Starting phenix.real_space_refine
on Fri Aug 22 13:23:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zpp_60351/08_2025/8zpp_60351.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zpp_60351/08_2025/8zpp_60351.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zpp_60351/08_2025/8zpp_60351.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zpp_60351/08_2025/8zpp_60351.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zpp_60351/08_2025/8zpp_60351.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zpp_60351/08_2025/8zpp_60351.map"
  }
  resolution = 3.6
  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=   0.051
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      16      5.16       5
     C    2082      2.51       5
     N     540      2.21       5
     O     628      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3266
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1532
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 192, 1532
          Classifications: {'peptide': 192}
          Link IDs: {'PTRANS': 11, 'TRANS': 180}
    Chain: "H"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 928
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 3, 'TRANS': 115}
    Chain: "L"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 806
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 6, 'TRANS': 101}
  Time building chain proxies: 1.16, per 1000 atoms: 0.36
  Number of scatterers: 3266
  At special positions: 0
  Unit cell: (70.3, 68.4, 95, 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      16     16.00
     O     628      8.00
     N     540      7.00
     C    2082      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  89 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.28
  Conformation dependent library (CDL) restraints added in 108.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  760

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 7 sheets defined
      11.2% alpha, 33.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 365 through 372
      removed outlier: 4.076A  pdb=" N   TYR A 369 " --> pdb=" O   TYR A 365 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ASN A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ALA A 372 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 407
      No H-bonds generated for 'chain 'A' and resid 405 through 407'
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 438 through 443
      removed outlier: 3.521A  pdb=" N   SER A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 30 through 32
      No H-bonds generated for 'chain 'L' and resid 30 through 32'
    Processing helix  chain 'L' and resid 80 through 84
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.623A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.726A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   LYS H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   TRP H  47 " --> pdb=" O   LYS H  38 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.893A  pdb=" N   TYR H 109 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 6
      removed outlier: 5.524A  pdb=" N   THR L  70 " --> pdb=" O   VAL L  25 " (cutoff:3.500A)
      removed outlier: 10.577A  pdb=" N   SER L  27 " --> pdb=" O   SER L  68 " (cutoff:3.500A)
      removed outlier: 10.555A  pdb=" N   SER L  68 " --> pdb=" O   SER L  27 " (cutoff:3.500A)
      removed outlier: 10.911A  pdb=" N   ILE L  29 " --> pdb=" O   SER L  66 " (cutoff:3.500A)
      removed outlier: 11.591A  pdb=" N   SER L  66 " --> pdb=" O   ILE L  29 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 5.525A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 106 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   TYR L  87 " --> pdb=" O   THR L 103 " (cutoff:3.500A)
      removed outlier: 5.499A  pdb=" N   GLN L  38 " --> pdb=" O   PRO L  47 " (cutoff:3.500A)

    95 hydrogen bonds defined for protein.
    225 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: 0.31

  Time building geometry restraints manager: 0.36 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: 1022
        1.34 -     1.46: 775
        1.46 -     1.57: 1539
        1.57 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 3356
  Sorted by residual:
  bond pdb=" CG  MET L  79 "
       pdb=" SD  MET L  79 "
    ideal  model  delta    sigma   weight residual
    1.803  1.707  0.096 2.50e-02 1.60e+03 1.48e+01
  bond pdb=" SD  MET L  79 "
       pdb=" CE  MET L  79 "
    ideal  model  delta    sigma   weight residual
    1.791  1.697  0.094 2.50e-02 1.60e+03 1.43e+01
  bond pdb=" CG  LEU H  70 "
       pdb=" CD2 LEU H  70 "
    ideal  model  delta    sigma   weight residual
    1.521  1.400  0.121 3.30e-02 9.18e+02 1.34e+01
  bond pdb=" CA  LEU H  70 "
       pdb=" C   LEU H  70 "
    ideal  model  delta    sigma   weight residual
    1.524  1.559 -0.035 1.23e-02 6.61e+03 8.19e+00
  bond pdb=" C   MET L  11 "
       pdb=" N   ALA L  12 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.32e-02 5.74e+03 6.61e+00
  ... (remaining 3351 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 4251
        1.28 -     2.55: 243
        2.55 -     3.83: 42
        3.83 -     5.11: 18
        5.11 -     6.39: 8
  Bond angle restraints: 4562
  Sorted by residual:
  angle pdb=" N   LEU H  70 "
        pdb=" CA  LEU H  70 "
        pdb=" C   LEU H  70 "
      ideal   model   delta    sigma   weight residual
     108.73  114.63   -5.90 1.63e+00 3.76e-01 1.31e+01
  angle pdb=" C   VAL A 486 "
        pdb=" N   ASN A 487 "
        pdb=" CA  ASN A 487 "
      ideal   model   delta    sigma   weight residual
     121.54  127.93   -6.39 1.91e+00 2.74e-01 1.12e+01
  angle pdb=" C   PRO H  53 "
        pdb=" CA  PRO H  53 "
        pdb=" CB  PRO H  53 "
      ideal   model   delta    sigma   weight residual
     111.85  115.90   -4.05 1.42e+00 4.96e-01 8.14e+00
  angle pdb=" CA  TYR L  95 "
        pdb=" CB  TYR L  95 "
        pdb=" CG  TYR L  95 "
      ideal   model   delta    sigma   weight residual
     113.90  109.00    4.90 1.80e+00 3.09e-01 7.43e+00
  angle pdb=" C   PHE A 371 "
        pdb=" N   ALA A 372 "
        pdb=" CA  ALA A 372 "
      ideal   model   delta    sigma   weight residual
     123.11  118.40    4.71 1.79e+00 3.12e-01 6.93e+00
  ... (remaining 4557 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.81: 1794
       16.81 -    33.63: 123
       33.63 -    50.44: 35
       50.44 -    67.25: 4
       67.25 -    84.06: 1
  Dihedral angle restraints: 1957
    sinusoidal: 750
      harmonic: 1207
  Sorted by residual:
  dihedral pdb=" CA  GLY L  94 "
           pdb=" C   GLY L  94 "
           pdb=" N   TYR L  95 "
           pdb=" CA  TYR L  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.22  -21.78     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  PHE A 490 "
           pdb=" C   PHE A 490 "
           pdb=" N   PRO A 491 "
           pdb=" CA  PRO A 491 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.87  -18.13     0      5.00e+00 4.00e-02 1.31e+01
  dihedral pdb=" CA  LEU A 461 "
           pdb=" C   LEU A 461 "
           pdb=" N   LYS A 462 "
           pdb=" CA  LYS A 462 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.09   17.91     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 1954 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 409
       0.069 -    0.139: 63
       0.139 -    0.208: 2
       0.208 -    0.278: 2
       0.278 -    0.347: 2
  Chirality restraints: 478
  Sorted by residual:
  chirality pdb=" CG  LEU H  70 "
            pdb=" CB  LEU H  70 "
            pdb=" CD1 LEU H  70 "
            pdb=" CD2 LEU H  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" CA  PRO H  53 "
            pdb=" N   PRO H  53 "
            pdb=" C   PRO H  53 "
            pdb=" CB  PRO H  53 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.43    0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  THR H  71 "
            pdb=" N   THR H  71 "
            pdb=" C   THR H  71 "
            pdb=" CB  THR H  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.26 2.00e-01 2.50e+01 1.74e+00
  ... (remaining 475 not shown)

  Planarity restraints: 589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 429 "    0.014 2.00e-02 2.50e+03   1.00e-02 1.75e+00
        pdb=" CG  PHE A 429 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 429 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 429 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 429 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 429 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 429 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 524 "    0.007 2.00e-02 2.50e+03   1.30e-02 1.68e+00
        pdb=" C   VAL A 524 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   VAL A 524 "    0.008 2.00e-02 2.50e+03
        pdb=" N   CYS A 525 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR L  95 "    0.010 2.00e-02 2.50e+03   7.59e-03 1.15e+00
        pdb=" CG  TYR L  95 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD1 TYR L  95 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR L  95 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR L  95 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR L  95 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR L  95 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR L  95 "    0.001 2.00e-02 2.50e+03
  ... (remaining 586 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 737
        2.77 -     3.30: 3078
        3.30 -     3.84: 5522
        3.84 -     4.37: 6617
        4.37 -     4.90: 11471
  Nonbonded interactions: 27425
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 398 "
            pdb=" OH  TYR A 423 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   ASP L  83 "
            pdb=" OH  TYR L  87 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OD2 ASP H  73 "
            pdb=" N   SER H  76 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" O   ILE L  29 "
            pdb=" OH  TYR L  72 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   GLY L  51 "
            pdb=" OG1 THR L  52 "
     model   vdw
     2.317 3.040
  ... (remaining 27420 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:             6.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.760
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.121   3362  Z= 0.349
  Angle     :  0.754   6.386   4574  Z= 0.412
  Chirality :  0.052   0.347    478
  Planarity :  0.004   0.032    589
  Dihedral  : 12.662  84.065   1179
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.25 %
    Favored  : 87.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.42), residues: 413
  helix: -3.07 (0.75), residues: 27
  sheet: -0.13 (0.40), residues: 172
  loop :  0.39 (0.44), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG L  62 
 TYR   0.018   0.002   TYR L  95 
 PHE   0.022   0.002   PHE A 429 
 TRP   0.012   0.002   TRP H  47 
 HIS   0.004   0.002   HIS L  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00794 ( 3356)
  covalent geometry    : angle       0.75361 ( 4562)
  SS BOND              : bond        0.00146 (    6)
  SS BOND              : angle       0.74032 (   12)
  hydrogen bonds       : bond        0.28071 (   90)
  hydrogen bonds       : angle      10.44505 (  225)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.075 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8881 (tppp) cc_final: 0.8149 (tptp)
REVERT: A  455 LEU cc_start: 0.9002 (tp) cc_final: 0.8711 (tp)
REVERT: A  523 THR cc_start: 0.8257 (p) cc_final: 0.7957 (p)
REVERT: H    3 GLN cc_start: 0.8447 (pp30) cc_final: 0.8028 (pp30)
REVERT: H  114 THR cc_start: 0.9027 (m) cc_final: 0.8513 (m)
REVERT: L  104 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8423 (ttpp)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0602
  time to fit residues: 8.1458
Evaluate side-chains
  93 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.1980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    0.1980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
H  50 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.153582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.135772 restraints weight = 4616.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.139362 restraints weight = 2555.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.141586 restraints weight = 1670.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.143415 restraints weight = 1236.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.144581 restraints weight = 965.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3362  Z= 0.165
  Angle     :  0.641   5.856   4574  Z= 0.345
  Chirality :  0.048   0.177    478
  Planarity :  0.004   0.033    589
  Dihedral  :  5.378  26.087    462
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 19.94 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.16 (0.43), residues: 413
  helix: -2.68 (0.87), residues: 21
  sheet: -0.19 (0.40), residues: 172
  loop :  0.43 (0.44), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 457 
 TYR   0.013   0.001   TYR H  32 
 PHE   0.019   0.002   PHE H  64 
 TRP   0.012   0.002   TRP A 436 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3356)
  covalent geometry    : angle       0.63739 ( 4562)
  SS BOND              : bond        0.00182 (    6)
  SS BOND              : angle       1.40422 (   12)
  hydrogen bonds       : bond        0.04707 (   90)
  hydrogen bonds       : angle       7.18546 (  225)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8906 (tppp) cc_final: 0.8247 (tptp)
REVERT: A  523 THR cc_start: 0.7965 (p) cc_final: 0.7727 (p)
REVERT: H    3 GLN cc_start: 0.8216 (pp30) cc_final: 0.7696 (pp30)
REVERT: H    6 GLN cc_start: 0.8086 (tt0) cc_final: 0.7800 (tt0)
REVERT: H   46 GLU cc_start: 0.8029 (pt0) cc_final: 0.7810 (pt0)
REVERT: H  112 GLN cc_start: 0.8282 (pm20) cc_final: 0.8044 (pm20)
REVERT: H  114 THR cc_start: 0.9034 (m) cc_final: 0.8492 (m)
  outliers start: 9
  outliers final: 5
  residues processed: 112
  average time/residue: 0.0532
  time to fit residues: 7.0537
Evaluate side-chains
  101 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   71 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   28 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN
H  39 GLN
L  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.151929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.133929 restraints weight = 4628.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.137482 restraints weight = 2556.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.139953 restraints weight = 1678.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.141613 restraints weight = 1227.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.142685 restraints weight = 968.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   3362  Z= 0.248
  Angle     :  0.666   5.813   4574  Z= 0.355
  Chirality :  0.048   0.154    478
  Planarity :  0.004   0.038    589
  Dihedral  :  5.406  19.713    462
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 22.51 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.43), residues: 413
  helix: -2.57 (0.92), residues: 21
  sheet: -0.40 (0.40), residues: 173
  loop :  0.27 (0.45), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 357 
 TYR   0.017   0.002   TYR H 106 
 PHE   0.014   0.001   PHE A 429 
 TRP   0.012   0.002   TRP H  47 
 HIS   0.002   0.001   HIS L  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 3356)
  covalent geometry    : angle       0.66386 ( 4562)
  SS BOND              : bond        0.00301 (    6)
  SS BOND              : angle       1.30969 (   12)
  hydrogen bonds       : bond        0.04436 (   90)
  hydrogen bonds       : angle       7.10410 (  225)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8983 (tppp) cc_final: 0.8305 (tptp)
REVERT: A  420 ASP cc_start: 0.8443 (m-30) cc_final: 0.8227 (m-30)
REVERT: A  466 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.6844 (ttt180)
REVERT: A  523 THR cc_start: 0.8247 (p) cc_final: 0.7990 (p)
REVERT: H    3 GLN cc_start: 0.8158 (pp30) cc_final: 0.7850 (pp30)
REVERT: H    6 GLN cc_start: 0.8318 (tt0) cc_final: 0.8041 (tt0)
REVERT: H   38 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7737 (ttmm)
REVERT: H   46 GLU cc_start: 0.8096 (pt0) cc_final: 0.7871 (pt0)
REVERT: H  112 GLN cc_start: 0.8284 (pm20) cc_final: 0.8045 (pm20)
REVERT: H  114 THR cc_start: 0.9048 (m) cc_final: 0.8690 (m)
  outliers start: 14
  outliers final: 12
  residues processed: 102
  average time/residue: 0.0568
  time to fit residues: 6.8682
Evaluate side-chains
  105 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  448 ASN
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   38 LYS
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   93 VAL
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   98 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    0.1980
   chunk 38 optimal weight:    0.5980
   chunk 34 optimal weight:    0.0670
   chunk 37 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 14 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.4518

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN
H  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.152384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.134744 restraints weight = 4671.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.138290 restraints weight = 2574.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.140598 restraints weight = 1689.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.142256 restraints weight = 1243.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.143277 restraints weight = 985.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3362  Z= 0.161
  Angle     :  0.583   5.968   4574  Z= 0.312
  Chirality :  0.045   0.141    478
  Planarity :  0.004   0.035    589
  Dihedral  :  5.136  19.449    462
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 23.36 %
    Favored  : 73.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.42), residues: 413
  helix: -1.47 (1.42), residues: 13
  sheet: -0.38 (0.39), residues: 171
  loop :  0.20 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 357 
 TYR   0.014   0.001   TYR A 365 
 PHE   0.011   0.001   PHE A 377 
 TRP   0.011   0.002   TRP H  47 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3356)
  covalent geometry    : angle       0.58212 ( 4562)
  SS BOND              : bond        0.00274 (    6)
  SS BOND              : angle       0.96347 (   12)
  hydrogen bonds       : bond        0.03599 (   90)
  hydrogen bonds       : angle       6.66384 (  225)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8960 (tppp) cc_final: 0.8296 (tptp)
REVERT: A  420 ASP cc_start: 0.8459 (m-30) cc_final: 0.8231 (m-30)
REVERT: A  523 THR cc_start: 0.8077 (p) cc_final: 0.7823 (p)
REVERT: H    6 GLN cc_start: 0.8214 (tt0) cc_final: 0.7950 (tt0)
REVERT: H   34 MET cc_start: 0.7968 (tpt) cc_final: 0.7350 (tpt)
REVERT: H   46 GLU cc_start: 0.8127 (pt0) cc_final: 0.7881 (pt0)
REVERT: H  114 THR cc_start: 0.9014 (m) cc_final: 0.8624 (m)
  outliers start: 10
  outliers final: 8
  residues processed: 104
  average time/residue: 0.0555
  time to fit residues: 6.9805
Evaluate side-chains
  105 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   76 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 3 optimal weight:    0.0670
   chunk 7 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 30 optimal weight:    0.2980
   chunk 5 optimal weight:    0.0170
   chunk 20 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.3356

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 460 ASN
A 493 GLN
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   1 GLN
H  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.153751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.135065 restraints weight = 4667.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.138744 restraints weight = 2571.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.141266 restraints weight = 1687.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.143017 restraints weight = 1238.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.144094 restraints weight = 983.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3362  Z= 0.138
  Angle     :  0.591   6.017   4574  Z= 0.309
  Chirality :  0.045   0.137    478
  Planarity :  0.004   0.034    589
  Dihedral  :  4.961  18.784    462
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 23.08 %
    Favored  : 72.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.43), residues: 413
  helix: -1.37 (1.45), residues: 13
  sheet: -0.34 (0.39), residues: 171
  loop :  0.20 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 357 
 TYR   0.013   0.001   TYR L  50 
 PHE   0.012   0.001   PHE A 377 
 TRP   0.011   0.001   TRP H 110 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3356)
  covalent geometry    : angle       0.58980 ( 4562)
  SS BOND              : bond        0.00241 (    6)
  SS BOND              : angle       0.81470 (   12)
  hydrogen bonds       : bond        0.03357 (   90)
  hydrogen bonds       : angle       6.24242 (  225)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8951 (tppp) cc_final: 0.8244 (tptp)
REVERT: A  462 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7599 (ttpp)
REVERT: A  466 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6681 (ttt180)
REVERT: A  523 THR cc_start: 0.8054 (p) cc_final: 0.7790 (p)
REVERT: H    3 GLN cc_start: 0.8108 (pp30) cc_final: 0.7727 (pp30)
REVERT: H   34 MET cc_start: 0.8029 (tpt) cc_final: 0.7425 (tpt)
REVERT: L  104 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8341 (ttpt)
  outliers start: 16
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0660
  time to fit residues: 8.2885
Evaluate side-chains
  109 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  448 ASN
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  466 ARG
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   76 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0870
   chunk 7 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 460 ASN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   1 GLN
H  31 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.151498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.132549 restraints weight = 4707.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.136227 restraints weight = 2621.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.138474 restraints weight = 1731.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.140391 restraints weight = 1299.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.141494 restraints weight = 1028.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   3362  Z= 0.204
  Angle     :  0.637   6.033   4574  Z= 0.331
  Chirality :  0.046   0.146    478
  Planarity :  0.004   0.034    589
  Dihedral  :  5.176  18.832    462
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 25.07 %
    Favored  : 70.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.43), residues: 413
  helix: -1.61 (1.36), residues: 13
  sheet: -0.44 (0.39), residues: 171
  loop :  0.19 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 357 
 TYR   0.014   0.002   TYR L  50 
 PHE   0.011   0.001   PHE A 429 
 TRP   0.020   0.002   TRP A 353 
 HIS   0.002   0.001   HIS L  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 3356)
  covalent geometry    : angle       0.63673 ( 4562)
  SS BOND              : bond        0.00214 (    6)
  SS BOND              : angle       0.82564 (   12)
  hydrogen bonds       : bond        0.03498 (   90)
  hydrogen bonds       : angle       6.39789 (  225)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8969 (tppp) cc_final: 0.8244 (tptp)
REVERT: A  420 ASP cc_start: 0.8514 (m-30) cc_final: 0.8289 (m-30)
REVERT: A  523 THR cc_start: 0.8207 (p) cc_final: 0.7921 (p)
REVERT: H    3 GLN cc_start: 0.8081 (pp30) cc_final: 0.7684 (pp30)
REVERT: L  104 LYS cc_start: 0.8635 (ttpp) cc_final: 0.8397 (ttpt)
  outliers start: 17
  outliers final: 13
  residues processed: 104
  average time/residue: 0.0596
  time to fit residues: 7.4061
Evaluate side-chains
  107 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  448 ASN
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   45 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   76 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0770
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   1 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.152727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.133718 restraints weight = 4780.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.137288 restraints weight = 2694.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.139825 restraints weight = 1805.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.141493 restraints weight = 1338.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.142588 restraints weight = 1076.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.3724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3362  Z= 0.178
  Angle     :  0.625   6.249   4574  Z= 0.329
  Chirality :  0.046   0.143    478
  Planarity :  0.004   0.034    589
  Dihedral  :  5.040  18.440    462
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 25.64 %
    Favored  : 70.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.43), residues: 413
  helix: -1.68 (1.34), residues: 13
  sheet: -0.52 (0.39), residues: 171
  loop :  0.19 (0.44), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 357 
 TYR   0.014   0.001   TYR L  50 
 PHE   0.019   0.002   PHE H  64 
 TRP   0.016   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 3356)
  covalent geometry    : angle       0.62438 ( 4562)
  SS BOND              : bond        0.00365 (    6)
  SS BOND              : angle       0.74821 (   12)
  hydrogen bonds       : bond        0.03227 (   90)
  hydrogen bonds       : angle       6.24644 (  225)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8959 (tppp) cc_final: 0.8246 (tptp)
REVERT: A  462 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7690 (ttpp)
REVERT: A  523 THR cc_start: 0.8194 (p) cc_final: 0.7928 (p)
REVERT: H    3 GLN cc_start: 0.8118 (pp30) cc_final: 0.7696 (pp30)
REVERT: H   34 MET cc_start: 0.8163 (tpt) cc_final: 0.7563 (tpt)
REVERT: L  104 LYS cc_start: 0.8601 (ttpp) cc_final: 0.8357 (ttpt)
  outliers start: 14
  outliers final: 11
  residues processed: 104
  average time/residue: 0.0558
  time to fit residues: 6.9869
Evaluate side-chains
  103 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   76 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 18 optimal weight:    0.2980
   chunk 10 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 31 optimal weight:    0.1980
   chunk 34 optimal weight:    0.0000
   chunk 6 optimal weight:    0.5980
   chunk 9 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 38 optimal weight:    0.4980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.155964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.137922 restraints weight = 4725.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.141562 restraints weight = 2582.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.144044 restraints weight = 1689.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.145855 restraints weight = 1233.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.146730 restraints weight = 963.088|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.3988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3362  Z= 0.135
  Angle     :  0.600   6.307   4574  Z= 0.314
  Chirality :  0.045   0.141    478
  Planarity :  0.004   0.033    589
  Dihedral  :  4.840  17.346    462
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 26.50 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.43), residues: 413
  helix: -1.59 (1.35), residues: 13
  sheet: -0.49 (0.39), residues: 171
  loop :  0.22 (0.45), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 357 
 TYR   0.020   0.001   TYR A 473 
 PHE   0.010   0.001   PHE A 374 
 TRP   0.014   0.001   TRP A 353 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3356)
  covalent geometry    : angle       0.59975 ( 4562)
  SS BOND              : bond        0.00253 (    6)
  SS BOND              : angle       0.73754 (   12)
  hydrogen bonds       : bond        0.03013 (   90)
  hydrogen bonds       : angle       6.08356 (  225)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8944 (tppp) cc_final: 0.8251 (tptp)
REVERT: A  462 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7650 (ttpp)
REVERT: A  523 THR cc_start: 0.8131 (p) cc_final: 0.7866 (p)
REVERT: H    3 GLN cc_start: 0.8049 (pp30) cc_final: 0.7785 (pp30)
REVERT: L  104 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8321 (ttpt)
  outliers start: 13
  outliers final: 9
  residues processed: 104
  average time/residue: 0.0582
  time to fit residues: 7.2690
Evaluate side-chains
  104 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   76 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0970
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 5 optimal weight:    0.3980
   chunk 30 optimal weight:    0.6980
   chunk 31 optimal weight:    0.3980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.154435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.135520 restraints weight = 4769.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.139182 restraints weight = 2661.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.141766 restraints weight = 1758.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.143273 restraints weight = 1290.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.144662 restraints weight = 1041.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7579
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3362  Z= 0.161
  Angle     :  0.639   6.506   4574  Z= 0.332
  Chirality :  0.046   0.142    478
  Planarity :  0.004   0.033    589
  Dihedral  :  4.977  17.080    462
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 26.50 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.42 (0.43), residues: 413
  helix: -1.92 (1.22), residues: 13
  sheet: -0.55 (0.40), residues: 170
  loop :  0.21 (0.45), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 357 
 TYR   0.018   0.001   TYR A 473 
 PHE   0.016   0.001   PHE A 374 
 TRP   0.013   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 3356)
  covalent geometry    : angle       0.63874 ( 4562)
  SS BOND              : bond        0.00257 (    6)
  SS BOND              : angle       0.79101 (   12)
  hydrogen bonds       : bond        0.03084 (   90)
  hydrogen bonds       : angle       6.05825 (  225)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8948 (tppp) cc_final: 0.8213 (tptp)
REVERT: A  462 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7679 (ttpp)
REVERT: A  523 THR cc_start: 0.8228 (p) cc_final: 0.7943 (p)
REVERT: L  104 LYS cc_start: 0.8608 (ttpp) cc_final: 0.8347 (ttpt)
  outliers start: 13
  outliers final: 11
  residues processed: 101
  average time/residue: 0.0701
  time to fit residues: 8.4445
Evaluate side-chains
  105 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain A residue  500 THR
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   76 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0870
   chunk 9 optimal weight:    0.0670
   chunk 4 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0010
   chunk 2 optimal weight:    0.3980
   chunk 13 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.2302

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  31 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.154557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.134391 restraints weight = 4702.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.138235 restraints weight = 2657.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.140849 restraints weight = 1776.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.142534 restraints weight = 1315.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.144008 restraints weight = 1060.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3362  Z= 0.126
  Angle     :  0.614   6.428   4574  Z= 0.320
  Chirality :  0.045   0.146    478
  Planarity :  0.004   0.032    589
  Dihedral  :  4.761  16.776    462
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 28.21 %
    Favored  : 68.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.43), residues: 413
  helix: -2.66 (1.01), residues: 13
  sheet: -0.32 (0.41), residues: 160
  loop :  0.08 (0.43), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  40 
 TYR   0.018   0.001   TYR A 473 
 PHE   0.017   0.001   PHE A 374 
 TRP   0.013   0.001   TRP A 353 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 3356)
  covalent geometry    : angle       0.61361 ( 4562)
  SS BOND              : bond        0.00475 (    6)
  SS BOND              : angle       0.85775 (   12)
  hydrogen bonds       : bond        0.02875 (   90)
  hydrogen bonds       : angle       5.81110 (  225)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  378 LYS cc_start: 0.8917 (tppp) cc_final: 0.8143 (tptp)
REVERT: A  462 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7552 (ttpp)
REVERT: A  523 THR cc_start: 0.8097 (p) cc_final: 0.7809 (p)
  outliers start: 11
  outliers final: 10
  residues processed: 100
  average time/residue: 0.0638
  time to fit residues: 7.5798
Evaluate side-chains
  105 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  493 GLN
Chi-restraints excluded: chain H residue   35 ASN
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   27 SER
Chi-restraints excluded: chain L residue   28 SER
Chi-restraints excluded: chain L residue   53 SER
Chi-restraints excluded: chain L residue   76 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 17 optimal weight:    0.1980
   chunk 33 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0770
   chunk 2 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 405 ASN
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 460 ASN
** A 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.151179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.131439 restraints weight = 4804.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.135031 restraints weight = 2674.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.137724 restraints weight = 1788.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.139387 restraints weight = 1316.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.140763 restraints weight = 1055.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.4207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3362  Z= 0.175
  Angle     :  0.644   6.546   4574  Z= 0.337
  Chirality :  0.046   0.146    478
  Planarity :  0.004   0.033    589
  Dihedral  :  4.964  16.703    462
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 27.35 %
    Favored  : 68.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.43), residues: 413
  helix: -2.86 (0.99), residues: 13
  sheet: -0.57 (0.39), residues: 170
  loop :  0.13 (0.45), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 357 
 TYR   0.014   0.001   TYR A 473 
 PHE   0.014   0.001   PHE A 374 
 TRP   0.011   0.002   TRP A 353 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 3356)
  covalent geometry    : angle       0.64248 ( 4562)
  SS BOND              : bond        0.00355 (    6)
  SS BOND              : angle       1.03617 (   12)
  hydrogen bonds       : bond        0.03115 (   90)
  hydrogen bonds       : angle       6.04654 (  225)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 782.57 seconds
wall clock time: 14 minutes 13.39 seconds (853.39 seconds total)