Starting phenix.real_space_refine
on Tue Feb  3 14:22:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vnd_65208/02_2026/9vnd_65208.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vnd_65208/02_2026/9vnd_65208.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vnd_65208/02_2026/9vnd_65208.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vnd_65208/02_2026/9vnd_65208.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vnd_65208/02_2026/9vnd_65208.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vnd_65208/02_2026/9vnd_65208.map"
  }
  resolution = 3.3
  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=   0.002 sd=   0.124
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      19      5.16       5
     C    2399      2.51       5
     N     592      2.21       5
     O     675      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3685
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "B"
      Number of atoms: 697
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 697
          Classifications: {'peptide': 87}
          Link IDs: {'PTRANS': 3, 'TRANS': 83}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 735
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 426
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 426
          Classifications: {'peptide': 53}
          Link IDs: {'TRANS': 52}
          Chain breaks: 3
    Chain: "D"
      Number of atoms: 351
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 351
          Classifications: {'peptide': 43}
          Link IDs: {'TRANS': 42}
          Chain breaks: 4
    Chain: "J"
      Number of atoms: 651
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 651
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 4, 'TRANS': 74}
          Chain breaks: 4
    Chain: "E"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 454
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 2, 'TRANS': 53}
          Chain breaks: 4
    Chain: "F"
      Number of atoms: 371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 371
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
          Chain breaks: 2
  Time building chain proxies: 1.00, per 1000 atoms: 0.27
  Number of scatterers: 3685
  At special positions: 0
  Unit cell: (58.912, 87.316, 92.576, 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      19     16.00
     O     675      8.00
     N     592      7.00
     C    2399      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 125.0 milliseconds
  

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  846

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 8 sheets defined
      5.0% alpha, 33.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'B' and resid 65 through 70
    Processing helix  chain 'J' and resid 9 through 19
    Processing helix  chain 'E' and resid 65 through 70
    Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25
    Processing sheet with id=AA2, first strand: chain 'C' and resid 120 through 123
      removed outlier: 5.854A  pdb=" N   THR C  53 " --> pdb=" O   SER C  34 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   SER C  34 " --> pdb=" O   THR C  53 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   ASN B  95 " --> pdb=" O   ASP B 120 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASP B 120 " --> pdb=" O   ASN B  95 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   TYR B  97 " --> pdb=" O   SER B 118 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   VAL B 116 " --> pdb=" O   ILE B  99 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   PHE B 101 " --> pdb=" O   GLN B 114 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   GLN B 114 " --> pdb=" O   PHE B 101 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ARG B 103 " --> pdb=" O   GLU B 112 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   GLU B 112 " --> pdb=" O   ARG B 103 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   HIS B  28 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE A 106 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 27 through 28
      removed outlier: 4.539A  pdb=" N   SER C   6 " --> pdb=" O   LEU C  28 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 107 through 110
    Processing sheet with id=AA5, first strand: chain 'A' and resid 31 through 33
      removed outlier: 3.795A  pdb=" N   CYS A  31 " --> pdb=" O   TYR D 108 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 31 through 34
      removed outlier: 6.415A  pdb=" N   CYS E  98 " --> pdb=" O   SER E 118 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   SER E 118 " --> pdb=" O   CYS E  98 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ARG E 100 " --> pdb=" O   VAL E 116 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'J' and resid 180 through 182
      removed outlier: 4.251A  pdb=" N   TYR J  42 " --> pdb=" O   ILE J  60 " (cutoff:3.500A)
      removed outlier: 6.532A  pdb=" N   TYR J  57 " --> pdb=" O   TRP J 191 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 29 through 33

    121 hydrogen bonds defined for protein.
    309 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:
        1.23 -     1.34: 1111
        1.34 -     1.46: 877
        1.46 -     1.58: 1730
        1.58 -     1.69: 0
        1.69 -     1.81: 27
  Bond restraints: 3745
  Sorted by residual:
  bond pdb=" CB  GLU C  97 "
       pdb=" CG  GLU C  97 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.04e+00
  bond pdb=" N   GLY C 112 "
       pdb=" CA  GLY C 112 "
    ideal  model  delta    sigma   weight residual
    1.449  1.464 -0.015 1.45e-02 4.76e+03 1.02e+00
  bond pdb=" CG  GLU C  97 "
       pdb=" CD  GLU C  97 "
    ideal  model  delta    sigma   weight residual
    1.516  1.539 -0.023 2.50e-02 1.60e+03 8.17e-01
  bond pdb=" CA  LYS C 126 "
       pdb=" CB  LYS C 126 "
    ideal  model  delta    sigma   weight residual
    1.530  1.548 -0.018 2.22e-02 2.03e+03 6.88e-01
  bond pdb=" CB  LYS C 126 "
       pdb=" CG  LYS C 126 "
    ideal  model  delta    sigma   weight residual
    1.520  1.544 -0.024 3.00e-02 1.11e+03 6.48e-01
  ... (remaining 3740 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 4914
        1.59 -     3.18: 96
        3.18 -     4.77: 13
        4.77 -     6.36: 4
        6.36 -     7.96: 3
  Bond angle restraints: 5030
  Sorted by residual:
  angle pdb=" CA  LYS C 126 "
        pdb=" CB  LYS C 126 "
        pdb=" CG  LYS C 126 "
      ideal   model   delta    sigma   weight residual
     114.10  120.48   -6.38 2.00e+00 2.50e-01 1.02e+01
  angle pdb=" C   PRO B  61 "
        pdb=" N   GLU B  62 "
        pdb=" CA  GLU B  62 "
      ideal   model   delta    sigma   weight residual
     121.54  126.28   -4.74 1.91e+00 2.74e-01 6.17e+00
  angle pdb=" CB  GLU C  97 "
        pdb=" CG  GLU C  97 "
        pdb=" CD  GLU C  97 "
      ideal   model   delta    sigma   weight residual
     112.60  116.56   -3.96 1.70e+00 3.46e-01 5.44e+00
  angle pdb=" CA  LEU J  41 "
        pdb=" CB  LEU J  41 "
        pdb=" CG  LEU J  41 "
      ideal   model   delta    sigma   weight residual
     116.30  124.26   -7.96 3.50e+00 8.16e-02 5.17e+00
  angle pdb=" CA  GLU B  62 "
        pdb=" CB  GLU B  62 "
        pdb=" CG  GLU B  62 "
      ideal   model   delta    sigma   weight residual
     114.10  118.63   -4.53 2.00e+00 2.50e-01 5.14e+00
  ... (remaining 5025 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 1765
       17.87 -    35.74: 293
       35.74 -    53.61: 93
       53.61 -    71.47: 16
       71.47 -    89.34: 7
  Dihedral angle restraints: 2174
    sinusoidal: 872
      harmonic: 1302
  Sorted by residual:
  dihedral pdb=" CA  TYR F 108 "
           pdb=" C   TYR F 108 "
           pdb=" N   THR F 109 "
           pdb=" CA  THR F 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.65  -19.35     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  PRO B  61 "
           pdb=" C   PRO B  61 "
           pdb=" N   GLU B  62 "
           pdb=" CA  GLU B  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.69   16.31     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CB  GLU A 107 "
           pdb=" CG  GLU A 107 "
           pdb=" CD  GLU A 107 "
           pdb=" OE1 GLU A 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.34  -89.34     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 2171 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 315
       0.026 -    0.053: 152
       0.053 -    0.079: 52
       0.079 -    0.106: 36
       0.106 -    0.132: 25
  Chirality restraints: 580
  Sorted by residual:
  chirality pdb=" CA  ILE F 121 "
            pdb=" N   ILE F 121 "
            pdb=" C   ILE F 121 "
            pdb=" CB  ILE F 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CB  ILE A 116 "
            pdb=" CA  ILE A 116 "
            pdb=" CG1 ILE A 116 "
            pdb=" CG2 ILE A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.13 2.00e-01 2.50e+01 4.33e-01
  chirality pdb=" CA  ILE J 182 "
            pdb=" N   ILE J 182 "
            pdb=" C   ILE J 182 "
            pdb=" CB  ILE J 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.09e-01
  ... (remaining 577 not shown)

  Planarity restraints: 604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE J  60 "   -0.048 5.00e-02 4.00e+02   7.37e-02 8.68e+00
        pdb=" N   PRO J  61 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO J  61 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO J  61 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 116 "   -0.006 2.00e-02 2.50e+03   1.11e-02 1.23e+00
        pdb=" C   ILE A 116 "    0.019 2.00e-02 2.50e+03
        pdb=" O   ILE A 116 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   HIS A 117 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  17 "    0.008 2.00e-02 2.50e+03   7.10e-03 8.82e-01
        pdb=" CG  PHE B  17 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  17 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  17 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  17 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  17 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  17 "    0.002 2.00e-02 2.50e+03
  ... (remaining 601 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 444
        2.76 -     3.30: 3214
        3.30 -     3.83: 5743
        3.83 -     4.37: 6681
        4.37 -     4.90: 12010
  Nonbonded interactions: 28092
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B 100 "
            pdb=" OD1 ASN C  36 "
     model   vdw
     2.225 3.120
  nonbonded pdb=" OG  SER D  34 "
            pdb=" OD1 ASN E 102 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   GLU A  29 "
            pdb=" OG1 THR A  57 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" OD1 ASN B 102 "
            pdb=" OG  SER C  34 "
     model   vdw
     2.374 3.040
  nonbonded pdb=" N   GLN D  37 "
            pdb=" O   ILE E  99 "
     model   vdw
     2.378 3.120
  ... (remaining 28087 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.220
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6706
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3745  Z= 0.111
  Angle     :  0.578   7.956   5030  Z= 0.299
  Chirality :  0.045   0.132    580
  Planarity :  0.004   0.074    604
  Dihedral  : 19.746  89.343   1328
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  : 39.01 %
    Favored  : 60.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.34 (0.41), residues: 397
  helix: -1.25 (1.05), residues: 25
  sheet: -1.32 (0.41), residues: 188
  loop : -3.36 (0.36), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 100 
 TYR   0.012   0.001   TYR C 108 
 PHE   0.017   0.001   PHE B  17 
 TRP   0.004   0.001   TRP E  67 
 HIS   0.007   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 3745)
  covalent geometry    : angle       0.57786 ( 5030)
  hydrogen bonds       : bond        0.16271 (  121)
  hydrogen bonds       : angle       8.67629 (  309)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 95
  time to evaluate  : 0.083 
Fit side-chains
REVERT: B  111 LEU cc_start: 0.7822 (mt) cc_final: 0.7372 (mt)
REVERT: A  107 GLU cc_start: 0.7617 (tt0) cc_final: 0.7387 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0389
  time to fit residues: 4.7687
Evaluate side-chains
  92 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0970
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 114 GLN
C 123 GLN
D  30 ASN
J  18 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.216934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.209596 restraints weight = 4119.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.4225 rms_B_bonded: 0.76
r_work: 0.4143 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.4040 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6799
moved from start:          0.0916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3745  Z= 0.132
  Angle     :  0.585   7.947   5030  Z= 0.305
  Chirality :  0.045   0.140    580
  Planarity :  0.003   0.050    604
  Dihedral  :  4.639  18.456    468
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 37.53 %
    Favored  : 57.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.28 (0.41), residues: 397
  helix: -0.91 (1.08), residues: 25
  sheet: -1.34 (0.41), residues: 192
  loop : -3.33 (0.36), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 100 
 TYR   0.014   0.001   TYR C 108 
 PHE   0.021   0.002   PHE D  33 
 TRP   0.004   0.001   TRP E  16 
 HIS   0.009   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3745)
  covalent geometry    : angle       0.58493 ( 5030)
  hydrogen bonds       : bond        0.03424 (  121)
  hydrogen bonds       : angle       6.91325 (  309)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.085 
Fit side-chains
REVERT: D   33 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7202 (p90)
REVERT: J   39 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.5551 (tt0)
  outliers start: 21
  outliers final: 13
  residues processed: 103
  average time/residue: 0.0523
  time to fit residues: 6.9308
Evaluate side-chains
  104 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue  112 GLU
Chi-restraints excluded: chain C residue   27 GLU
Chi-restraints excluded: chain C residue   96 PHE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain D residue   33 PHE
Chi-restraints excluded: chain D residue   83 ILE
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   79 THR
Chi-restraints excluded: chain J residue  179 ILE
Chi-restraints excluded: chain E residue   33 PHE
Chi-restraints excluded: chain F residue   63 GLN
Chi-restraints excluded: chain F residue  120 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 33 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 37 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.4306 r_free = 0.4306 target = 0.217069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.209857 restraints weight = 4047.994|
|-----------------------------------------------------------------------------|
r_work (start): 0.4231 rms_B_bonded: 0.74
r_work: 0.4143 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.4037 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6804
moved from start:          0.1027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3745  Z= 0.126
  Angle     :  0.580   8.122   5030  Z= 0.298
  Chirality :  0.045   0.143    580
  Planarity :  0.003   0.039    604
  Dihedral  :  4.637  19.106    468
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 38.02 %
    Favored  : 56.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.27 (0.41), residues: 397
  helix: -0.72 (1.11), residues: 25
  sheet: -1.34 (0.41), residues: 192
  loop : -3.35 (0.36), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 100 
 TYR   0.014   0.001   TYR C 108 
 PHE   0.021   0.002   PHE D  33 
 TRP   0.003   0.001   TRP E  16 
 HIS   0.009   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 3745)
  covalent geometry    : angle       0.57968 ( 5030)
  hydrogen bonds       : bond        0.03108 (  121)
  hydrogen bonds       : angle       6.56768 (  309)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.137 
Fit side-chains
REVERT: C   54 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6672 (tp)
REVERT: D   33 PHE cc_start: 0.7611 (OUTLIER) cc_final: 0.7223 (p90)
REVERT: J   39 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5605 (tt0)
REVERT: F  125 ARG cc_start: 0.6340 (OUTLIER) cc_final: 0.5924 (ptt-90)
  outliers start: 24
  outliers final: 15
  residues processed: 107
  average time/residue: 0.0467
  time to fit residues: 6.3716
Evaluate side-chains
  110 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue  112 GLU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   27 GLU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   96 PHE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain D residue   33 PHE
Chi-restraints excluded: chain D residue   83 ILE
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   72 ILE
Chi-restraints excluded: chain J residue   79 THR
Chi-restraints excluded: chain J residue  179 ILE
Chi-restraints excluded: chain E residue   33 PHE
Chi-restraints excluded: chain F residue   63 GLN
Chi-restraints excluded: chain F residue  125 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 29 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0970
   chunk 28 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 25 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 102 ASN
B 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.216468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.207663 restraints weight = 4086.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.4216 rms_B_bonded: 0.87
r_work: 0.4130 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.4019 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6807
moved from start:          0.1212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3745  Z= 0.130
  Angle     :  0.572   8.272   5030  Z= 0.297
  Chirality :  0.045   0.147    580
  Planarity :  0.003   0.032    604
  Dihedral  :  4.685  19.626    468
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  7.16 %
    Allowed  : 37.28 %
    Favored  : 55.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.35 (0.41), residues: 397
  helix: -0.83 (1.11), residues: 25
  sheet: -1.42 (0.41), residues: 192
  loop : -3.36 (0.36), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 100 
 TYR   0.014   0.001   TYR C 108 
 PHE   0.021   0.002   PHE D  33 
 TRP   0.003   0.001   TRP E  16 
 HIS   0.009   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3745)
  covalent geometry    : angle       0.57243 ( 5030)
  hydrogen bonds       : bond        0.02984 (  121)
  hydrogen bonds       : angle       6.46061 (  309)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.147 
Fit side-chains
REVERT: C   54 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6673 (tp)
REVERT: C   84 CYS cc_start: 0.7425 (m) cc_final: 0.6951 (t)
REVERT: D   33 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.7067 (p90)
REVERT: J   39 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5556 (tt0)
REVERT: J  189 GLU cc_start: 0.5427 (OUTLIER) cc_final: 0.4866 (mt-10)
REVERT: E  117 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.7873 (mm)
REVERT: F  125 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.5967 (ptt-90)
  outliers start: 29
  outliers final: 16
  residues processed: 107
  average time/residue: 0.0575
  time to fit residues: 7.8885
Evaluate side-chains
  114 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   17 PHE
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue  112 GLU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   27 GLU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   96 PHE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain D residue   33 PHE
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   72 ILE
Chi-restraints excluded: chain J residue   79 THR
Chi-restraints excluded: chain J residue  179 ILE
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain E residue   33 PHE
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   53 THR
Chi-restraints excluded: chain F residue   63 GLN
Chi-restraints excluded: chain F residue  125 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4302 r_free = 0.4302 target = 0.216534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.209516 restraints weight = 4089.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.4231 rms_B_bonded: 0.72
r_work: 0.4151 rms_B_bonded: 1.71 restraints_weight: 0.5000
r_work: 0.4049 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.4049
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6792
moved from start:          0.1272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3745  Z= 0.126
  Angle     :  0.566   8.330   5030  Z= 0.293
  Chirality :  0.045   0.154    580
  Planarity :  0.003   0.026    604
  Dihedral  :  4.645  19.928    468
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  8.40 %
    Allowed  : 36.30 %
    Favored  : 55.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.36 (0.41), residues: 397
  helix: -0.77 (1.12), residues: 25
  sheet: -1.39 (0.41), residues: 189
  loop : -3.39 (0.35), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 100 
 TYR   0.014   0.001   TYR C 108 
 PHE   0.021   0.002   PHE D  33 
 TRP   0.003   0.001   TRP E  16 
 HIS   0.009   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3745)
  covalent geometry    : angle       0.56577 ( 5030)
  hydrogen bonds       : bond        0.02920 (  121)
  hydrogen bonds       : angle       6.36710 (  309)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 92
  time to evaluate  : 0.134 
Fit side-chains
REVERT: C   54 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6706 (tp)
REVERT: C   84 CYS cc_start: 0.7291 (m) cc_final: 0.6908 (t)
REVERT: A  126 LYS cc_start: 0.5131 (OUTLIER) cc_final: 0.4651 (tptp)
REVERT: D   33 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7060 (p90)
REVERT: J   39 GLU cc_start: 0.6617 (OUTLIER) cc_final: 0.5568 (tt0)
REVERT: J  189 GLU cc_start: 0.5328 (OUTLIER) cc_final: 0.4790 (mt-10)
REVERT: E  117 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7855 (mm)
REVERT: F  125 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.5950 (ptt-90)
  outliers start: 34
  outliers final: 20
  residues processed: 110
  average time/residue: 0.0640
  time to fit residues: 8.7463
Evaluate side-chains
  118 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   75 ASN
Chi-restraints excluded: chain B residue  112 GLU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain C residue   27 GLU
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   96 PHE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain A residue  126 LYS
Chi-restraints excluded: chain D residue   33 PHE
Chi-restraints excluded: chain D residue   83 ILE
Chi-restraints excluded: chain D residue  101 CYS
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   72 ILE
Chi-restraints excluded: chain J residue   79 THR
Chi-restraints excluded: chain J residue  179 ILE
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain E residue   30 ASP
Chi-restraints excluded: chain E residue   33 PHE
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   53 THR
Chi-restraints excluded: chain F residue   63 GLN
Chi-restraints excluded: chain F residue  120 ILE
Chi-restraints excluded: chain F residue  125 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
B 114 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.216543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.210056 restraints weight = 4150.207|
|-----------------------------------------------------------------------------|
r_work (start): 0.4207 rms_B_bonded: 0.68
r_work: 0.4140 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.4052 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6759
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3745  Z= 0.127
  Angle     :  0.568   8.357   5030  Z= 0.293
  Chirality :  0.045   0.155    580
  Planarity :  0.003   0.024    604
  Dihedral  :  4.646  20.013    468
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 36.54 %
    Favored  : 56.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.37 (0.41), residues: 397
  helix: -0.74 (1.12), residues: 25
  sheet: -1.40 (0.41), residues: 189
  loop : -3.40 (0.35), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 100 
 TYR   0.014   0.001   TYR C 108 
 PHE   0.021   0.002   PHE D  33 
 TRP   0.003   0.001   TRP B  67 
 HIS   0.009   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3745)
  covalent geometry    : angle       0.56754 ( 5030)
  hydrogen bonds       : bond        0.02871 (  121)
  hydrogen bonds       : angle       6.32801 (  309)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 91
  time to evaluate  : 0.081 
Fit side-chains
REVERT: C   54 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6672 (tp)
REVERT: C   84 CYS cc_start: 0.7176 (m) cc_final: 0.6844 (t)
REVERT: D   33 PHE cc_start: 0.7487 (OUTLIER) cc_final: 0.7055 (p90)
REVERT: J   39 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5581 (tt0)
REVERT: J  189 GLU cc_start: 0.5311 (OUTLIER) cc_final: 0.4779 (mt-10)
REVERT: E  117 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7841 (mm)
REVERT: F  125 ARG cc_start: 0.6409 (OUTLIER) cc_final: 0.6041 (ptt-90)
  outliers start: 30
  outliers final: 18
  residues processed: 106
  average time/residue: 0.0476
  time to fit residues: 6.3109
Evaluate side-chains
  114 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 90
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   75 ASN
Chi-restraints excluded: chain B residue  112 GLU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   96 PHE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain D residue   33 PHE
Chi-restraints excluded: chain D residue   83 ILE
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   72 ILE
Chi-restraints excluded: chain J residue   79 THR
Chi-restraints excluded: chain J residue  179 ILE
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain E residue   30 ASP
Chi-restraints excluded: chain E residue   33 PHE
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   53 THR
Chi-restraints excluded: chain F residue   63 GLN
Chi-restraints excluded: chain F residue  120 ILE
Chi-restraints excluded: chain F residue  125 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 3 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
B  32 ASN
J  18 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.215021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.208345 restraints weight = 4288.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.4207 rms_B_bonded: 0.71
r_work: 0.4137 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.4048 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6779
moved from start:          0.1428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3745  Z= 0.134
  Angle     :  0.580   8.439   5030  Z= 0.300
  Chirality :  0.045   0.165    580
  Planarity :  0.003   0.022    604
  Dihedral  :  4.691  20.177    468
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  7.41 %
    Allowed  : 37.28 %
    Favored  : 55.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.39 (0.41), residues: 397
  helix: -0.86 (1.11), residues: 25
  sheet: -1.42 (0.41), residues: 189
  loop : -3.40 (0.35), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 100 
 TYR   0.014   0.001   TYR C 108 
 PHE   0.021   0.002   PHE D  33 
 TRP   0.003   0.001   TRP B  67 
 HIS   0.008   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3745)
  covalent geometry    : angle       0.58018 ( 5030)
  hydrogen bonds       : bond        0.02907 (  121)
  hydrogen bonds       : angle       6.36805 (  309)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.083 
Fit side-chains
REVERT: C   54 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6744 (tp)
REVERT: C   84 CYS cc_start: 0.7133 (m) cc_final: 0.6833 (t)
REVERT: A  126 LYS cc_start: 0.5176 (OUTLIER) cc_final: 0.4667 (tptp)
REVERT: D   33 PHE cc_start: 0.7490 (OUTLIER) cc_final: 0.7068 (p90)
REVERT: J   39 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.5593 (tt0)
REVERT: J   62 PHE cc_start: 0.6757 (OUTLIER) cc_final: 0.5857 (m-10)
REVERT: J  189 GLU cc_start: 0.5407 (OUTLIER) cc_final: 0.4873 (mt-10)
REVERT: E  117 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.7852 (mm)
REVERT: F  125 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.6062 (ptt-90)
  outliers start: 30
  outliers final: 19
  residues processed: 108
  average time/residue: 0.0505
  time to fit residues: 6.7896
Evaluate side-chains
  119 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 ASP
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   75 ASN
Chi-restraints excluded: chain B residue  112 GLU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   96 PHE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain A residue  126 LYS
Chi-restraints excluded: chain D residue   33 PHE
Chi-restraints excluded: chain D residue   83 ILE
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   62 PHE
Chi-restraints excluded: chain J residue   72 ILE
Chi-restraints excluded: chain J residue   79 THR
Chi-restraints excluded: chain J residue  179 ILE
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain E residue   30 ASP
Chi-restraints excluded: chain E residue   33 PHE
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   53 THR
Chi-restraints excluded: chain F residue   63 GLN
Chi-restraints excluded: chain F residue  120 ILE
Chi-restraints excluded: chain F residue  125 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 41 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0980
   chunk 9 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0020
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.4988

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

Flipped N/Q/H residues before XYZ refinement:
B 114 GLN
J  18 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.220442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.213930 restraints weight = 4204.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.4252 rms_B_bonded: 0.69
r_work: 0.4188 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.4104 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   3745  Z= 0.099
  Angle     :  0.535   7.966   5030  Z= 0.278
  Chirality :  0.044   0.138    580
  Planarity :  0.003   0.023    604
  Dihedral  :  4.402  19.834    468
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 39.51 %
    Favored  : 55.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.41), residues: 397
  helix: -0.73 (1.13), residues: 25
  sheet: -1.07 (0.46), residues: 162
  loop : -3.23 (0.33), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 100 
 TYR   0.010   0.001   TYR C 108 
 PHE   0.021   0.001   PHE D  33 
 TRP   0.003   0.001   TRP E  16 
 HIS   0.009   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 3745)
  covalent geometry    : angle       0.53472 ( 5030)
  hydrogen bonds       : bond        0.02639 (  121)
  hydrogen bonds       : angle       5.96083 (  309)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.152 
Fit side-chains
REVERT: B  111 LEU cc_start: 0.7420 (mt) cc_final: 0.6943 (mt)
REVERT: C   29 GLU cc_start: 0.7313 (tp30) cc_final: 0.7075 (tp30)
REVERT: A  126 LYS cc_start: 0.4887 (OUTLIER) cc_final: 0.4404 (tptp)
REVERT: D   32 HIS cc_start: 0.7726 (m-70) cc_final: 0.6767 (t70)
REVERT: D   33 PHE cc_start: 0.7397 (OUTLIER) cc_final: 0.6967 (p90)
REVERT: J   62 PHE cc_start: 0.6729 (OUTLIER) cc_final: 0.5918 (m-10)
REVERT: E   33 PHE cc_start: 0.7931 (OUTLIER) cc_final: 0.7494 (p90)
REVERT: E  117 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7800 (mm)
REVERT: F  125 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.5923 (ptt-90)
  outliers start: 21
  outliers final: 13
  residues processed: 101
  average time/residue: 0.0630
  time to fit residues: 8.0014
Evaluate side-chains
  107 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   75 ASN
Chi-restraints excluded: chain B residue  112 GLU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain C residue   96 PHE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain A residue  126 LYS
Chi-restraints excluded: chain D residue   33 PHE
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain J residue   62 PHE
Chi-restraints excluded: chain J residue   79 THR
Chi-restraints excluded: chain J residue  179 ILE
Chi-restraints excluded: chain J residue  181 ILE
Chi-restraints excluded: chain E residue   33 PHE
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   53 THR
Chi-restraints excluded: chain F residue   61 LEU
Chi-restraints excluded: chain F residue  125 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.3980
   chunk 36 optimal weight:    4.9990
   chunk 2 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 26 optimal weight:    0.4980
   chunk 41 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
B 114 GLN
J  18 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.218720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.212368 restraints weight = 4123.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.4263 rms_B_bonded: 0.67
r_work: 0.4187 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.4099 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.4099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6744
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3745  Z= 0.117
  Angle     :  0.556   8.234   5030  Z= 0.286
  Chirality :  0.044   0.158    580
  Planarity :  0.003   0.025    604
  Dihedral  :  4.549  20.067    468
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.31 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 38.52 %
    Favored  : 55.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.12 (0.41), residues: 397
  helix: -0.72 (1.11), residues: 25
  sheet: -1.07 (0.46), residues: 163
  loop : -3.20 (0.33), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 100 
 TYR   0.013   0.001   TYR C 108 
 PHE   0.021   0.002   PHE D  33 
 TRP   0.005   0.001   TRP E  16 
 HIS   0.009   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 3745)
  covalent geometry    : angle       0.55593 ( 5030)
  hydrogen bonds       : bond        0.02733 (  121)
  hydrogen bonds       : angle       6.08334 (  309)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.167 
Fit side-chains
REVERT: B  111 LEU cc_start: 0.7534 (mt) cc_final: 0.7108 (mt)
REVERT: A  126 LYS cc_start: 0.5064 (OUTLIER) cc_final: 0.4549 (tptp)
REVERT: D   32 HIS cc_start: 0.7752 (m-70) cc_final: 0.6792 (t70)
REVERT: D   33 PHE cc_start: 0.7447 (OUTLIER) cc_final: 0.6974 (p90)
REVERT: J   39 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5536 (tt0)
REVERT: J   62 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.6037 (m-10)
REVERT: E  117 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7807 (mm)
REVERT: F  125 ARG cc_start: 0.6386 (OUTLIER) cc_final: 0.5961 (ptt-90)
  outliers start: 24
  outliers final: 16
  residues processed: 100
  average time/residue: 0.0429
  time to fit residues: 5.4843
Evaluate side-chains
  109 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   75 ASN
Chi-restraints excluded: chain B residue  112 GLU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain C residue   96 PHE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain A residue  126 LYS
Chi-restraints excluded: chain D residue   33 PHE
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   44 ILE
Chi-restraints excluded: chain J residue   62 PHE
Chi-restraints excluded: chain J residue   79 THR
Chi-restraints excluded: chain J residue  179 ILE
Chi-restraints excluded: chain J residue  181 ILE
Chi-restraints excluded: chain E residue   33 PHE
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   53 THR
Chi-restraints excluded: chain F residue   61 LEU
Chi-restraints excluded: chain F residue   63 GLN
Chi-restraints excluded: chain F residue  125 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    0.3980
   chunk 36 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0060
   chunk 1 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
J  18 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.218135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.211685 restraints weight = 4185.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.4241 rms_B_bonded: 0.68
r_work: 0.4174 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.4083 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
moved from start:          0.1545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3745  Z= 0.107
  Angle     :  0.551   8.086   5030  Z= 0.281
  Chirality :  0.044   0.143    580
  Planarity :  0.003   0.029    604
  Dihedral  :  4.450  19.863    468
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 39.26 %
    Favored  : 55.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.02 (0.41), residues: 397
  helix: -0.70 (1.12), residues: 25
  sheet: -0.95 (0.46), residues: 162
  loop : -3.16 (0.33), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 100 
 TYR   0.012   0.001   TYR C 108 
 PHE   0.020   0.002   PHE D  33 
 TRP   0.004   0.001   TRP E  16 
 HIS   0.009   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 3745)
  covalent geometry    : angle       0.55138 ( 5030)
  hydrogen bonds       : bond        0.02669 (  121)
  hydrogen bonds       : angle       5.96227 (  309)

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

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

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  794 Ramachandran restraints generated.
    397 Oldfield, 0 Emsley, 397 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 87
  time to evaluate  : 0.172 
Fit side-chains
REVERT: B  111 LEU cc_start: 0.7486 (mt) cc_final: 0.7016 (mt)
REVERT: C   54 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6540 (tp)
REVERT: A  126 LYS cc_start: 0.4947 (OUTLIER) cc_final: 0.3597 (tptp)
REVERT: D   32 HIS cc_start: 0.7748 (m-70) cc_final: 0.6785 (t70)
REVERT: D   33 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.6936 (p90)
REVERT: J   39 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5537 (tt0)
REVERT: J   62 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.6034 (m-10)
REVERT: J  189 GLU cc_start: 0.5290 (OUTLIER) cc_final: 0.4754 (mm-30)
REVERT: E   33 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7322 (p90)
REVERT: E  117 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7800 (mm)
REVERT: F  125 ARG cc_start: 0.6364 (OUTLIER) cc_final: 0.5982 (ptt-90)
  outliers start: 23
  outliers final: 14
  residues processed: 98
  average time/residue: 0.0570
  time to fit residues: 7.0021
Evaluate side-chains
  109 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 86
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   31 ILE
Chi-restraints excluded: chain B residue   75 ASN
Chi-restraints excluded: chain B residue  112 GLU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   10 ILE
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   96 PHE
Chi-restraints excluded: chain C residue  120 ILE
Chi-restraints excluded: chain A residue  126 LYS
Chi-restraints excluded: chain D residue   33 PHE
Chi-restraints excluded: chain J residue   23 THR
Chi-restraints excluded: chain J residue   39 GLU
Chi-restraints excluded: chain J residue   62 PHE
Chi-restraints excluded: chain J residue   79 THR
Chi-restraints excluded: chain J residue  179 ILE
Chi-restraints excluded: chain J residue  181 ILE
Chi-restraints excluded: chain J residue  189 GLU
Chi-restraints excluded: chain E residue   33 PHE
Chi-restraints excluded: chain E residue  117 ILE
Chi-restraints excluded: chain F residue   53 THR
Chi-restraints excluded: chain F residue   61 LEU
Chi-restraints excluded: chain F residue   63 GLN
Chi-restraints excluded: chain F residue  125 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0970
   chunk 17 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
B 114 GLN
J  18 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.219860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.211877 restraints weight = 4106.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.4223 rms_B_bonded: 0.80
r_work: 0.4148 rms_B_bonded: 1.74 restraints_weight: 0.5000
r_work: 0.4054 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6731
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3745  Z= 0.109
  Angle     :  0.553   8.125   5030  Z= 0.282
  Chirality :  0.044   0.149    580
  Planarity :  0.003   0.028    604
  Dihedral  :  4.454  19.872    468
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 39.51 %
    Favored  : 54.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.99 (0.41), residues: 397
  helix: -0.65 (1.12), residues: 25
  sheet: -0.93 (0.46), residues: 162
  loop : -3.15 (0.33), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 100 
 TYR   0.012   0.001   TYR C 108 
 PHE   0.020   0.002   PHE D  33 
 TRP   0.004   0.001   TRP E  16 
 HIS   0.009   0.001   HIS A 117 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3745)
  covalent geometry    : angle       0.55254 ( 5030)
  hydrogen bonds       : bond        0.02680 (  121)
  hydrogen bonds       : angle       5.95459 (  309)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 976.88 seconds
wall clock time: 17 minutes 29.39 seconds (1049.39 seconds total)