CYS cc_start: 0.8271 (t) cc_final: 0.7928 (t)
REVERT: A  570 LYS cc_start: 0.8235 (mttt) cc_final: 0.7876 (ttmm)
  outliers start: 21
  outliers final: 14
  residues processed: 177
  average time/residue: 0.0591
  time to fit residues: 12.6604
Evaluate side-chains
  181 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ARG
Chi-restraints excluded: chain A residue  186 TYR
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  592 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.108837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.090648 restraints weight = 8858.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.094259 restraints weight = 4945.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.096740 restraints weight = 3172.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.098400 restraints weight = 2231.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.099669 restraints weight = 1690.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3879  Z= 0.163
  Angle     :  0.607   6.212   5212  Z= 0.326
  Chirality :  0.038   0.135    563
  Planarity :  0.004   0.041    683
  Dihedral  :  4.451  35.896    515
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 25.68 %
    Favored  : 69.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.83 (0.40), residues: 473
  helix:  2.65 (0.26), residues: 402
  sheet:  None (None), residues: 0
  loop : -3.14 (0.56), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 447 
 TYR   0.018   0.002   TYR A 513 
 PHE   0.015   0.001   PHE A 338 
 TRP   0.008   0.002   TRP A 169 
 HIS   0.004   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.16 ( 3879)
  covalent geometry    : angle       0.60689 /  0.33 ( 5212)
  hydrogen bonds       : bond        0.03563 /  2.35 (  294)
  hydrogen bonds       : angle       3.55973 /  2.56 (  882)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 168
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 TYR cc_start: 0.8524 (m-80) cc_final: 0.7694 (m-80)
REVERT: A  137 TYR cc_start: 0.7898 (m-80) cc_final: 0.7308 (m-80)
REVERT: A  157 GLN cc_start: 0.8488 (pt0) cc_final: 0.7624 (pt0)
REVERT: A  159 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6709 (ttt-90)
REVERT: A  163 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.7113 (m-80)
REVERT: A  170 LYS cc_start: 0.8728 (pttt) cc_final: 0.8287 (ptpt)
REVERT: A  174 GLN cc_start: 0.8576 (mt0) cc_final: 0.8143 (mt0)
REVERT: A  178 LYS cc_start: 0.8969 (ttpt) cc_final: 0.8386 (ttpt)
REVERT: A  181 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8265 (mt-10)
REVERT: A  182 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8091 (mm)
REVERT: A  186 TYR cc_start: 0.7878 (OUTLIER) cc_final: 0.7514 (t80)
REVERT: A  195 LYS cc_start: 0.8604 (mmtp) cc_final: 0.8049 (mttt)
REVERT: A  211 THR cc_start: 0.8712 (m) cc_final: 0.8446 (p)
REVERT: A  229 ASP cc_start: 0.7518 (t0) cc_final: 0.7265 (t0)
REVERT: A  247 ARG cc_start: 0.7615 (ttp-110) cc_final: 0.7279 (ttp-110)
REVERT: A  308 GLU cc_start: 0.6768 (mp0) cc_final: 0.6230 (mp0)
REVERT: A  309 ASN cc_start: 0.8131 (m-40) cc_final: 0.7895 (t0)
REVERT: A  354 LYS cc_start: 0.8767 (tptm) cc_final: 0.8478 (ttmm)
REVERT: A  370 LEU cc_start: 0.8881 (mt) cc_final: 0.8662 (mt)
REVERT: A  373 ARG cc_start: 0.8462 (ttt-90) cc_final: 0.7821 (ttt90)
REVERT: A  376 MET cc_start: 0.8038 (tmm) cc_final: 0.7551 (tmm)
REVERT: A  380 GLN cc_start: 0.8478 (tp40) cc_final: 0.8274 (tp40)
REVERT: A  382 GLN cc_start: 0.7409 (tm-30) cc_final: 0.7032 (tm-30)
REVERT: A  389 ASP cc_start: 0.7607 (t0) cc_final: 0.7360 (t0)
REVERT: A  390 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8235 (t80)
REVERT: A  407 ARG cc_start: 0.8112 (ttp-110) cc_final: 0.7452 (ttp-110)
REVERT: A  462 MET cc_start: 0.6924 (ptm) cc_final: 0.6311 (ptm)
REVERT: A  466 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8148 (mt-10)
REVERT: A  477 GLU cc_start: 0.7848 (mp0) cc_final: 0.7635 (mp0)
REVERT: A  486 LEU cc_start: 0.8361 (mt) cc_final: 0.7959 (mt)
REVERT: A  498 MET cc_start: 0.7894 (mmt) cc_final: 0.7498 (mmt)
REVERT: A  509 ASN cc_start: 0.8197 (t0) cc_final: 0.7796 (t0)
REVERT: A  529 ARG cc_start: 0.6832 (mmt180) cc_final: 0.4829 (tpp-160)
REVERT: A  531 LEU cc_start: 0.8270 (mm) cc_final: 0.8056 (mm)
REVERT: A  532 GLU cc_start: 0.7537 (pt0) cc_final: 0.6896 (pt0)
REVERT: A  539 GLU cc_start: 0.8460 (tp30) cc_final: 0.7515 (mm-30)
REVERT: A  542 ASN cc_start: 0.8648 (p0) cc_final: 0.8373 (p0)
REVERT: A  544 CYS cc_start: 0.8260 (t) cc_final: 0.7862 (t)
REVERT: A  570 LYS cc_start: 0.8253 (mttt) cc_final: 0.7842 (ttmm)
  outliers start: 21
  outliers final: 14
  residues processed: 179
  average time/residue: 0.0816
  time to fit residues: 17.4602
Evaluate side-chains
  188 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 169
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ARG
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  186 TYR
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  592 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 29 optimal weight:    8.9990
   chunk 18 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 39 optimal weight:    0.4980
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.6380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.109131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.091333 restraints weight = 8816.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.094866 restraints weight = 4889.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.097322 restraints weight = 3111.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.099019 restraints weight = 2170.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.100195 restraints weight = 1628.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3879  Z= 0.151
  Angle     :  0.630  10.218   5212  Z= 0.329
  Chirality :  0.039   0.224    563
  Planarity :  0.004   0.040    683
  Dihedral  :  4.442  35.329    515
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 27.41 %
    Favored  : 67.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.79 (0.40), residues: 473
  helix:  2.62 (0.26), residues: 402
  sheet:  None (None), residues: 0
  loop : -3.15 (0.57), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 558 
 TYR   0.014   0.001   TYR A 446 
 PHE   0.017   0.002   PHE A 472 
 TRP   0.008   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.15 ( 3879)
  covalent geometry    : angle       0.63027 /  0.33 ( 5212)
  hydrogen bonds       : bond        0.03466 /  2.27 (  294)
  hydrogen bonds       : angle       3.56780 /  2.60 (  882)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 168
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 TYR cc_start: 0.8526 (m-80) cc_final: 0.7759 (m-80)
REVERT: A  137 TYR cc_start: 0.7866 (m-80) cc_final: 0.7284 (m-80)
REVERT: A  157 GLN cc_start: 0.8461 (pt0) cc_final: 0.7570 (pt0)
REVERT: A  159 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.6660 (ttt-90)
REVERT: A  163 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7038 (m-80)
REVERT: A  170 LYS cc_start: 0.8725 (pttt) cc_final: 0.8286 (ptpt)
REVERT: A  174 GLN cc_start: 0.8544 (mt0) cc_final: 0.8118 (mt0)
REVERT: A  178 LYS cc_start: 0.8973 (ttpt) cc_final: 0.8394 (ttpt)
REVERT: A  181 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8230 (mt-10)
REVERT: A  182 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8082 (mm)
REVERT: A  186 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7471 (t80)
REVERT: A  211 THR cc_start: 0.8656 (m) cc_final: 0.8434 (p)
REVERT: A  229 ASP cc_start: 0.7497 (t0) cc_final: 0.7241 (t0)
REVERT: A  247 ARG cc_start: 0.7594 (ttp-110) cc_final: 0.7251 (ttp-110)
REVERT: A  248 GLU cc_start: 0.8122 (tp30) cc_final: 0.7540 (tp30)
REVERT: A  251 MET cc_start: 0.8007 (tpp) cc_final: 0.7790 (tpp)
REVERT: A  308 GLU cc_start: 0.6775 (mp0) cc_final: 0.6265 (mp0)
REVERT: A  354 LYS cc_start: 0.8753 (tptm) cc_final: 0.8446 (ttmm)
REVERT: A  370 LEU cc_start: 0.8914 (mt) cc_final: 0.8655 (mt)
REVERT: A  373 ARG cc_start: 0.8475 (ttt-90) cc_final: 0.7844 (ttt90)
REVERT: A  376 MET cc_start: 0.8036 (tmm) cc_final: 0.7534 (tmm)
REVERT: A  382 GLN cc_start: 0.7416 (tm-30) cc_final: 0.7020 (tm-30)
REVERT: A  389 ASP cc_start: 0.7574 (t0) cc_final: 0.7301 (t0)
REVERT: A  390 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8231 (t80)
REVERT: A  407 ARG cc_start: 0.8081 (ttp-110) cc_final: 0.7415 (ttp-110)
REVERT: A  462 MET cc_start: 0.6903 (ptm) cc_final: 0.6200 (ptm)
REVERT: A  466 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8104 (mt-10)
REVERT: A  477 GLU cc_start: 0.7847 (mp0) cc_final: 0.7633 (mp0)
REVERT: A  486 LEU cc_start: 0.8352 (mt) cc_final: 0.7948 (mt)
REVERT: A  498 MET cc_start: 0.7882 (mmt) cc_final: 0.7493 (mmt)
REVERT: A  506 GLU cc_start: 0.8399 (tp30) cc_final: 0.7990 (tp30)
REVERT: A  529 ARG cc_start: 0.6855 (mmt180) cc_final: 0.4837 (tpp-160)
REVERT: A  531 LEU cc_start: 0.8216 (mm) cc_final: 0.8001 (mm)
REVERT: A  532 GLU cc_start: 0.7520 (pt0) cc_final: 0.6937 (pt0)
REVERT: A  539 GLU cc_start: 0.8434 (tp30) cc_final: 0.7446 (mm-30)
REVERT: A  542 ASN cc_start: 0.8645 (p0) cc_final: 0.8353 (p0)
REVERT: A  544 CYS cc_start: 0.8231 (t) cc_final: 0.7833 (t)
REVERT: A  570 LYS cc_start: 0.8237 (mttt) cc_final: 0.7872 (ttmm)
  outliers start: 21
  outliers final: 14
  residues processed: 177
  average time/residue: 0.0816
  time to fit residues: 17.3114
Evaluate side-chains
  184 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ARG
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  186 TYR
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  265 THR
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  592 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 45 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   overall best weight:    0.7380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.108824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.091139 restraints weight = 8797.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.094602 restraints weight = 4851.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.096940 restraints weight = 3094.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.098647 restraints weight = 2177.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.099837 restraints weight = 1635.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3879  Z= 0.166
  Angle     :  0.642   7.357   5212  Z= 0.339
  Chirality :  0.039   0.178    563
  Planarity :  0.004   0.042    683
  Dihedral  :  4.475  35.094    515
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 27.90 %
    Favored  : 66.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.71 (0.40), residues: 473
  helix:  2.57 (0.26), residues: 402
  sheet:  None (None), residues: 0
  loop : -3.18 (0.58), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 558 
 TYR   0.015   0.002   TYR A 446 
 PHE   0.011   0.001   PHE A 338 
 TRP   0.007   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.17 ( 3879)
  covalent geometry    : angle       0.64214 /  0.34 ( 5212)
  hydrogen bonds       : bond        0.03662 /  2.39 (  294)
  hydrogen bonds       : angle       3.63940 /  2.64 (  882)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 162
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 TYR cc_start: 0.8530 (m-80) cc_final: 0.7892 (m-80)
REVERT: A  137 TYR cc_start: 0.7897 (m-80) cc_final: 0.7424 (m-80)
REVERT: A  157 GLN cc_start: 0.8493 (pt0) cc_final: 0.7578 (pt0)
REVERT: A  159 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.6688 (ttt-90)
REVERT: A  163 PHE cc_start: 0.7579 (OUTLIER) cc_final: 0.7074 (m-80)
REVERT: A  170 LYS cc_start: 0.8726 (pttt) cc_final: 0.8284 (ptpt)
REVERT: A  174 GLN cc_start: 0.8556 (mt0) cc_final: 0.8132 (mt0)
REVERT: A  178 LYS cc_start: 0.8972 (ttpt) cc_final: 0.8387 (ttpt)
REVERT: A  181 GLU cc_start: 0.8476 (mt-10) cc_final: 0.8208 (mt-10)
REVERT: A  182 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8100 (mm)
REVERT: A  186 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7480 (t80)
REVERT: A  205 GLU cc_start: 0.7793 (mp0) cc_final: 0.7400 (mp0)
REVERT: A  211 THR cc_start: 0.8667 (m) cc_final: 0.8455 (p)
REVERT: A  229 ASP cc_start: 0.7505 (t0) cc_final: 0.7253 (t0)
REVERT: A  247 ARG cc_start: 0.7548 (ttp-110) cc_final: 0.7199 (ttp-110)
REVERT: A  251 MET cc_start: 0.7996 (tpp) cc_final: 0.7790 (tpp)
REVERT: A  308 GLU cc_start: 0.6778 (mp0) cc_final: 0.6228 (mp0)
REVERT: A  309 ASN cc_start: 0.8208 (m-40) cc_final: 0.7945 (t0)
REVERT: A  354 LYS cc_start: 0.8739 (tptm) cc_final: 0.8440 (ttmm)
REVERT: A  366 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.7843 (mtm-85)
REVERT: A  370 LEU cc_start: 0.8885 (mt) cc_final: 0.8652 (mt)
REVERT: A  373 ARG cc_start: 0.8476 (ttt-90) cc_final: 0.7839 (ttt90)
REVERT: A  376 MET cc_start: 0.8042 (tmm) cc_final: 0.7546 (tmm)
REVERT: A  382 GLN cc_start: 0.7438 (tm-30) cc_final: 0.7043 (tm-30)
REVERT: A  389 ASP cc_start: 0.7581 (t0) cc_final: 0.7318 (t0)
REVERT: A  390 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.8258 (t80)
REVERT: A  391 ASN cc_start: 0.8409 (t0) cc_final: 0.8157 (t0)
REVERT: A  407 ARG cc_start: 0.8096 (ttp-110) cc_final: 0.7432 (ttp-110)
REVERT: A  462 MET cc_start: 0.6879 (ptm) cc_final: 0.6455 (ptm)
REVERT: A  466 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8051 (mt-10)
REVERT: A  486 LEU cc_start: 0.8345 (mt) cc_final: 0.7954 (mt)
REVERT: A  498 MET cc_start: 0.7892 (mmt) cc_final: 0.7495 (mmt)
REVERT: A  506 GLU cc_start: 0.8420 (tp30) cc_final: 0.7914 (tp30)
REVERT: A  529 ARG cc_start: 0.6886 (mmt180) cc_final: 0.4856 (tpp-160)
REVERT: A  531 LEU cc_start: 0.8225 (mm) cc_final: 0.8009 (mm)
REVERT: A  532 GLU cc_start: 0.7533 (pt0) cc_final: 0.6938 (pt0)
REVERT: A  539 GLU cc_start: 0.8445 (tp30) cc_final: 0.7436 (mm-30)
REVERT: A  544 CYS cc_start: 0.8240 (t) cc_final: 0.7881 (t)
REVERT: A  570 LYS cc_start: 0.8244 (mttt) cc_final: 0.7836 (ttmm)
REVERT: A  589 ASP cc_start: 0.7982 (t0) cc_final: 0.7601 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 172
  average time/residue: 0.0877
  time to fit residues: 17.9251
Evaluate side-chains
  186 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 ARG
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  186 TYR
Chi-restraints excluded: chain A residue  225 MET
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  245 LYS
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  592 HIS
Chi-restraints excluded: chain A residue  595 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0970
   chunk 29 optimal weight:    0.1980
   chunk 3 optimal weight:    0.0000
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.3582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 459 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.110804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.092797 restraints weight = 8804.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.096403 restraints weight = 4904.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.098869 restraints weight = 3162.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.100520 restraints weight = 2235.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.101821 restraints weight = 1702.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3879  Z= 0.127
  Angle     :  0.617   7.157   5212  Z= 0.324
  Chirality :  0.037   0.152    563
  Planarity :  0.004   0.037    683
  Dihedral  :  4.282  29.792    515
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 29.38 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.79 (0.40), residues: 473
  helix:  2.61 (0.26), residues: 403
  sheet:  None (None), residues: 0
  loop : -3.13 (0.59), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 558 
 TYR   0.016   0.001   TYR A 298 
 PHE   0.020   0.001   PHE A 472 
 TRP   0.006   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00290 /  0.13 ( 3879)
  covalent geometry    : angle       0.61666 /  0.32 ( 5212)
  hydrogen bonds       : bond        0.03031 /  1.96 (  294)
  hydrogen bonds       : angle       3.39968 /  2.48 (  882)

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

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

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  946 Ramachandran restraints generated.
    473 Oldfield, 0 Emsley, 473 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 169
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 TYR cc_start: 0.8504 (m-80) cc_final: 0.7957 (m-80)
REVERT: A  137 TYR cc_start: 0.7905 (m-80) cc_final: 0.7409 (m-80)
REVERT: A  157 GLN cc_start: 0.8513 (pt0) cc_final: 0.7500 (pt0)
REVERT: A  163 PHE cc_start: 0.7525 (OUTLIER) cc_final: 0.7208 (m-80)
REVERT: A  170 LYS cc_start: 0.8691 (pttt) cc_final: 0.8273 (ptpt)
REVERT: A  174 GLN cc_start: 0.8558 (mt0) cc_final: 0.8115 (mt0)
REVERT: A  178 LYS cc_start: 0.8955 (ttpt) cc_final: 0.8304 (ttpt)
REVERT: A  181 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8233 (mt-10)
REVERT: A  182 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8085 (mm)
REVERT: A  186 TYR cc_start: 0.7799 (OUTLIER) cc_final: 0.7469 (t80)
REVERT: A  192 ARG cc_start: 0.7897 (ttm110) cc_final: 0.7350 (mtp-110)
REVERT: A  211 THR cc_start: 0.8631 (m) cc_final: 0.8398 (p)
REVERT: A  229 ASP cc_start: 0.7484 (t0) cc_final: 0.7220 (t0)
REVERT: A  247 ARG cc_start: 0.7539 (ttp-110) cc_final: 0.7187 (ttp-110)
REVERT: A  308 GLU cc_start: 0.6665 (mp0) cc_final: 0.6118 (mp0)
REVERT: A  354 LYS cc_start: 0.8693 (tptm) cc_final: 0.8401 (ttmm)
REVERT: A  366 ARG cc_start: 0.8383 (mtm-85) cc_final: 0.7841 (mtm-85)
REVERT: A  370 LEU cc_start: 0.8874 (mt) cc_final: 0.8621 (mt)
REVERT: A  376 MET cc_start: 0.8042 (tmm) cc_final: 0.7527 (tmm)
REVERT: A  382 GLN cc_start: 0.7435 (tm-30) cc_final: 0.7016 (tm-30)
REVERT: A  389 ASP cc_start: 0.7545 (t0) cc_final: 0.7258 (t0)
REVERT: A  390 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.8244 (t80)
REVERT: A  407 ARG cc_start: 0.7961 (ttp-110) cc_final: 0.7308 (ttp-110)
REVERT: A  459 GLN cc_start: 0.8588 (mm110) cc_final: 0.8103 (mm-40)
REVERT: A  462 MET cc_start: 0.6895 (ptm) cc_final: 0.6195 (ptm)
REVERT: A  466 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8065 (mt-10)
REVERT: A  486 LEU cc_start: 0.8304 (mt) cc_final: 0.7890 (mt)
REVERT: A  497 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7850 (mt-10)
REVERT: A  498 MET cc_start: 0.7860 (mmt) cc_final: 0.7485 (mmt)
REVERT: A  506 GLU cc_start: 0.8353 (tp30) cc_final: 0.7740 (tp30)
REVERT: A  529 ARG cc_start: 0.6836 (mmt180) cc_final: 0.4798 (tpp-160)
REVERT: A  531 LEU cc_start: 0.8149 (mm) cc_final: 0.7935 (mm)
REVERT: A  532 GLU cc_start: 0.7483 (pt0) cc_final: 0.6891 (pt0)
REVERT: A  539 GLU cc_start: 0.8345 (tp30) cc_final: 0.7386 (mm-30)
REVERT: A  542 ASN cc_start: 0.8617 (p0) cc_final: 0.8313 (p0)
REVERT: A  544 CYS cc_start: 0.8180 (t) cc_final: 0.7789 (t)
REVERT: A  570 LYS cc_start: 0.8229 (mttt) cc_final: 0.7855 (ttmm)
REVERT: A  585 TYR cc_start: 0.7987 (m-80) cc_final: 0.7694 (m-80)
  outliers start: 16
  outliers final: 10
  residues processed: 175
  average time/residue: 0.0800
  time to fit residues: 16.7495
Evaluate side-chains
  179 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 165
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 PHE
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  186 TYR
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  257 ILE
Chi-restraints excluded: chain A residue  339 TYR
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain A residue  390 PHE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  415 ASP
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  592 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 47
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 3 optimal weight:    0.3980
   chunk 36 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 25 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.6580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.109406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.091561 restraints weight = 8837.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.095098 restraints weight = 4906.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.097470 restraints weight = 3139.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.099088 restraints weight = 2219.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.100351 restraints weight = 1690.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3879  Z= 0.157
  Angle     :  0.658   9.048   5212  Z= 0.343
  Chirality :  0.038   0.145    563
  Planarity :  0.004   0.041    683
  Dihedral  :  4.289  28.423    515
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 29.88 %
    Favored  : 66.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.72 (0.40), residues: 473
  helix:  2.57 (0.26), residues: 403
  sheet:  None (None), residues: 0
  loop : -3.20 (0.58), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 247 
 TYR   0.017   0.002   TYR A 327 
 PHE   0.011   0.001   PHE A 338 
 TRP   0.007   0.001   TRP A 169 
 HIS   0.004   0.001   HIS A 406 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.16 ( 3879)
  covalent geometry    : angle       0.65824 /  0.34 ( 5212)
  hydrogen bonds       : bond        0.03462 /  2.25 (  294)
  hydrogen bonds       : angle       3.56793 /  2.60 (  882)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 804.54 seconds
wall clock time: 14 minutes 33.08 seconds (873.08 seconds total)