Starting phenix.real_space_refine
on Fri Aug 22 16:41:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pq2_17819/08_2025/8pq2_17819_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pq2_17819/08_2025/8pq2_17819.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pq2_17819/08_2025/8pq2_17819.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pq2_17819/08_2025/8pq2_17819.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pq2_17819/08_2025/8pq2_17819_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pq2_17819/08_2025/8pq2_17819_trim.cif"
  }
  resolution = 3.85
  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=   0.018
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: 5
    Type Number    sf(0)   Gaussians
     S      15      5.16       5
     C    1962      2.51       5
     N     511      2.21       5
     O     577      1.98       5
     H    2891      0.53       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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5956
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 1752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 1752
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 1273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 1273
          Classifications: {'peptide': 85}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 78}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "C"
      Number of atoms: 2917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 2917
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 12, 'TRANS': 177}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.46, per 1000 atoms: 0.25
  Number of scatterers: 5956
  At special positions: 0
  Unit cell: (65.9412, 79.8903, 103.984, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     O     577      8.00
     N     511      7.00
     C    1962      6.00
     H    2891      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " 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
  Links applied
    NAG-ASN
      " NAG C 601 " - " ASN C 343 "
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 144.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  720

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 8 sheets defined
      6.7% alpha, 34.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.913A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 371
      removed outlier: 3.562A  pdb=" N   VAL C 367 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE C 371 " --> pdb=" O   ILE C 368 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 387
      removed outlier: 3.668A  pdb=" N   LEU C 387 " --> pdb=" O   PRO C 384 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.474A  pdb=" N   SER C 408 " --> pdb=" O   ASN C 405 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 8
    Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59
      removed outlier: 6.250A  pdb=" N   LEU H  45 " --> pdb=" O   SER H  40 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   SER H  40 " --> pdb=" O   LEU H  45 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   CYS H  95 " --> pdb=" O   TRP H 111 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   TRP H 111 " --> pdb=" O   CYS H  95 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   ARG H  97 " --> pdb=" O   ASP H 109 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   SER H  99 " --> pdb=" O   ARG H 107 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   ARG H 107 " --> pdb=" O   SER H  99 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 59
      removed outlier: 6.250A  pdb=" N   LEU H  45 " --> pdb=" O   SER H  40 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   SER H  40 " --> pdb=" O   LEU H  45 " (cutoff:3.500A)
      removed outlier: 4.839A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 19 through 24
      removed outlier: 4.192A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  75 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ILE L  75 " --> pdb=" O   VAL L  19 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 34 through 39
      removed outlier: 6.635A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   LYS L  39 " --> pdb=" O   ALA L  43 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   ALA L  43 " --> pdb=" O   LYS L  39 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 354 through 358
    Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474

    94 hydrogen bonds defined for protein.
    222 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: 1.48

  Time building geometry restraints manager: 0.76 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 2881
        1.04 -     1.23: 89
        1.23 -     1.43: 1332
        1.43 -     1.63: 1726
        1.63 -     1.82: 18
  Bond restraints: 6046
  Sorted by residual:
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.430 -0.024 2.00e-02 2.50e+03 1.50e+00
  bond pdb=" C5  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.22e+00
  bond pdb=" C3  NAG C 601 "
       pdb=" O3  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.94e-01
  bond pdb=" C2  NAG C 601 "
       pdb=" N2  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.439  1.454 -0.015 2.00e-02 2.50e+03 5.45e-01
  bond pdb=" C4  NAG C 601 "
       pdb=" O4  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.409  1.423 -0.014 2.00e-02 2.50e+03 4.81e-01
  ... (remaining 6041 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.88: 9868
        0.88 -     1.76: 883
        1.76 -     2.65: 45
        2.65 -     3.53: 16
        3.53 -     4.41: 11
  Bond angle restraints: 10823
  Sorted by residual:
  angle pdb=" N   THR L  69 "
        pdb=" CA  THR L  69 "
        pdb=" CB  THR L  69 "
      ideal   model   delta    sigma   weight residual
     113.89  109.86    4.03 1.93e+00 2.68e-01 4.35e+00
  angle pdb=" C   GLY L  68 "
        pdb=" N   THR L  69 "
        pdb=" CA  THR L  69 "
      ideal   model   delta    sigma   weight residual
     124.82  121.83    2.99 1.78e+00 3.16e-01 2.83e+00
  angle pdb=" C   SER L  60 "
        pdb=" CA  SER L  60 "
        pdb=" CB  SER L  60 "
      ideal   model   delta    sigma   weight residual
     111.50  109.34    2.16 1.29e+00 6.01e-01 2.79e+00
  angle pdb=" C   PHE H  33 "
        pdb=" N   TRP H  34 "
        pdb=" CA  TRP H  34 "
      ideal   model   delta    sigma   weight residual
     122.77  120.73    2.04 1.41e+00 5.03e-01 2.10e+00
  angle pdb=" C   ALA L  43 "
        pdb=" CA  ALA L  43 "
        pdb=" CB  ALA L  43 "
      ideal   model   delta    sigma   weight residual
     109.46  111.70   -2.24 1.64e+00 3.72e-01 1.87e+00
  ... (remaining 10818 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 2773
       17.34 -    34.68: 109
       34.68 -    52.02: 54
       52.02 -    69.36: 19
       69.36 -    86.69: 3
  Dihedral angle restraints: 2958
    sinusoidal: 1542
      harmonic: 1416
  Sorted by residual:
  dihedral pdb=" CA  PRO L  59 "
           pdb=" C   PRO L  59 "
           pdb=" N   SER L  60 "
           pdb=" CA  SER L  60 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.97  -17.03     0      5.00e+00 4.00e-02 1.16e+01
  dihedral pdb=" N   LYS L  39 "
           pdb=" CA  LYS L  39 "
           pdb=" CB  LYS L  39 "
           pdb=" CG  LYS L  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.36   57.36     3      1.50e+01 4.44e-03 9.44e+00
  dihedral pdb=" CB  LYS L  39 "
           pdb=" CG  LYS L  39 "
           pdb=" CD  LYS L  39 "
           pdb=" CE  LYS L  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.99  -56.01     3      1.50e+01 4.44e-03 9.38e+00
  ... (remaining 2955 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 259
       0.029 -    0.058: 147
       0.058 -    0.087: 21
       0.087 -    0.116: 30
       0.116 -    0.145: 7
  Chirality restraints: 464
  Sorted by residual:
  chirality pdb=" C1  NAG C 601 "
            pdb=" ND2 ASN C 343 "
            pdb=" C2  NAG C 601 "
            pdb=" O5  NAG C 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 5.23e-01
  chirality pdb=" CA  ILE C 434 "
            pdb=" N   ILE C 434 "
            pdb=" C   ILE C 434 "
            pdb=" CB  ILE C 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.37e-01
  chirality pdb=" CA  VAL C 362 "
            pdb=" N   VAL C 362 "
            pdb=" C   VAL C 362 "
            pdb=" CB  VAL C 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.01e-01
  ... (remaining 461 not shown)

  Planarity restraints: 916
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 336 "   -0.019 5.00e-02 4.00e+02   2.84e-02 1.29e+00
        pdb=" N   PRO C 337 "    0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO C 337 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO C 337 "   -0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL L  58 "   -0.016 5.00e-02 4.00e+02   2.38e-02 9.07e-01
        pdb=" N   PRO L  59 "    0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO L  59 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO L  59 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR L  36 "    0.005 2.00e-02 2.50e+03   9.23e-03 8.52e-01
        pdb=" C   TYR L  36 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   TYR L  36 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLN L  37 "    0.005 2.00e-02 2.50e+03
  ... (remaining 913 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 345
        2.20 -     2.80: 11960
        2.80 -     3.40: 14397
        3.40 -     4.00: 19307
        4.00 -     4.60: 28938
  Nonbonded interactions: 74947
  Sorted by model distance:
  nonbonded pdb=" HE2 HIS C 339 "
            pdb=" O7  NAG C 601 "
     model   vdw
     1.602 2.450
  nonbonded pdb=" OD1 ASP H  98 "
            pdb=" H   GLY H 108 "
     model   vdw
     1.623 2.450
  nonbonded pdb=" OE1 GLN C 493 "
            pdb=" H   SER C 494 "
     model   vdw
     1.668 2.450
  nonbonded pdb="HH22 ARG H  66 "
            pdb=" OD2 ASP H  89 "
     model   vdw
     1.670 2.450
  nonbonded pdb="HH12 ARG C 457 "
            pdb=" OD2 ASP C 467 "
     model   vdw
     1.690 2.450
  ... (remaining 74942 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:             3.210
  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:             0.030
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.600
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:1.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
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      :  0.002   0.024   3161  Z= 0.112
  Angle     :  0.512   4.411   4314  Z= 0.265
  Chirality :  0.043   0.145    464
  Planarity :  0.003   0.028    551
  Dihedral  : 10.370  74.805   1115
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  :  3.33 %
    Favored  : 93.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.04 (0.40), residues: 384
  helix: -2.37 (1.01), residues: 29
  sheet: -0.21 (0.45), residues: 116
  loop : -1.91 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 457 
 TYR   0.008   0.001   TYR H  94 
 PHE   0.007   0.001   PHE H  33 
 TRP   0.007   0.001   TRP H   7 
 HIS   0.001   0.000   HIS C 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 3155)
  covalent geometry    : angle       0.50976 ( 4301)
  SS BOND              : bond        0.00317 (    5)
  SS BOND              : angle       0.97274 (   10)
  hydrogen bonds       : bond        0.08489 (   81)
  hydrogen bonds       : angle       5.25376 (  222)
  link_NAG-ASN         : bond        0.00181 (    1)
  link_NAG-ASN         : angle       0.97674 (    3)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  424 is missing expected H atoms. Skipping.
Evaluate side-chains
  82 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.8186 (m) cc_final: 0.7806 (p)
REVERT: L   85 THR cc_start: 0.8472 (m) cc_final: 0.7975 (p)
REVERT: C  353 TRP cc_start: 0.9135 (p-90) cc_final: 0.8921 (p-90)
REVERT: C  474 GLN cc_start: 0.7895 (tt0) cc_final: 0.7378 (tt0)
  outliers start: 9
  outliers final: 4
  residues processed: 79
  average time/residue: 0.1530
  time to fit residues: 14.2445
Evaluate side-chains
  55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   86 THR
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   81 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
H  58 ASN
C 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.110526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.092933 restraints weight = 17030.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.097246 restraints weight = 8171.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.100212 restraints weight = 5011.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.102305 restraints weight = 3461.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.103814 restraints weight = 2568.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3161  Z= 0.144
  Angle     :  0.565   5.155   4314  Z= 0.289
  Chirality :  0.044   0.146    464
  Planarity :  0.004   0.040    551
  Dihedral  :  6.924  73.371    458
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.72 %
    Favored  : 88.28 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 10.00 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.13 (0.40), residues: 384
  helix: -3.04 (0.94), residues: 29
  sheet: -0.42 (0.45), residues: 123
  loop : -1.82 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 509 
 TYR   0.011   0.001   TYR H  94 
 PHE   0.028   0.002   PHE H  29 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.003   0.001   HIS C 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 3155)
  covalent geometry    : angle       0.55736 ( 4301)
  SS BOND              : bond        0.00820 (    5)
  SS BOND              : angle       1.95101 (   10)
  hydrogen bonds       : bond        0.03508 (   81)
  hydrogen bonds       : angle       4.93893 (  222)
  link_NAG-ASN         : bond        0.00241 (    1)
  link_NAG-ASN         : angle       1.21529 (    3)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  424 is missing expected H atoms. Skipping.
Evaluate side-chains
  60 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   59 TYR cc_start: 0.8620 (m-10) cc_final: 0.8386 (m-10)
REVERT: L   74 THR cc_start: 0.8211 (m) cc_final: 0.7870 (p)
REVERT: C  474 GLN cc_start: 0.8121 (tt0) cc_final: 0.7626 (tt0)
  outliers start: 7
  outliers final: 6
  residues processed: 58
  average time/residue: 0.1337
  time to fit residues: 9.3691
Evaluate side-chains
  55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   86 THR
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue   94 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
L  37 GLN
L  50 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.108751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.091294 restraints weight = 16985.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.095553 restraints weight = 8237.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.098508 restraints weight = 5056.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.100513 restraints weight = 3505.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.101943 restraints weight = 2625.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3161  Z= 0.161
  Angle     :  0.559   5.603   4314  Z= 0.287
  Chirality :  0.044   0.151    464
  Planarity :  0.004   0.032    551
  Dihedral  :  7.014  77.179    458
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.46 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 11.52 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.11 (0.40), residues: 384
  helix: -2.27 (1.14), residues: 23
  sheet: -0.34 (0.45), residues: 119
  loop : -1.98 (0.37), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 509 
 TYR   0.013   0.001   TYR H  94 
 PHE   0.016   0.001   PHE H  29 
 TRP   0.009   0.001   TRP L  35 
 HIS   0.001   0.001   HIS L  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3155)
  covalent geometry    : angle       0.55557 ( 4301)
  SS BOND              : bond        0.00525 (    5)
  SS BOND              : angle       1.37581 (   10)
  hydrogen bonds       : bond        0.03532 (   81)
  hydrogen bonds       : angle       4.95503 (  222)
  link_NAG-ASN         : bond        0.00322 (    1)
  link_NAG-ASN         : angle       1.14137 (    3)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  424 is missing expected H atoms. Skipping.
Evaluate side-chains
  60 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   59 TYR cc_start: 0.8645 (m-10) cc_final: 0.8403 (m-10)
REVERT: L   74 THR cc_start: 0.8254 (m) cc_final: 0.7887 (p)
REVERT: C  378 LYS cc_start: 0.7699 (ttmm) cc_final: 0.7344 (ttmm)
REVERT: C  474 GLN cc_start: 0.8201 (tt0) cc_final: 0.7958 (tt0)
  outliers start: 11
  outliers final: 7
  residues processed: 57
  average time/residue: 0.1341
  time to fit residues: 9.3111
Evaluate side-chains
  55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   61 ARG
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue   94 LEU
Chi-restraints excluded: chain C residue  361 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 33 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
L  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.108631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.091047 restraints weight = 17099.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.095272 restraints weight = 8205.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.098235 restraints weight = 5045.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.100305 restraints weight = 3496.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.101767 restraints weight = 2609.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3161  Z= 0.150
  Angle     :  0.552   5.696   4314  Z= 0.283
  Chirality :  0.044   0.151    464
  Planarity :  0.004   0.032    551
  Dihedral  :  6.815  77.230    457
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.72 %
    Favored  : 88.28 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 12.12 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.12 (0.40), residues: 384
  helix: -2.27 (1.14), residues: 23
  sheet: -0.32 (0.46), residues: 119
  loop : -2.00 (0.36), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 509 
 TYR   0.013   0.001   TYR H  94 
 PHE   0.015   0.001   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.001   0.001   HIS C 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 3155)
  covalent geometry    : angle       0.54805 ( 4301)
  SS BOND              : bond        0.00434 (    5)
  SS BOND              : angle       1.28853 (   10)
  hydrogen bonds       : bond        0.03456 (   81)
  hydrogen bonds       : angle       4.93058 (  222)
  link_NAG-ASN         : bond        0.00310 (    1)
  link_NAG-ASN         : angle       1.12793 (    3)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  424 is missing expected H atoms. Skipping.
Evaluate side-chains
  59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 48
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   59 TYR cc_start: 0.8599 (m-10) cc_final: 0.8383 (m-10)
REVERT: L   74 THR cc_start: 0.8258 (m) cc_final: 0.7880 (p)
REVERT: C  378 LYS cc_start: 0.7660 (ttmm) cc_final: 0.7292 (ttmm)
  outliers start: 11
  outliers final: 8
  residues processed: 55
  average time/residue: 0.1349
  time to fit residues: 8.9407
Evaluate side-chains
  55 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   50 HIS
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue   94 LEU
Chi-restraints excluded: chain C residue  361 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.3980
   chunk 32 optimal weight:    0.0070
   chunk 22 optimal weight:    0.9980
   chunk 34 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 28 optimal weight:    0.4980
   overall best weight:    0.4398

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

Flipped N/Q/H residues before XYZ refinement:
L  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.110072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.092276 restraints weight = 17168.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.096606 restraints weight = 8262.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.099650 restraints weight = 5074.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.101716 restraints weight = 3492.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.103158 restraints weight = 2609.169|
|-----------------------------------------------------------------------------|
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   3161  Z= 0.103
  Angle     :  0.529   5.753   4314  Z= 0.271
  Chirality :  0.044   0.145    464
  Planarity :  0.004   0.034    551
  Dihedral  :  6.234  77.385    453
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.38 %
    Favored  : 90.62 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 12.12 %
    Favored  : 84.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.06 (0.40), residues: 384
  helix: -2.16 (1.16), residues: 23
  sheet: -0.20 (0.46), residues: 115
  loop : -1.98 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 509 
 TYR   0.014   0.001   TYR L  49 
 PHE   0.032   0.001   PHE H  29 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.002   0.001   HIS L  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3155)
  covalent geometry    : angle       0.52651 ( 4301)
  SS BOND              : bond        0.00362 (    5)
  SS BOND              : angle       1.02865 (   10)
  hydrogen bonds       : bond        0.03088 (   81)
  hydrogen bonds       : angle       4.83121 (  222)
  link_NAG-ASN         : bond        0.00308 (    1)
  link_NAG-ASN         : angle       0.88482 (    3)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  424 is missing expected H atoms. Skipping.
Evaluate side-chains
  59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   61 ARG cc_start: 0.7288 (tpp-160) cc_final: 0.6855 (tpp-160)
REVERT: L   74 THR cc_start: 0.8244 (m) cc_final: 0.7888 (p)
REVERT: C  378 LYS cc_start: 0.7619 (ttmm) cc_final: 0.7265 (ttmm)
  outliers start: 10
  outliers final: 7
  residues processed: 56
  average time/residue: 0.1432
  time to fit residues: 9.6067
Evaluate side-chains
  54 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue   94 LEU
Chi-restraints excluded: chain C residue  361 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0370
   chunk 2 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.6058

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

Flipped N/Q/H residues before XYZ refinement:
L  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.109425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.091745 restraints weight = 16909.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.096047 restraints weight = 8236.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.099007 restraints weight = 5063.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.101003 restraints weight = 3512.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.102530 restraints weight = 2652.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3161  Z= 0.119
  Angle     :  0.527   5.583   4314  Z= 0.269
  Chirality :  0.044   0.147    464
  Planarity :  0.004   0.034    551
  Dihedral  :  6.168  77.138    453
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.42 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 11.82 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.09 (0.40), residues: 384
  helix: -2.14 (1.15), residues: 23
  sheet: -0.35 (0.45), residues: 119
  loop : -1.96 (0.37), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 509 
 TYR   0.011   0.001   TYR H  94 
 PHE   0.027   0.001   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.001   0.000   HIS C 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3155)
  covalent geometry    : angle       0.52477 ( 4301)
  SS BOND              : bond        0.00371 (    5)
  SS BOND              : angle       1.03086 (   10)
  hydrogen bonds       : bond        0.03182 (   81)
  hydrogen bonds       : angle       4.80997 (  222)
  link_NAG-ASN         : bond        0.00314 (    1)
  link_NAG-ASN         : angle       0.89484 (    3)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  424 is missing expected H atoms. Skipping.
Evaluate side-chains
  61 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 48
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.8257 (m) cc_final: 0.7891 (p)
REVERT: C  378 LYS cc_start: 0.7640 (ttmm) cc_final: 0.7268 (ttmm)
  outliers start: 13
  outliers final: 9
  residues processed: 57
  average time/residue: 0.1544
  time to fit residues: 10.4545
Evaluate side-chains
  56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   86 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue   94 LEU
Chi-restraints excluded: chain C residue  361 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 10 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    0.4980
   chunk 37 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
L  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.109677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.091991 restraints weight = 17075.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.096227 restraints weight = 8267.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.099191 restraints weight = 5107.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.101313 restraints weight = 3543.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.102707 restraints weight = 2628.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   3161  Z= 0.125
  Angle     :  0.544   5.493   4314  Z= 0.278
  Chirality :  0.044   0.153    464
  Planarity :  0.004   0.034    551
  Dihedral  :  6.341  77.263    453
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.68 %
    Favored  : 89.32 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 12.73 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.12 (0.40), residues: 384
  helix: -2.22 (1.14), residues: 23
  sheet: -0.27 (0.46), residues: 115
  loop : -2.00 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 509 
 TYR   0.014   0.001   TYR H  59 
 PHE   0.024   0.001   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.002   0.001   HIS C 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3155)
  covalent geometry    : angle       0.53794 ( 4301)
  SS BOND              : bond        0.00400 (    5)
  SS BOND              : angle       1.66464 (   10)
  hydrogen bonds       : bond        0.03161 (   81)
  hydrogen bonds       : angle       4.81132 (  222)
  link_NAG-ASN         : bond        0.00326 (    1)
  link_NAG-ASN         : angle       0.92015 (    3)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  424 is missing expected H atoms. Skipping.
Evaluate side-chains
  58 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.8259 (m) cc_final: 0.7892 (p)
REVERT: C  378 LYS cc_start: 0.7635 (ttmm) cc_final: 0.7260 (ttmm)
  outliers start: 10
  outliers final: 8
  residues processed: 54
  average time/residue: 0.1485
  time to fit residues: 9.5663
Evaluate side-chains
  56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   86 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue   94 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
L  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.108812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.091234 restraints weight = 17020.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.095430 restraints weight = 8256.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.098390 restraints weight = 5106.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.100400 restraints weight = 3546.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.101779 restraints weight = 2666.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3161  Z= 0.143
  Angle     :  0.543   5.388   4314  Z= 0.279
  Chirality :  0.044   0.156    464
  Planarity :  0.004   0.034    551
  Dihedral  :  6.402  77.411    453
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.16 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 12.42 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.20 (0.39), residues: 384
  helix: -2.28 (1.13), residues: 23
  sheet: -0.30 (0.46), residues: 115
  loop : -2.07 (0.36), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 509 
 TYR   0.012   0.001   TYR H  94 
 PHE   0.023   0.001   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.001   0.001   HIS C 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3155)
  covalent geometry    : angle       0.54117 ( 4301)
  SS BOND              : bond        0.00454 (    5)
  SS BOND              : angle       0.99537 (   10)
  hydrogen bonds       : bond        0.03338 (   81)
  hydrogen bonds       : angle       4.82666 (  222)
  link_NAG-ASN         : bond        0.00307 (    1)
  link_NAG-ASN         : angle       0.95176 (    3)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  424 is missing expected H atoms. Skipping.
Evaluate side-chains
  59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.8273 (m) cc_final: 0.7897 (p)
REVERT: C  378 LYS cc_start: 0.7656 (ttmm) cc_final: 0.7273 (ttmm)
  outliers start: 10
  outliers final: 9
  residues processed: 55
  average time/residue: 0.1569
  time to fit residues: 10.1180
Evaluate side-chains
  56 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   86 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue   94 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
L  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.108593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.090744 restraints weight = 17204.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.094990 restraints weight = 8412.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.097927 restraints weight = 5213.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.100002 restraints weight = 3644.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.101445 restraints weight = 2737.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3161  Z= 0.145
  Angle     :  0.561   5.618   4314  Z= 0.288
  Chirality :  0.044   0.159    464
  Planarity :  0.004   0.033    551
  Dihedral  :  6.378  77.707    453
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.46 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 11.82 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.25 (0.39), residues: 384
  helix: -2.29 (1.12), residues: 23
  sheet: -0.33 (0.46), residues: 115
  loop : -2.12 (0.35), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 509 
 TYR   0.012   0.001   TYR H  94 
 PHE   0.040   0.002   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.001   0.001   HIS C 339 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 3155)
  covalent geometry    : angle       0.55861 ( 4301)
  SS BOND              : bond        0.00459 (    5)
  SS BOND              : angle       1.20524 (   10)
  hydrogen bonds       : bond        0.03381 (   81)
  hydrogen bonds       : angle       4.84608 (  222)
  link_NAG-ASN         : bond        0.00305 (    1)
  link_NAG-ASN         : angle       0.98523 (    3)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  424 is missing expected H atoms. Skipping.
Evaluate side-chains
  62 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.8274 (m) cc_final: 0.7890 (p)
REVERT: C  378 LYS cc_start: 0.7637 (ttmm) cc_final: 0.7260 (ttmm)
  outliers start: 12
  outliers final: 10
  residues processed: 58
  average time/residue: 0.1294
  time to fit residues: 9.0944
Evaluate side-chains
  59 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 49
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain H residue   86 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue   94 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 22 optimal weight:    0.0270
   chunk 12 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 32 optimal weight:    0.6980
   chunk 17 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
L  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.109746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.091815 restraints weight = 17071.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.096122 restraints weight = 8373.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.099102 restraints weight = 5194.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.101171 restraints weight = 3620.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.102596 restraints weight = 2719.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3161  Z= 0.111
  Angle     :  0.541   5.593   4314  Z= 0.277
  Chirality :  0.044   0.155    464
  Planarity :  0.004   0.034    551
  Dihedral  :  6.290  77.671    453
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 11.82 %
    Favored  : 84.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.21 (0.39), residues: 384
  helix: -2.29 (1.11), residues: 24
  sheet: -0.27 (0.46), residues: 115
  loop : -2.10 (0.36), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 509 
 TYR   0.010   0.001   TYR H  94 
 PHE   0.039   0.001   PHE H  29 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.002   0.001   HIS L  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3155)
  covalent geometry    : angle       0.53949 ( 4301)
  SS BOND              : bond        0.00424 (    5)
  SS BOND              : angle       1.03969 (   10)
  hydrogen bonds       : bond        0.03129 (   81)
  hydrogen bonds       : angle       4.78599 (  222)
  link_NAG-ASN         : bond        0.00299 (    1)
  link_NAG-ASN         : angle       0.84029 (    3)

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

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

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  768 Ramachandran restraints generated.
    384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  424 is missing expected H atoms. Skipping.
Evaluate side-chains
  62 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   74 THR cc_start: 0.8263 (m) cc_final: 0.7864 (p)
REVERT: C  378 LYS cc_start: 0.7616 (ttmm) cc_final: 0.7248 (ttmm)
  outliers start: 12
  outliers final: 10
  residues processed: 58
  average time/residue: 0.1576
  time to fit residues: 10.7876
Evaluate side-chains
  57 residues out of total 335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   82 LEU
Chi-restraints excluded: chain H residue   86 THR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   21 VAL
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   77 SER
Chi-restraints excluded: chain L residue   81 GLU
Chi-restraints excluded: chain L residue   94 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 38
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0980
   chunk 0 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   chunk 1 optimal weight:    0.2980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
L  50 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.109638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.091729 restraints weight = 17041.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.096030 restraints weight = 8314.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.099019 restraints weight = 5144.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.101093 restraints weight = 3583.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.102599 restraints weight = 2692.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3161  Z= 0.115
  Angle     :  0.543   5.720   4314  Z= 0.277
  Chirality :  0.044   0.156    464
  Planarity :  0.004   0.035    551
  Dihedral  :  6.215  77.305    453
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.42 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 13.03 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.19 (0.40), residues: 384
  helix: -2.17 (1.13), residues: 24
  sheet: -0.25 (0.46), residues: 115
  loop : -2.11 (0.36), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 509 
 TYR   0.010   0.001   TYR H  94 
 PHE   0.038   0.001   PHE H  29 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.002   0.001   HIS L  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 3155)
  covalent geometry    : angle       0.54148 ( 4301)
  SS BOND              : bond        0.00422 (    5)
  SS BOND              : angle       1.03634 (   10)
  hydrogen bonds       : bond        0.03114 (   81)
  hydrogen bonds       : angle       4.73995 (  222)
  link_NAG-ASN         : bond        0.00298 (    1)
  link_NAG-ASN         : angle       0.79509 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1532.87 seconds
wall clock time: 26 minutes 41.66 seconds (1601.66 seconds total)