Starting phenix.real_space_refine
on Tue Mar  3 11:33:05 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wef_32449/03_2026/7wef_32449.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wef_32449/03_2026/7wef_32449.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wef_32449/03_2026/7wef_32449.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wef_32449/03_2026/7wef_32449.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wef_32449/03_2026/7wef_32449.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wef_32449/03_2026/7wef_32449.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    2119      2.51       5
     N     565      2.21       5
     O     629      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3328
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 902
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 902
          Classifications: {'peptide': 120}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 114}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "E"
      Number of atoms: 1610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1610
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 12, 'TRANS': 188}
    Chain: "L"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 816
          Classifications: {'peptide': 111}
          Link IDs: {'PTRANS': 8, 'TRANS': 102}
  Time building chain proxies: 0.83, per 1000 atoms: 0.25
  Number of scatterers: 3328
  At special positions: 0
  Unit cell: (79.18, 85.6, 86.67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      15     16.00
     O     629      8.00
     N     565      7.00
     C    2119      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - 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: 0.20
  Conformation dependent library (CDL) restraints added in 133.6 milliseconds
  

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  782

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 8 sheets defined
      7.2% alpha, 28.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.672A  pdb=" N   HIS C  32 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.993A  pdb=" N   THR C  90 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 337 through 343
    Processing helix  chain 'E' and resid 366 through 371
      removed outlier: 3.776A  pdb=" N   ASN E 370 " --> pdb=" O   SER E 366 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 404 through 411
      removed outlier: 3.940A  pdb=" N   ARG E 408 " --> pdb=" O   ASP E 405 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ALA E 411 " --> pdb=" O   ARG E 408 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5
      removed outlier: 4.209A  pdb=" N   GLN C   3 " --> pdb=" O   SER C  25 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   SER C  25 " --> pdb=" O   GLN C   3 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   TYR C  79 " --> pdb=" O   THR C  70 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 57 through 59
      removed outlier: 6.346A  pdb=" N   TRP C  36 " --> pdb=" O   MET C  48 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ILE C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   ILE C  34 " --> pdb=" O   ILE C  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358
      removed outlier: 3.993A  pdb=" N   ASN E 354 " --> pdb=" O   SER E 399 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   SER E 399 " --> pdb=" O   ASN E 354 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   VAL E 395 " --> pdb=" O   ILE E 358 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474
      removed outlier: 3.584A  pdb=" N   TYR E 473 " --> pdb=" O   TYR E 489 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   TYR E 489 " --> pdb=" O   TYR E 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.041A  pdb=" N   GLN L  38 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   LEU L  47 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12
      removed outlier: 3.528A  pdb=" N   ALA L  91 " --> pdb=" O   VAL L 102 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL L 102 " --> pdb=" O   ALA L  91 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 23
      removed outlier: 3.557A  pdb=" N   VAL L  18 " --> pdb=" O   ILE L  76 " (cutoff:3.500A)

    87 hydrogen bonds defined for protein.
    213 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: 0.42

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1066
        1.35 -     1.47: 943
        1.47 -     1.59: 1395
        1.59 -     1.71: 0
        1.71 -     1.84: 18
  Bond restraints: 3422
  Sorted by residual:
  bond pdb=" N   LEU C 104 "
       pdb=" CA  LEU C 104 "
    ideal  model  delta    sigma   weight residual
    1.465  1.452  0.013 1.31e-02 5.83e+03 9.85e-01
  bond pdb=" CB  CYS E 379 "
       pdb=" SG  CYS E 379 "
    ideal  model  delta    sigma   weight residual
    1.808  1.837 -0.029 3.30e-02 9.18e+02 7.49e-01
  bond pdb=" CA  THR E 333 "
       pdb=" CB  THR E 333 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 6.96e-01
  bond pdb=" CA  ILE L  76 "
       pdb=" CB  ILE L  76 "
    ideal  model  delta    sigma   weight residual
    1.540  1.529  0.011 1.36e-02 5.41e+03 6.45e-01
  bond pdb=" CB  TRP C  47 "
       pdb=" CG  TRP C  47 "
    ideal  model  delta    sigma   weight residual
    1.498  1.475  0.023 3.10e-02 1.04e+03 5.72e-01
  ... (remaining 3417 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 4315
        1.04 -     2.07: 254
        2.07 -     3.11: 60
        3.11 -     4.14: 29
        4.14 -     5.18: 4
  Bond angle restraints: 4662
  Sorted by residual:
  angle pdb=" C   ARG C  64 "
        pdb=" N   ASP C  65 "
        pdb=" CA  ASP C  65 "
      ideal   model   delta    sigma   weight residual
     121.54  126.02   -4.48 1.91e+00 2.74e-01 5.51e+00
  angle pdb=" C   ILE E 332 "
        pdb=" N   THR E 333 "
        pdb=" CA  THR E 333 "
      ideal   model   delta    sigma   weight residual
     121.54  125.79   -4.25 1.91e+00 2.74e-01 4.95e+00
  angle pdb=" CA  PHE C 107 "
        pdb=" C   PHE C 107 "
        pdb=" N   ASP C 108 "
      ideal   model   delta    sigma   weight residual
     115.29  117.80   -2.51 1.18e+00 7.18e-01 4.54e+00
  angle pdb=" C   MET C  69 "
        pdb=" CA  MET C  69 "
        pdb=" CB  MET C  69 "
      ideal   model   delta    sigma   weight residual
     110.24  113.20   -2.96 1.46e+00 4.69e-01 4.10e+00
  angle pdb=" CA  PHE C 107 "
        pdb=" C   PHE C 107 "
        pdb=" O   PHE C 107 "
      ideal   model   delta    sigma   weight residual
     122.36  119.97    2.39 1.21e+00 6.83e-01 3.91e+00
  ... (remaining 4657 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.33: 1805
       16.33 -    32.66: 148
       32.66 -    48.99: 38
       48.99 -    65.32: 4
       65.32 -    81.65: 5
  Dihedral angle restraints: 2000
    sinusoidal: 763
      harmonic: 1237
  Sorted by residual:
  dihedral pdb=" CB  CYS E 480 "
           pdb=" SG  CYS E 480 "
           pdb=" SG  CYS E 488 "
           pdb=" CB  CYS E 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.95  -66.95     1      1.00e+01 1.00e-02 5.84e+01
  dihedral pdb=" CA  ILE C  51 "
           pdb=" C   ILE C  51 "
           pdb=" N   ASN C  52 "
           pdb=" CA  ASN C  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.64   17.36     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  ASP E 428 "
           pdb=" C   ASP E 428 "
           pdb=" N   PHE E 429 "
           pdb=" CA  PHE E 429 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.76  -16.24     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 1997 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 278
       0.030 -    0.060: 143
       0.060 -    0.090: 51
       0.090 -    0.120: 19
       0.120 -    0.150: 5
  Chirality restraints: 496
  Sorted by residual:
  chirality pdb=" CA  ILE C  51 "
            pdb=" N   ILE C  51 "
            pdb=" C   ILE C  51 "
            pdb=" CB  ILE C  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.61e-01
  chirality pdb=" CA  ILE L  20 "
            pdb=" N   ILE L  20 "
            pdb=" C   ILE L  20 "
            pdb=" CB  ILE L  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  ILE E 434 "
            pdb=" N   ILE E 434 "
            pdb=" C   ILE E 434 "
            pdb=" CB  ILE E 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 493 not shown)

  Planarity restraints: 604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C  47 "    0.012 2.00e-02 2.50e+03   1.66e-02 6.86e+00
        pdb=" CG  TRP C  47 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP C  47 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP C  47 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP C  47 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP C  47 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP C  47 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C  47 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP C  47 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  72 "   -0.025 5.00e-02 4.00e+02   3.73e-02 2.22e+00
        pdb=" N   PRO C  73 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO C  73 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  73 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 108 "    0.023 5.00e-02 4.00e+02   3.42e-02 1.87e+00
        pdb=" N   PRO C 109 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO C 109 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 109 "    0.019 5.00e-02 4.00e+02
  ... (remaining 601 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 592
        2.77 -     3.30: 2922
        3.30 -     3.84: 4973
        3.84 -     4.37: 5725
        4.37 -     4.90: 10342
  Nonbonded interactions: 24554
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN E 439 "
            pdb=" OE1 GLN E 506 "
     model   vdw
     2.239 3.120
  nonbonded pdb=" OG1 THR C  28 "
            pdb=" OG  SER C  31 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   THR C  28 "
            pdb=" OG  SER C  31 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   ASN L  53 "
            pdb=" NH1 ARG L  55 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" OH  TYR E 369 "
            pdb=" O   PRO E 384 "
     model   vdw
     2.326 3.040
  ... (remaining 24549 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:             1.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.660
  Find NCS groups from input model:        0.020
  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:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3428  Z= 0.152
  Angle     :  0.627   5.176   4674  Z= 0.336
  Chirality :  0.043   0.150    496
  Planarity :  0.004   0.037    604
  Dihedral  : 12.721  81.647   1200
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  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: -1.27 (0.41), residues: 426
  helix: -3.97 (0.48), residues: 26
  sheet:  0.64 (0.49), residues: 135
  loop : -1.38 (0.37), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 509 
 TYR   0.015   0.001   TYR E 453 
 PHE   0.012   0.002   PHE E 374 
 TRP   0.042   0.003   TRP C  47 
 HIS   0.002   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3422)
  covalent geometry    : angle       0.62392 ( 4662)
  SS BOND              : bond        0.00354 (    6)
  SS BOND              : angle       1.35629 (   12)
  hydrogen bonds       : bond        0.18861 (   82)
  hydrogen bonds       : angle       6.38883 (  213)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.120 
Fit side-chains
REVERT: C  106 TRP cc_start: 0.8053 (p-90) cc_final: 0.7845 (p-90)
REVERT: E  346 ARG cc_start: 0.7386 (ttp80) cc_final: 0.6968 (ptm-80)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0630
  time to fit residues: 4.7126
Evaluate side-chains
  56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0770
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.140347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.116653 restraints weight = 4640.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.119763 restraints weight = 2985.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.122067 restraints weight = 2170.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.123727 restraints weight = 1717.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.124822 restraints weight = 1443.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.0899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3428  Z= 0.139
  Angle     :  0.591   5.407   4674  Z= 0.307
  Chirality :  0.043   0.163    496
  Planarity :  0.004   0.038    604
  Dihedral  :  4.612  17.135    474
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  7.82 %
    Favored  : 90.50 %
  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 are not related in a simple way.
  whole: -1.12 (0.41), residues: 426
  helix: -3.84 (0.51), residues: 27
  sheet:  0.85 (0.49), residues: 133
  loop : -1.31 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  66 
 TYR   0.008   0.001   TYR L  50 
 PHE   0.010   0.001   PHE E 400 
 TRP   0.012   0.002   TRP C 103 
 HIS   0.002   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3422)
  covalent geometry    : angle       0.58682 ( 4662)
  SS BOND              : bond        0.00483 (    6)
  SS BOND              : angle       1.43713 (   12)
  hydrogen bonds       : bond        0.03794 (   82)
  hydrogen bonds       : angle       5.53493 (  213)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.118 
Fit side-chains
REVERT: E  346 ARG cc_start: 0.7380 (ttp80) cc_final: 0.7094 (ptm-80)
REVERT: E  369 TYR cc_start: 0.5052 (m-80) cc_final: 0.4838 (m-80)
REVERT: E  406 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7826 (tt0)
  outliers start: 6
  outliers final: 5
  residues processed: 61
  average time/residue: 0.0632
  time to fit residues: 4.7287
Evaluate side-chains
  58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    7 SER
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue  107 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.9784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.136142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.112491 restraints weight = 4786.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.115467 restraints weight = 3116.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.117658 restraints weight = 2290.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.119268 restraints weight = 1825.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.120347 restraints weight = 1544.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3428  Z= 0.187
  Angle     :  0.629   5.266   4674  Z= 0.326
  Chirality :  0.044   0.154    496
  Planarity :  0.004   0.036    604
  Dihedral  :  4.841  19.325    474
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.17 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.40), residues: 426
  helix: -3.17 (0.72), residues: 21
  sheet:  0.75 (0.48), residues: 133
  loop : -1.56 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C  64 
 TYR   0.010   0.002   TYR E 423 
 PHE   0.017   0.002   PHE E 429 
 TRP   0.018   0.003   TRP C 103 
 HIS   0.004   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 3422)
  covalent geometry    : angle       0.62544 ( 4662)
  SS BOND              : bond        0.00209 (    6)
  SS BOND              : angle       1.46107 (   12)
  hydrogen bonds       : bond        0.03850 (   82)
  hydrogen bonds       : angle       5.41824 (  213)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.128 
Fit side-chains
REVERT: E  346 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7175 (ptm-80)
  outliers start: 7
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0661
  time to fit residues: 4.7513
Evaluate side-chains
  58 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain L residue  110 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9990
   chunk 25 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.151886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.130832 restraints weight = 4697.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.133457 restraints weight = 3237.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.135410 restraints weight = 2470.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.136836 restraints weight = 2024.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.137663 restraints weight = 1741.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3428  Z= 0.130
  Angle     :  0.568   5.345   4674  Z= 0.294
  Chirality :  0.042   0.159    496
  Planarity :  0.004   0.036    604
  Dihedral  :  4.608  20.690    474
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 13.13 %
    Favored  : 84.36 %
  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 are not related in a simple way.
  whole: -1.23 (0.40), residues: 426
  helix: -3.06 (0.77), residues: 21
  sheet:  0.72 (0.48), residues: 134
  loop : -1.53 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  66 
 TYR   0.009   0.001   TYR E 423 
 PHE   0.009   0.001   PHE E 429 
 TRP   0.020   0.002   TRP C 106 
 HIS   0.003   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3422)
  covalent geometry    : angle       0.56531 ( 4662)
  SS BOND              : bond        0.00222 (    6)
  SS BOND              : angle       1.24803 (   12)
  hydrogen bonds       : bond        0.03262 (   82)
  hydrogen bonds       : angle       5.15335 (  213)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.117 
Fit side-chains
REVERT: E  346 ARG cc_start: 0.7398 (ttp80) cc_final: 0.7188 (ptm-80)
REVERT: E  406 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7560 (mt-10)
  outliers start: 9
  outliers final: 8
  residues processed: 62
  average time/residue: 0.0526
  time to fit residues: 4.2250
Evaluate side-chains
  63 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain L residue  110 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 34 optimal weight:    6.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 506 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 = 0.3704 r_free = 0.3704 target = 0.135609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.112420 restraints weight = 4729.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.115407 restraints weight = 3129.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.117454 restraints weight = 2304.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.118597 restraints weight = 1860.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.120092 restraints weight = 1612.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7467
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3428  Z= 0.155
  Angle     :  0.604   5.413   4674  Z= 0.311
  Chirality :  0.043   0.153    496
  Planarity :  0.004   0.034    604
  Dihedral  :  4.751  23.277    474
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 13.13 %
    Favored  : 83.52 %
  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: -1.40 (0.41), residues: 426
  helix: -3.09 (0.78), residues: 21
  sheet:  0.21 (0.46), residues: 150
  loop : -1.51 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 466 
 TYR   0.009   0.001   TYR C  79 
 PHE   0.012   0.002   PHE C 107 
 TRP   0.023   0.003   TRP L 101 
 HIS   0.003   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 3422)
  covalent geometry    : angle       0.60147 ( 4662)
  SS BOND              : bond        0.00191 (    6)
  SS BOND              : angle       1.26234 (   12)
  hydrogen bonds       : bond        0.03374 (   82)
  hydrogen bonds       : angle       5.03384 (  213)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.124 
Fit side-chains
REVERT: E  346 ARG cc_start: 0.7470 (ttp80) cc_final: 0.7222 (ptm-80)
  outliers start: 12
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0573
  time to fit residues: 4.6548
Evaluate side-chains
  63 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue  110 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 31 optimal weight:    0.1980
   chunk 30 optimal weight:    0.6980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 506 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 = 0.3712 r_free = 0.3712 target = 0.136373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.112990 restraints weight = 4682.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.115951 restraints weight = 3102.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.118128 restraints weight = 2298.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.119765 restraints weight = 1838.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.120572 restraints weight = 1558.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3428  Z= 0.142
  Angle     :  0.590   5.393   4674  Z= 0.305
  Chirality :  0.043   0.155    496
  Planarity :  0.004   0.036    604
  Dihedral  :  4.670  24.078    474
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 12.85 %
    Favored  : 83.80 %
  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 are not related in a simple way.
  whole: -1.40 (0.41), residues: 426
  helix: -3.09 (0.80), residues: 21
  sheet:  0.24 (0.46), residues: 149
  loop : -1.53 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 493 
 TYR   0.009   0.001   TYR C  94 
 PHE   0.010   0.001   PHE C  63 
 TRP   0.021   0.002   TRP C 106 
 HIS   0.003   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3422)
  covalent geometry    : angle       0.58816 ( 4662)
  SS BOND              : bond        0.00204 (    6)
  SS BOND              : angle       1.16980 (   12)
  hydrogen bonds       : bond        0.03292 (   82)
  hydrogen bonds       : angle       4.95495 (  213)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 57
  time to evaluate  : 0.119 
Fit side-chains
REVERT: E  346 ARG cc_start: 0.7473 (ttp80) cc_final: 0.7222 (ptm-80)
  outliers start: 12
  outliers final: 11
  residues processed: 65
  average time/residue: 0.0585
  time to fit residues: 4.7562
Evaluate side-chains
  67 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 56
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   71 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue  110 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    0.2980
   chunk 41 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 16 optimal weight:    0.3980
   chunk 22 optimal weight:    0.3980
   chunk 10 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 506 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 = 0.3727 r_free = 0.3727 target = 0.137537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.114331 restraints weight = 4803.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.117262 restraints weight = 3182.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.119452 restraints weight = 2355.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120878 restraints weight = 1878.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.122102 restraints weight = 1604.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3428  Z= 0.118
  Angle     :  0.561   5.888   4674  Z= 0.290
  Chirality :  0.042   0.156    496
  Planarity :  0.004   0.036    604
  Dihedral  :  4.464  23.416    474
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 13.41 %
    Favored  : 83.24 %
  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: -1.36 (0.41), residues: 426
  helix: -3.19 (0.80), residues: 21
  sheet:  0.24 (0.46), residues: 150
  loop : -1.46 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG E 355 
 TYR   0.010   0.001   TYR C  79 
 PHE   0.009   0.001   PHE C  63 
 TRP   0.025   0.002   TRP C 106 
 HIS   0.002   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3422)
  covalent geometry    : angle       0.55909 ( 4662)
  SS BOND              : bond        0.00216 (    6)
  SS BOND              : angle       1.04858 (   12)
  hydrogen bonds       : bond        0.03015 (   82)
  hydrogen bonds       : angle       4.78644 (  213)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.124 
Fit side-chains
REVERT: C   10 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6849 (pm20)
REVERT: C  106 TRP cc_start: 0.7886 (p-90) cc_final: 0.7675 (p-90)
REVERT: E  346 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7251 (ptm-80)
REVERT: E  417 LYS cc_start: 0.8938 (ttpp) cc_final: 0.8577 (ttpp)
  outliers start: 12
  outliers final: 10
  residues processed: 66
  average time/residue: 0.0579
  time to fit residues: 4.8010
Evaluate side-chains
  68 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   10 GLU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue  110 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0570
   chunk 25 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0870
   chunk 10 optimal weight:    0.7980
   chunk 21 optimal weight:    0.5980
   chunk 38 optimal weight:    0.4980
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.4076

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

Flipped N/Q/H residues before XYZ refinement:
** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 506 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 = 0.3722 r_free = 0.3722 target = 0.137310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.114095 restraints weight = 4830.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.117042 restraints weight = 3200.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.119254 restraints weight = 2370.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.120695 restraints weight = 1891.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.121890 restraints weight = 1613.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3428  Z= 0.111
  Angle     :  0.552   5.361   4674  Z= 0.285
  Chirality :  0.042   0.155    496
  Planarity :  0.004   0.036    604
  Dihedral  :  4.345  22.852    474
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.34 %
    Favored  : 93.66 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 13.97 %
    Favored  : 82.96 %
  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: -1.33 (0.40), residues: 426
  helix: -3.17 (0.82), residues: 21
  sheet:  0.41 (0.47), residues: 140
  loop : -1.48 (0.36), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  86 
 TYR   0.007   0.001   TYR L  50 
 PHE   0.007   0.001   PHE C  63 
 TRP   0.020   0.002   TRP C 106 
 HIS   0.002   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3422)
  covalent geometry    : angle       0.55023 ( 4662)
  SS BOND              : bond        0.00218 (    6)
  SS BOND              : angle       1.01900 (   12)
  hydrogen bonds       : bond        0.02998 (   82)
  hydrogen bonds       : angle       4.69226 (  213)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.128 
Fit side-chains
REVERT: C   10 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6879 (pm20)
REVERT: C  106 TRP cc_start: 0.7874 (p-90) cc_final: 0.7645 (p-90)
REVERT: E  346 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7250 (ptm-80)
REVERT: E  417 LYS cc_start: 0.8932 (ttpp) cc_final: 0.8578 (ttpp)
  outliers start: 11
  outliers final: 10
  residues processed: 66
  average time/residue: 0.0601
  time to fit residues: 5.0170
Evaluate side-chains
  65 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   10 GLU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue  110 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 27 optimal weight:    0.4980
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.136253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.112775 restraints weight = 4754.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.115722 restraints weight = 3149.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.117785 restraints weight = 2328.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.119307 restraints weight = 1872.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120597 restraints weight = 1594.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7453
moved from start:          0.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3428  Z= 0.143
  Angle     :  0.595   6.660   4674  Z= 0.307
  Chirality :  0.043   0.149    496
  Planarity :  0.004   0.035    604
  Dihedral  :  4.470  24.649    474
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 14.25 %
    Favored  : 82.12 %
  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: -1.43 (0.40), residues: 426
  helix: -3.22 (0.80), residues: 21
  sheet:  0.11 (0.45), residues: 150
  loop : -1.46 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  86 
 TYR   0.009   0.001   TYR C  79 
 PHE   0.015   0.002   PHE C  63 
 TRP   0.023   0.002   TRP L 101 
 HIS   0.002   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3422)
  covalent geometry    : angle       0.59264 ( 4662)
  SS BOND              : bond        0.00186 (    6)
  SS BOND              : angle       1.11508 (   12)
  hydrogen bonds       : bond        0.03212 (   82)
  hydrogen bonds       : angle       4.70611 (  213)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.101 
Fit side-chains
REVERT: E  346 ARG cc_start: 0.7489 (ttp80) cc_final: 0.7222 (ptm-80)
REVERT: E  417 LYS cc_start: 0.9003 (ttpp) cc_final: 0.8573 (ttpp)
  outliers start: 13
  outliers final: 11
  residues processed: 66
  average time/residue: 0.0541
  time to fit residues: 4.4893
Evaluate side-chains
  68 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue  110 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    0.1980
   chunk 7 optimal weight:    0.4980
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.135552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.112628 restraints weight = 4748.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.115503 restraints weight = 3175.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.117459 restraints weight = 2356.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.118764 restraints weight = 1907.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.120212 restraints weight = 1641.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.2176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3428  Z= 0.145
  Angle     :  0.593   5.499   4674  Z= 0.310
  Chirality :  0.043   0.149    496
  Planarity :  0.004   0.036    604
  Dihedral  :  4.545  25.556    474
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 15.36 %
    Favored  : 81.01 %
  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: -1.43 (0.40), residues: 426
  helix: -3.20 (0.82), residues: 21
  sheet:  0.14 (0.46), residues: 150
  loop : -1.48 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  86 
 TYR   0.007   0.001   TYR L  50 
 PHE   0.014   0.002   PHE C  63 
 TRP   0.029   0.003   TRP C 106 
 HIS   0.002   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3422)
  covalent geometry    : angle       0.59145 ( 4662)
  SS BOND              : bond        0.00218 (    6)
  SS BOND              : angle       1.11123 (   12)
  hydrogen bonds       : bond        0.03251 (   82)
  hydrogen bonds       : angle       4.74043 (  213)

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

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

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  852 Ramachandran restraints generated.
    426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.129 
Fit side-chains
REVERT: E  346 ARG cc_start: 0.7483 (ttp80) cc_final: 0.7215 (ptm-80)
REVERT: E  417 LYS cc_start: 0.8943 (ttpp) cc_final: 0.8591 (ttpp)
  outliers start: 13
  outliers final: 13
  residues processed: 67
  average time/residue: 0.0609
  time to fit residues: 5.1419
Evaluate side-chains
  69 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   10 GLU
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   47 TRP
Chi-restraints excluded: chain C residue   69 MET
Chi-restraints excluded: chain C residue  114 THR
Chi-restraints excluded: chain E residue  385 THR
Chi-restraints excluded: chain E residue  433 VAL
Chi-restraints excluded: chain E residue  512 VAL
Chi-restraints excluded: chain E residue  524 VAL
Chi-restraints excluded: chain E residue  525 CYS
Chi-restraints excluded: chain L residue   96 LEU
Chi-restraints excluded: chain L residue  110 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 4 optimal weight:    0.4980
   chunk 26 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.135587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.112285 restraints weight = 4856.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.115149 restraints weight = 3172.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.117481 restraints weight = 2341.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.118916 restraints weight = 1855.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.120238 restraints weight = 1579.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3428  Z= 0.142
  Angle     :  0.597   5.740   4674  Z= 0.314
  Chirality :  0.043   0.151    496
  Planarity :  0.004   0.039    604
  Dihedral  :  4.581  26.011    474
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 15.92 %
    Favored  : 80.45 %
  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: -1.41 (0.41), residues: 426
  helix: -3.21 (0.81), residues: 21
  sheet:  0.14 (0.46), residues: 150
  loop : -1.46 (0.37), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  86 
 TYR   0.009   0.001   TYR C  79 
 PHE   0.021   0.002   PHE C  63 
 TRP   0.042   0.003   TRP C 106 
 HIS   0.002   0.001   HIS E 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3422)
  covalent geometry    : angle       0.59460 ( 4662)
  SS BOND              : bond        0.00216 (    6)
  SS BOND              : angle       1.29847 (   12)
  hydrogen bonds       : bond        0.03323 (   82)
  hydrogen bonds       : angle       4.72775 (  213)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 883.58 seconds
wall clock time: 15 minutes 47.44 seconds (947.44 seconds total)