Starting phenix.real_space_refine
on Tue Feb  3 15:40:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kvz_62605/02_2026/9kvz_62605.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kvz_62605/02_2026/9kvz_62605.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kvz_62605/02_2026/9kvz_62605.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kvz_62605/02_2026/9kvz_62605.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kvz_62605/02_2026/9kvz_62605.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kvz_62605/02_2026/9kvz_62605.cif"
  }
  resolution = 2.94
  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=   0.008
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      32      5.16       5
     C    2892      2.51       5
     N     720      2.21       5
     O     782      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 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: 4426
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 2213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2213
          Classifications: {'peptide': 290}
          Link IDs: {'PTRANS': 13, 'TRANS': 276}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2213
          Classifications: {'peptide': 290}
          Link IDs: {'PTRANS': 13, 'TRANS': 276}
          Chain breaks: 2
  Time building chain proxies: 1.08, per 1000 atoms: 0.24
  Number of scatterers: 4426
  At special positions: 0
  Unit cell: (74.56, 60.58, 109.976, 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      32     16.00
     O     782      8.00
     N     720      7.00
     C    2892      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 273 " - pdb=" SG  CYS B 277 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 404 " - pdb=" SG  CYS B 409 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 273 " - pdb=" SG  CYS A 277 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 404 " - pdb=" SG  CYS A 409 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 394.9 milliseconds
  

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1088

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 2 sheets defined
      67.4% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'B' and resid 12 through 33
      removed outlier: 4.047A  pdb=" N   VAL B  16 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TYR B  30 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 61
    Processing helix  chain 'B' and resid 76 through 104
    Processing helix  chain 'B' and resid 112 through 133
    Processing helix  chain 'B' and resid 244 through 265
      removed outlier: 4.481A  pdb=" N   ASP B 248 " --> pdb=" O   HIS B 244 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   ALA B 249 " --> pdb=" O   VAL B 245 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 277
    Processing helix  chain 'B' and resid 278 through 307
      Proline residue:  B 297  - end of helix
    Processing helix  chain 'B' and resid 315 through 326
    Processing helix  chain 'B' and resid 359 through 373
    Processing helix  chain 'B' and resid 406 through 413
      removed outlier: 3.592A  pdb=" N   LYS B 411 " --> pdb=" O   GLY B 408 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   LEU B 413 " --> pdb=" O   ALA B 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 12 through 33
      removed outlier: 3.966A  pdb=" N   VAL A  16 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   TYR A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 34 through 61
    Processing helix  chain 'A' and resid 76 through 106
    Processing helix  chain 'A' and resid 112 through 133
    Processing helix  chain 'A' and resid 244 through 265
    Processing helix  chain 'A' and resid 274 through 277
    Processing helix  chain 'A' and resid 278 through 307
      Proline residue:  A 297  - end of helix
    Processing helix  chain 'A' and resid 315 through 326
    Processing helix  chain 'A' and resid 359 through 373
    Processing helix  chain 'A' and resid 395 through 399
      removed outlier: 3.899A  pdb=" N   LEU A 398 " --> pdb=" O   ASP A 395 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU A 399 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 395 through 399'
    Processing helix  chain 'A' and resid 406 through 413
      removed outlier: 3.584A  pdb=" N   LYS A 411 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 331 through 341
      removed outlier: 5.533A  pdb=" N   VAL B 332 " --> pdb=" O   LYS B 352 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LYS B 352 " --> pdb=" O   VAL B 332 " (cutoff:3.500A)
      removed outlier: 4.894A  pdb=" N   GLU B 334 " --> pdb=" O   HIS B 350 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   HIS B 350 " --> pdb=" O   GLU B 334 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LYS B 344 " --> pdb=" O   LEU B 340 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASN B 377 " --> pdb=" O   ILE B 345 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 331 through 341
      removed outlier: 5.541A  pdb=" N   VAL A 332 " --> pdb=" O   LYS A 352 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LYS A 352 " --> pdb=" O   VAL A 332 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   GLU A 334 " --> pdb=" O   HIS A 350 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   HIS A 350 " --> pdb=" O   GLU A 334 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   LYS A 344 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASN A 377 " --> pdb=" O   ILE A 345 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    933 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: 0.69

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1350
        1.34 -     1.45: 520
        1.45 -     1.57: 2592
        1.57 -     1.69: 0
        1.69 -     1.81: 46
  Bond restraints: 4508
  Sorted by residual:
  bond pdb=" N   CYS A 414 "
       pdb=" CA  CYS A 414 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.029 1.23e-02 6.61e+03 5.66e+00
  bond pdb=" N   GLN B 412 "
       pdb=" CA  GLN B 412 "
    ideal  model  delta    sigma   weight residual
    1.462  1.487 -0.025 1.15e-02 7.56e+03 4.91e+00
  bond pdb=" N   CYS A 415 "
       pdb=" CA  CYS A 415 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.41e-02 5.03e+03 4.86e+00
  bond pdb=" C   PRO B 416 "
       pdb=" O   PRO B 416 "
    ideal  model  delta    sigma   weight residual
    1.240  1.217  0.023 1.12e-02 7.97e+03 4.26e+00
  bond pdb=" C   CYS A 415 "
       pdb=" N   PRO A 416 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.023 1.18e-02 7.18e+03 3.96e+00
  ... (remaining 4503 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 5968
        1.54 -     3.09: 125
        3.09 -     4.63: 25
        4.63 -     6.18: 9
        6.18 -     7.72: 7
  Bond angle restraints: 6134
  Sorted by residual:
  angle pdb=" CA  CYS A 414 "
        pdb=" C   CYS A 414 "
        pdb=" O   CYS A 414 "
      ideal   model   delta    sigma   weight residual
     121.19  117.19    4.00 1.10e+00 8.26e-01 1.32e+01
  angle pdb=" C   GLN A 412 "
        pdb=" N   LEU A 413 "
        pdb=" CA  LEU A 413 "
      ideal   model   delta    sigma   weight residual
     121.24  116.16    5.08 1.44e+00 4.82e-01 1.24e+01
  angle pdb=" CA  CYS B 414 "
        pdb=" C   CYS B 414 "
        pdb=" O   CYS B 414 "
      ideal   model   delta    sigma   weight residual
     121.56  117.86    3.70 1.09e+00 8.42e-01 1.15e+01
  angle pdb=" N   CYS A 414 "
        pdb=" CA  CYS A 414 "
        pdb=" C   CYS A 414 "
      ideal   model   delta    sigma   weight residual
     110.23  106.26    3.97 1.45e+00 4.76e-01 7.48e+00
  angle pdb=" CA  LYS B 411 "
        pdb=" C   LYS B 411 "
        pdb=" N   GLN B 412 "
      ideal   model   delta    sigma   weight residual
     117.17  113.95    3.22 1.18e+00 7.18e-01 7.44e+00
  ... (remaining 6129 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 2400
       17.87 -    35.75: 231
       35.75 -    53.62: 59
       53.62 -    71.49: 21
       71.49 -    89.36: 3
  Dihedral angle restraints: 2714
    sinusoidal: 1036
      harmonic: 1678
  Sorted by residual:
  dihedral pdb=" CB  CYS A 404 "
           pdb=" SG  CYS A 404 "
           pdb=" SG  CYS A 409 "
           pdb=" CB  CYS A 409 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -0.76  -85.24     1      1.00e+01 1.00e-02 8.80e+01
  dihedral pdb=" CB  CYS B 404 "
           pdb=" SG  CYS B 404 "
           pdb=" SG  CYS B 409 "
           pdb=" CB  CYS B 409 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -5.63  -80.37     1      1.00e+01 1.00e-02 7.99e+01
  dihedral pdb=" CB  GLU B 114 "
           pdb=" CG  GLU B 114 "
           pdb=" CD  GLU B 114 "
           pdb=" OE1 GLU B 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.36   89.36     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 2711 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 580
       0.044 -    0.089: 146
       0.089 -    0.133: 37
       0.133 -    0.178: 4
       0.178 -    0.222: 1
  Chirality restraints: 768
  Sorted by residual:
  chirality pdb=" CA  LEU B 413 "
            pdb=" N   LEU B 413 "
            pdb=" C   LEU B 413 "
            pdb=" CB  LEU B 413 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  CYS A 414 "
            pdb=" N   CYS A 414 "
            pdb=" C   CYS A 414 "
            pdb=" CB  CYS A 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.88e-01
  chirality pdb=" CA  CYS B 414 "
            pdb=" N   CYS B 414 "
            pdb=" C   CYS B 414 "
            pdb=" CB  CYS B 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.87e-01
  ... (remaining 765 not shown)

  Planarity restraints: 752
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 411 "    0.026 2.00e-02 2.50e+03   5.23e-02 2.73e+01
        pdb=" C   LYS B 411 "   -0.090 2.00e-02 2.50e+03
        pdb=" O   LYS B 411 "    0.035 2.00e-02 2.50e+03
        pdb=" N   GLN B 412 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 412 "   -0.019 2.00e-02 2.50e+03   3.77e-02 1.42e+01
        pdb=" C   GLN A 412 "    0.065 2.00e-02 2.50e+03
        pdb=" O   GLN A 412 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LEU A 413 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 415 "    0.023 5.00e-02 4.00e+02   3.48e-02 1.94e+00
        pdb=" N   PRO A 416 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 416 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 416 "    0.019 5.00e-02 4.00e+02
  ... (remaining 749 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 816
        2.77 -     3.30: 4418
        3.30 -     3.84: 7782
        3.84 -     4.37: 8629
        4.37 -     4.90: 15148
  Nonbonded interactions: 36793
  Sorted by model distance:
  nonbonded pdb=" O   MET A  14 "
            pdb=" OG1 THR A  18 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" NZ  LYS A 352 "
            pdb=" OD1 ASN A 401 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" O   TYR B 359 "
            pdb=" OG  SER B 363 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   TYR A 359 "
            pdb=" OG  SER A 363 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" NZ  LYS B 352 "
            pdb=" OD1 ASN B 401 "
     model   vdw
     2.278 3.120
  ... (remaining 36788 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.760
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.400
  Find NCS groups from input model:        0.070
  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:8.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4512  Z= 0.192
  Angle     :  0.629   7.721   6142  Z= 0.341
  Chirality :  0.042   0.222    768
  Planarity :  0.005   0.052    752
  Dihedral  : 16.080  89.364   1614
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 27.31 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.35), residues: 568
  helix:  2.32 (0.27), residues: 346
  sheet: -0.59 (0.68), residues: 52
  loop : -0.27 (0.47), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  66 
 TYR   0.013   0.001   TYR A 263 
 PHE   0.017   0.002   PHE A  21 
 TRP   0.009   0.001   TRP B 275 
 HIS   0.004   0.001   HIS A 333 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 4508)
  covalent geometry    : angle       0.62913 ( 6134)
  SS BOND              : bond        0.00275 (    4)
  SS BOND              : angle       0.67691 (    8)
  hydrogen bonds       : bond        0.13229 (  320)
  hydrogen bonds       : angle       5.26199 (  933)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 193
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.8198 (pp) cc_final: 0.7971 (pt)
  outliers start: 5
  outliers final: 0
  residues processed: 197
  average time/residue: 0.4994
  time to fit residues: 101.9656
Evaluate side-chains
  132 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.4980
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 127 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.104475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.084074 restraints weight = 9334.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 3.33
r_work: 0.3108 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4512  Z= 0.156
  Angle     :  0.678   8.601   6142  Z= 0.331
  Chirality :  0.043   0.171    768
  Planarity :  0.004   0.031    752
  Dihedral  :  3.789  13.255    610
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 28.92 %
    Favored  : 65.86 %
  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:  2.11 (0.35), residues: 568
  helix:  2.24 (0.26), residues: 356
  sheet: -0.28 (0.73), residues: 52
  loop :  0.15 (0.52), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  66 
 TYR   0.010   0.001   TYR A 263 
 PHE   0.013   0.001   PHE A  21 
 TRP   0.006   0.001   TRP B 338 
 HIS   0.002   0.001   HIS B 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4508)
  covalent geometry    : angle       0.67710 ( 6134)
  SS BOND              : bond        0.00367 (    4)
  SS BOND              : angle       1.37040 (    8)
  hydrogen bonds       : bond        0.04325 (  320)
  hydrogen bonds       : angle       3.96705 (  933)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 168
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 ASN cc_start: 0.8900 (t0) cc_final: 0.8637 (t160)
REVERT: B   99 GLU cc_start: 0.9257 (tp30) cc_final: 0.8887 (tp30)
REVERT: B  271 ASP cc_start: 0.9214 (m-30) cc_final: 0.8182 (m-30)
REVERT: B  318 GLU cc_start: 0.9196 (mt-10) cc_final: 0.8712 (mt-10)
REVERT: B  355 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6440 (pttm)
REVERT: B  357 ARG cc_start: 0.7806 (mtp-110) cc_final: 0.7474 (mtp-110)
REVERT: A   47 ASP cc_start: 0.8384 (m-30) cc_final: 0.8151 (m-30)
REVERT: A   66 ARG cc_start: 0.8745 (ptp-110) cc_final: 0.8491 (ptp-110)
REVERT: A   85 ASN cc_start: 0.8874 (t0) cc_final: 0.8588 (t160)
REVERT: A   99 GLU cc_start: 0.9259 (tp30) cc_final: 0.8669 (tp30)
REVERT: A  106 ARG cc_start: 0.7651 (mtm-85) cc_final: 0.7008 (mmt180)
REVERT: A  109 ARG cc_start: 0.8146 (ttm-80) cc_final: 0.7444 (ttm110)
REVERT: A  271 ASP cc_start: 0.9157 (m-30) cc_final: 0.8767 (m-30)
REVERT: A  298 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8489 (tt)
REVERT: A  318 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8706 (mt-10)
REVERT: A  412 GLN cc_start: 0.8695 (mp10) cc_final: 0.8375 (mp10)
  outliers start: 26
  outliers final: 7
  residues processed: 184
  average time/residue: 0.4759
  time to fit residues: 90.8558
Evaluate side-chains
  141 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  355 LYS
Chi-restraints excluded: chain A residue   21 PHE
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  293 SER
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  355 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 33 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3582 r_free = 0.3582 target = 0.101729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.082032 restraints weight = 9388.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 3.23
r_work: 0.3094 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.4822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   4512  Z= 0.157
  Angle     :  0.673  10.119   6142  Z= 0.333
  Chirality :  0.043   0.130    768
  Planarity :  0.004   0.037    752
  Dihedral  :  3.793  14.008    610
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  7.23 %
    Allowed  : 32.73 %
    Favored  : 60.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.36), residues: 568
  helix:  2.26 (0.26), residues: 358
  sheet: -0.20 (0.73), residues: 52
  loop :  0.38 (0.55), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 357 
 TYR   0.012   0.001   TYR B  59 
 PHE   0.010   0.001   PHE B  21 
 TRP   0.009   0.002   TRP A 338 
 HIS   0.002   0.001   HIS B 350 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 4508)
  covalent geometry    : angle       0.67186 ( 6134)
  SS BOND              : bond        0.00377 (    4)
  SS BOND              : angle       1.44482 (    8)
  hydrogen bonds       : bond        0.04108 (  320)
  hydrogen bonds       : angle       3.85582 (  933)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 149
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   59 TYR cc_start: 0.8980 (t80) cc_final: 0.8542 (t80)
REVERT: B   85 ASN cc_start: 0.8837 (t0) cc_final: 0.8589 (t160)
REVERT: B   89 LEU cc_start: 0.9198 (tp) cc_final: 0.8862 (tp)
REVERT: B   99 GLU cc_start: 0.9210 (tp30) cc_final: 0.8830 (tp30)
REVERT: B  244 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.6124 (p-80)
REVERT: B  321 SER cc_start: 0.9601 (OUTLIER) cc_final: 0.9321 (p)
REVERT: B  357 ARG cc_start: 0.7849 (mtp-110) cc_final: 0.7492 (mtp-110)
REVERT: A   47 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8111 (m-30)
REVERT: A   99 GLU cc_start: 0.9198 (tp30) cc_final: 0.8837 (tp30)
REVERT: A  106 ARG cc_start: 0.7854 (mtm-85) cc_final: 0.7127 (mmt-90)
REVERT: A  109 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7352 (ttp80)
REVERT: A  318 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8584 (mt-10)
REVERT: A  412 GLN cc_start: 0.8794 (mp10) cc_final: 0.8347 (mp10)
  outliers start: 36
  outliers final: 10
  residues processed: 168
  average time/residue: 0.4185
  time to fit residues: 73.2182
Evaluate side-chains
  140 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  355 LYS
Chi-restraints excluded: chain B residue  395 ASP
Chi-restraints excluded: chain A residue   47 ASP
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  348 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 40 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.099170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.079288 restraints weight = 9391.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 3.19
r_work: 0.3052 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.5395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068   4512  Z= 0.189
  Angle     :  0.703  10.408   6142  Z= 0.348
  Chirality :  0.045   0.186    768
  Planarity :  0.004   0.034    752
  Dihedral  :  3.825  14.543    610
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  7.43 %
    Allowed  : 33.94 %
    Favored  : 58.63 %
  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:  2.23 (0.35), residues: 568
  helix:  2.26 (0.26), residues: 356
  sheet: -0.33 (0.72), residues: 52
  loop :  0.43 (0.55), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 357 
 TYR   0.012   0.001   TYR A  72 
 PHE   0.012   0.001   PHE A  21 
 TRP   0.007   0.001   TRP B 338 
 HIS   0.003   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 4508)
  covalent geometry    : angle       0.70213 ( 6134)
  SS BOND              : bond        0.00225 (    4)
  SS BOND              : angle       1.05005 (    8)
  hydrogen bonds       : bond        0.04180 (  320)
  hydrogen bonds       : angle       3.93792 (  933)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 151
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 ASN cc_start: 0.8839 (t0) cc_final: 0.8625 (t160)
REVERT: B   99 GLU cc_start: 0.9221 (tp30) cc_final: 0.8666 (tp30)
REVERT: B  114 GLU cc_start: 0.8987 (pm20) cc_final: 0.8723 (pm20)
REVERT: B  244 HIS cc_start: 0.7634 (OUTLIER) cc_final: 0.6002 (p-80)
REVERT: B  274 ASN cc_start: 0.8473 (t0) cc_final: 0.8243 (t0)
REVERT: B  357 ARG cc_start: 0.7956 (mtp-110) cc_final: 0.7614 (mtp-110)
REVERT: A   48 LEU cc_start: 0.8641 (pp) cc_final: 0.8404 (pp)
REVERT: A   99 GLU cc_start: 0.9214 (tp30) cc_final: 0.8656 (tp30)
REVERT: A  106 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7183 (mmt-90)
REVERT: A  109 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8234 (ttm-80)
REVERT: A  271 ASP cc_start: 0.9134 (m-30) cc_final: 0.8884 (m-30)
REVERT: A  318 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8583 (mt-10)
REVERT: A  344 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7858 (mptm)
REVERT: A  412 GLN cc_start: 0.8912 (mp10) cc_final: 0.8435 (mp10)
  outliers start: 37
  outliers final: 12
  residues processed: 176
  average time/residue: 0.4346
  time to fit residues: 79.0790
Evaluate side-chains
  134 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  355 LYS
Chi-restraints excluded: chain A residue   21 PHE
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  294 SER
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  344 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 127 ASN
A  43 ASN
** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 276 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.100351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.080899 restraints weight = 9296.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 3.17
r_work: 0.3083 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.5717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.073   4512  Z= 0.154
  Angle     :  0.708  10.521   6142  Z= 0.348
  Chirality :  0.043   0.160    768
  Planarity :  0.004   0.046    752
  Dihedral  :  3.842  14.179    610
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 36.75 %
    Favored  : 57.23 %
  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:  2.26 (0.36), residues: 568
  helix:  2.33 (0.26), residues: 356
  sheet: -0.32 (0.72), residues: 52
  loop :  0.31 (0.56), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  66 
 TYR   0.012   0.001   TYR A  72 
 PHE   0.009   0.001   PHE A  88 
 TRP   0.005   0.001   TRP B 338 
 HIS   0.002   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 4508)
  covalent geometry    : angle       0.70620 ( 6134)
  SS BOND              : bond        0.00426 (    4)
  SS BOND              : angle       1.69690 (    8)
  hydrogen bonds       : bond        0.03918 (  320)
  hydrogen bonds       : angle       3.89828 (  933)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 147
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   99 GLU cc_start: 0.9162 (tp30) cc_final: 0.8767 (tp30)
REVERT: B  271 ASP cc_start: 0.9340 (m-30) cc_final: 0.8519 (m-30)
REVERT: B  315 ASN cc_start: 0.9300 (t0) cc_final: 0.8989 (t0)
REVERT: B  357 ARG cc_start: 0.8029 (mtp-110) cc_final: 0.7749 (mtp-110)
REVERT: B  412 GLN cc_start: 0.8912 (mp10) cc_final: 0.8575 (pm20)
REVERT: A   48 LEU cc_start: 0.8641 (pp) cc_final: 0.8431 (pp)
REVERT: A   99 GLU cc_start: 0.9193 (tp30) cc_final: 0.8742 (tp30)
REVERT: A  106 ARG cc_start: 0.7843 (mtm-85) cc_final: 0.7165 (mmt-90)
REVERT: A  344 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7791 (mptm)
REVERT: A  412 GLN cc_start: 0.8905 (mp10) cc_final: 0.8400 (mp10)
  outliers start: 30
  outliers final: 11
  residues processed: 165
  average time/residue: 0.4382
  time to fit residues: 74.9058
Evaluate side-chains
  150 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 138
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  355 LYS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  344 LYS
Chi-restraints excluded: chain A residue  406 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0970
   chunk 57 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.101651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.081649 restraints weight = 9504.713|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 3.30
r_work: 0.3096 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.5966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   4512  Z= 0.157
  Angle     :  0.751   9.148   6142  Z= 0.367
  Chirality :  0.044   0.156    768
  Planarity :  0.004   0.047    752
  Dihedral  :  3.830  14.297    610
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  6.83 %
    Allowed  : 38.76 %
    Favored  : 54.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.22 (0.36), residues: 568
  helix:  2.25 (0.26), residues: 358
  sheet: -0.16 (0.73), residues: 52
  loop :  0.32 (0.57), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  66 
 TYR   0.020   0.001   TYR B 263 
 PHE   0.012   0.001   PHE A 382 
 TRP   0.006   0.001   TRP B 338 
 HIS   0.002   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 4508)
  covalent geometry    : angle       0.74943 ( 6134)
  SS BOND              : bond        0.00262 (    4)
  SS BOND              : angle       1.49678 (    8)
  hydrogen bonds       : bond        0.03875 (  320)
  hydrogen bonds       : angle       3.87395 (  933)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 0.116 
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: B   14 MET cc_start: 0.8476 (tpp) cc_final: 0.8261 (tpt)
REVERT: B   99 GLU cc_start: 0.9183 (tp30) cc_final: 0.8769 (tp30)
REVERT: B  244 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.6086 (p-80)
REVERT: B  271 ASP cc_start: 0.8920 (m-30) cc_final: 0.8456 (m-30)
REVERT: B  315 ASN cc_start: 0.9220 (t0) cc_final: 0.8604 (t0)
REVERT: B  318 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8625 (mt-10)
REVERT: B  357 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7930 (mtm110)
REVERT: A   48 LEU cc_start: 0.8636 (pp) cc_final: 0.8433 (pp)
REVERT: A   99 GLU cc_start: 0.9193 (tp30) cc_final: 0.8680 (tp30)
REVERT: A  106 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7154 (mmt-90)
REVERT: A  270 GLU cc_start: 0.9421 (pm20) cc_final: 0.9120 (pm20)
REVERT: A  271 ASP cc_start: 0.9086 (m-30) cc_final: 0.8807 (m-30)
REVERT: A  318 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8665 (mt-10)
REVERT: A  344 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7735 (mptm)
REVERT: A  412 GLN cc_start: 0.8935 (mp10) cc_final: 0.8421 (mp10)
  outliers start: 34
  outliers final: 9
  residues processed: 164
  average time/residue: 0.4636
  time to fit residues: 78.6816
Evaluate side-chains
  143 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  355 LYS
Chi-restraints excluded: chain B residue  406 SER
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  344 LYS
Chi-restraints excluded: chain A residue  355 LYS
Chi-restraints excluded: chain A residue  406 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 12 optimal weight:    7.9990
   chunk 49 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.099669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.079271 restraints weight = 9372.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 3.28
r_work: 0.3059 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.6207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068   4512  Z= 0.186
  Angle     :  0.769   9.305   6142  Z= 0.385
  Chirality :  0.045   0.160    768
  Planarity :  0.005   0.054    752
  Dihedral  :  3.971  17.921    610
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 39.76 %
    Favored  : 55.02 %
  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:  2.11 (0.36), residues: 568
  helix:  2.21 (0.26), residues: 358
  sheet: -0.43 (0.71), residues: 52
  loop :  0.25 (0.56), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A  66 
 TYR   0.017   0.001   TYR A 353 
 PHE   0.012   0.001   PHE A  21 
 TRP   0.008   0.002   TRP B 338 
 HIS   0.003   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 4508)
  covalent geometry    : angle       0.76756 ( 6134)
  SS BOND              : bond        0.00318 (    4)
  SS BOND              : angle       1.64876 (    8)
  hydrogen bonds       : bond        0.04126 (  320)
  hydrogen bonds       : angle       4.00907 (  933)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 142
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   14 MET cc_start: 0.8605 (tpp) cc_final: 0.8395 (tpt)
REVERT: B   99 GLU cc_start: 0.9212 (tp30) cc_final: 0.8741 (tp30)
REVERT: B  244 HIS cc_start: 0.7679 (OUTLIER) cc_final: 0.6131 (p-80)
REVERT: B  271 ASP cc_start: 0.8748 (m-30) cc_final: 0.8498 (m-30)
REVERT: B  315 ASN cc_start: 0.9184 (t0) cc_final: 0.8835 (t0)
REVERT: B  357 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7904 (mtp-110)
REVERT: A   99 GLU cc_start: 0.9188 (tp30) cc_final: 0.8669 (tp30)
REVERT: A  106 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7169 (mmt-90)
REVERT: A  246 MET cc_start: 0.4998 (pmm) cc_final: 0.4747 (pmm)
REVERT: A  270 GLU cc_start: 0.9391 (pm20) cc_final: 0.9166 (pm20)
REVERT: A  271 ASP cc_start: 0.9014 (m-30) cc_final: 0.8792 (m-30)
REVERT: A  344 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7912 (mptm)
REVERT: A  355 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6502 (pttm)
REVERT: A  412 GLN cc_start: 0.8971 (mp10) cc_final: 0.8503 (mp10)
  outliers start: 26
  outliers final: 11
  residues processed: 160
  average time/residue: 0.5235
  time to fit residues: 86.5059
Evaluate side-chains
  148 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 134
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   85 ASN
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  355 LYS
Chi-restraints excluded: chain A residue   69 SER
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  344 LYS
Chi-restraints excluded: chain A residue  355 LYS
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  406 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 55 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.100822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.080561 restraints weight = 9323.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3232 rms_B_bonded: 3.28
r_work: 0.3093 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start:          0.6343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4512  Z= 0.170
  Angle     :  0.822   9.756   6142  Z= 0.401
  Chirality :  0.046   0.241    768
  Planarity :  0.005   0.078    752
  Dihedral  :  4.055  18.704    610
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 40.96 %
    Favored  : 54.62 %
  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:  2.00 (0.36), residues: 568
  helix:  2.07 (0.26), residues: 362
  sheet: -0.34 (0.70), residues: 52
  loop :  0.24 (0.56), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG B 109 
 TYR   0.020   0.002   TYR B 263 
 PHE   0.010   0.001   PHE A  21 
 TRP   0.006   0.001   TRP B 275 
 HIS   0.002   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 4508)
  covalent geometry    : angle       0.82025 ( 6134)
  SS BOND              : bond        0.00665 (    4)
  SS BOND              : angle       1.74460 (    8)
  hydrogen bonds       : bond        0.03976 (  320)
  hydrogen bonds       : angle       3.99254 (  933)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.118 
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: B   28 SER cc_start: 0.9645 (m) cc_final: 0.9151 (p)
REVERT: B   66 ARG cc_start: 0.8482 (tpp-160) cc_final: 0.8168 (mpt90)
REVERT: B   99 GLU cc_start: 0.9165 (tp30) cc_final: 0.8608 (tp30)
REVERT: B  244 HIS cc_start: 0.7722 (OUTLIER) cc_final: 0.6136 (p-80)
REVERT: B  315 ASN cc_start: 0.9214 (t0) cc_final: 0.8862 (t0)
REVERT: A   28 SER cc_start: 0.9653 (m) cc_final: 0.9095 (p)
REVERT: A   99 GLU cc_start: 0.9159 (tp30) cc_final: 0.8611 (tp30)
REVERT: A  106 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7123 (mmt-90)
REVERT: A  246 MET cc_start: 0.5077 (pmm) cc_final: 0.4819 (pmm)
REVERT: A  289 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.9017 (mp)
REVERT: A  298 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8697 (tp)
REVERT: A  344 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7770 (mptm)
REVERT: A  355 LYS cc_start: 0.6702 (OUTLIER) cc_final: 0.6440 (pttm)
REVERT: A  412 GLN cc_start: 0.8957 (mp10) cc_final: 0.8427 (mp10)
  outliers start: 22
  outliers final: 7
  residues processed: 148
  average time/residue: 0.4434
  time to fit residues: 67.7961
Evaluate side-chains
  138 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  355 LYS
Chi-restraints excluded: chain B residue  406 SER
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  344 LYS
Chi-restraints excluded: chain A residue  355 LYS
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  406 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 28 optimal weight:    0.3980
   chunk 21 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.101588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.082196 restraints weight = 9375.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 3.14
r_work: 0.3106 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.6469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   4512  Z= 0.175
  Angle     :  0.833   9.536   6142  Z= 0.410
  Chirality :  0.047   0.306    768
  Planarity :  0.005   0.074    752
  Dihedral  :  4.057  17.947    610
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 42.17 %
    Favored  : 53.82 %
  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:  2.19 (0.36), residues: 568
  helix:  2.23 (0.27), residues: 358
  sheet: -0.37 (0.70), residues: 52
  loop :  0.39 (0.56), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG B 109 
 TYR   0.023   0.002   TYR A 353 
 PHE   0.011   0.001   PHE A  21 
 TRP   0.008   0.001   TRP B 338 
 HIS   0.003   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 4508)
  covalent geometry    : angle       0.83116 ( 6134)
  SS BOND              : bond        0.00465 (    4)
  SS BOND              : angle       1.55007 (    8)
  hydrogen bonds       : bond        0.03939 (  320)
  hydrogen bonds       : angle       4.00022 (  933)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   28 SER cc_start: 0.9653 (m) cc_final: 0.9188 (p)
REVERT: B   66 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.8005 (mpt90)
REVERT: B   99 GLU cc_start: 0.9198 (tp30) cc_final: 0.8765 (tp30)
REVERT: B  244 HIS cc_start: 0.7658 (OUTLIER) cc_final: 0.6147 (p-80)
REVERT: B  315 ASN cc_start: 0.9217 (t0) cc_final: 0.8893 (t0)
REVERT: B  412 GLN cc_start: 0.8882 (mp10) cc_final: 0.8588 (pm20)
REVERT: A   28 SER cc_start: 0.9674 (m) cc_final: 0.9120 (p)
REVERT: A   99 GLU cc_start: 0.9169 (tp30) cc_final: 0.8773 (tp30)
REVERT: A  106 ARG cc_start: 0.7911 (mtm-85) cc_final: 0.7255 (mmt-90)
REVERT: A  109 ARG cc_start: 0.8528 (ttm-80) cc_final: 0.8230 (mmm-85)
REVERT: A  246 MET cc_start: 0.5208 (pmm) cc_final: 0.4939 (pmm)
REVERT: A  298 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8739 (tp)
REVERT: A  344 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7932 (mptm)
REVERT: A  355 LYS cc_start: 0.6760 (OUTLIER) cc_final: 0.6461 (pttm)
REVERT: A  412 GLN cc_start: 0.8979 (mp10) cc_final: 0.8492 (mp10)
  outliers start: 20
  outliers final: 8
  residues processed: 147
  average time/residue: 0.6299
  time to fit residues: 95.4397
Evaluate side-chains
  137 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   78 GLU
Chi-restraints excluded: chain B residue  121 VAL
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  246 MET
Chi-restraints excluded: chain B residue  265 LEU
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  355 LYS
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  344 LYS
Chi-restraints excluded: chain A residue  355 LYS
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  406 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 42 optimal weight:    0.3980
   chunk 23 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 7 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0270
   chunk 47 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
B 127 ASN
** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.104044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.084621 restraints weight = 9435.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3277 rms_B_bonded: 3.18
r_work: 0.3146 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.6677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090   4512  Z= 0.167
  Angle     :  0.882  11.605   6142  Z= 0.424
  Chirality :  0.048   0.332    768
  Planarity :  0.005   0.072    752
  Dihedral  :  4.031  17.045    610
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 42.97 %
    Favored  : 53.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.36), residues: 568
  helix:  2.22 (0.27), residues: 358
  sheet: -0.19 (0.71), residues: 52
  loop :  0.27 (0.55), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 109 
 TYR   0.026   0.002   TYR A 353 
 PHE   0.013   0.001   PHE B 382 
 TRP   0.005   0.001   TRP B 275 
 HIS   0.002   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 4508)
  covalent geometry    : angle       0.88109 ( 6134)
  SS BOND              : bond        0.00486 (    4)
  SS BOND              : angle       1.45455 (    8)
  hydrogen bonds       : bond        0.03852 (  320)
  hydrogen bonds       : angle       3.99731 (  933)

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

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

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1136 Ramachandran restraints generated.
    568 Oldfield, 0 Emsley, 568 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 138
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   14 MET cc_start: 0.8432 (tpp) cc_final: 0.8182 (tpt)
REVERT: B   28 SER cc_start: 0.9633 (m) cc_final: 0.9223 (p)
REVERT: B   99 GLU cc_start: 0.9188 (tp30) cc_final: 0.8736 (tp30)
REVERT: B  108 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8435 (mt-10)
REVERT: B  244 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.6146 (p-80)
REVERT: B  315 ASN cc_start: 0.9246 (t0) cc_final: 0.9006 (t0)
REVERT: B  412 GLN cc_start: 0.8865 (mp10) cc_final: 0.8562 (pm20)
REVERT: A   28 SER cc_start: 0.9649 (m) cc_final: 0.9191 (p)
REVERT: A   99 GLU cc_start: 0.9158 (tp30) cc_final: 0.8726 (tp30)
REVERT: A  103 ARG cc_start: 0.8222 (mtm180) cc_final: 0.7909 (mtp85)
REVERT: A  106 ARG cc_start: 0.7875 (mtm-85) cc_final: 0.7198 (mmt-90)
REVERT: A  109 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8021 (mtm-85)
REVERT: A  246 MET cc_start: 0.5179 (pmm) cc_final: 0.4922 (pmm)
REVERT: A  289 ILE cc_start: 0.9312 (OUTLIER) cc_final: 0.8985 (mp)
REVERT: A  298 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8611 (tp)
REVERT: A  344 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7832 (mptm)
REVERT: A  355 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6514 (pttm)
REVERT: A  357 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8058 (ptm160)
REVERT: A  412 GLN cc_start: 0.8951 (mp10) cc_final: 0.8429 (mp10)
  outliers start: 20
  outliers final: 6
  residues processed: 147
  average time/residue: 0.4764
  time to fit residues: 72.5654
Evaluate side-chains
  133 residues out of total 498 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 LEU
Chi-restraints excluded: chain B residue  244 HIS
Chi-restraints excluded: chain B residue  299 ILE
Chi-restraints excluded: chain B residue  406 SER
Chi-restraints excluded: chain A residue   78 GLU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  344 LYS
Chi-restraints excluded: chain A residue  355 LYS
Chi-restraints excluded: chain A residue  357 ARG
Chi-restraints excluded: chain A residue  385 VAL
Chi-restraints excluded: chain A residue  406 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  85 ASN
** B 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.102231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.082668 restraints weight = 9429.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 3.17
r_work: 0.3117 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.6738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088   4512  Z= 0.180
  Angle     :  0.902  12.025   6142  Z= 0.432
  Chirality :  0.049   0.332    768
  Planarity :  0.005   0.071    752
  Dihedral  :  4.044  18.643    610
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 44.98 %
    Favored  : 51.81 %
  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:  2.10 (0.36), residues: 568
  helix:  2.18 (0.27), residues: 358
  sheet: -0.27 (0.72), residues: 52
  loop :  0.25 (0.55), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 109 
 TYR   0.027   0.002   TYR A 353 
 PHE   0.014   0.001   PHE B 382 
 TRP   0.012   0.002   TRP B 275 
 HIS   0.003   0.001   HIS B 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 4508)
  covalent geometry    : angle       0.90150 ( 6134)
  SS BOND              : bond        0.00488 (    4)
  SS BOND              : angle       1.46745 (    8)
  hydrogen bonds       : bond        0.03997 (  320)
  hydrogen bonds       : angle       4.05643 (  933)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1815.37 seconds
wall clock time: 31 minutes 40.32 seconds (1900.32 seconds total)