Starting phenix.real_space_refine
on Tue Mar  3 11:35:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v27_31638/03_2026/7v27_31638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v27_31638/03_2026/7v27_31638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v27_31638/03_2026/7v27_31638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v27_31638/03_2026/7v27_31638.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v27_31638/03_2026/7v27_31638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v27_31638/03_2026/7v27_31638.cif"
  }
  resolution = 4.18
  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=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2065      2.51       5
     N     535      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3252
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    Chain: "B"
      Number of atoms: 920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 920
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 7, 'TRANS': 112}
    Chain: "A"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 782
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    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: 0.67, per 1000 atoms: 0.21
  Number of scatterers: 3252
  At special positions: 0
  Unit cell: (80.542, 58.576, 99.37, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O     636      8.00
     N     535      7.00
     C    2065      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    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=2.04
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  90 " 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: 0.16
  Conformation dependent library (CDL) restraints added in 87.4 milliseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 10 sheets defined
      5.5% alpha, 26.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.892A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   PHE C 342 " --> pdb=" O   PHE C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 349 through 353
      removed outlier: 3.642A  pdb=" N   TRP C 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'B' and resid 88 through 92
    Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 357
      removed outlier: 3.604A  pdb=" N   VAL C 512 " --> pdb=" O   ASP C 398 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 379 through 380
      removed outlier: 4.202A  pdb=" N   GLY C 431 " --> pdb=" O   TYR C 380 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454
      removed outlier: 4.024A  pdb=" N   TYR C 453 " --> pdb=" O   GLN C 493 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.680A  pdb=" N   ARG B   5 " --> pdb=" O   THR B  23 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.717A  pdb=" N   VAL B  12 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   THR B 114 " --> pdb=" O   TYR B  95 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   VAL B  36 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   LEU B  52 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   TRP B  38 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG B  60 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.717A  pdb=" N   VAL B  12 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   THR B 114 " --> pdb=" O   TYR B  95 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 11 through 12
    Processing sheet with id=AA8, first strand: chain 'A' and resid 19 through 22
      removed outlier: 3.639A  pdb=" N   SER A  67 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 48 through 50
      removed outlier: 6.028A  pdb=" N   LEU A  48 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   GLN A  39 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE A  50 " --> pdb=" O   TRP A  37 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 48 through 50
      removed outlier: 6.028A  pdb=" N   LEU A  48 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   GLN A  39 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE A  50 " --> pdb=" O   TRP A  37 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TYR A  88 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR A 104 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)

    72 hydrogen bonds defined for protein.
    171 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: 0.27

  Time building geometry restraints manager: 0.23 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1026
        1.35 -     1.47: 885
        1.47 -     1.59: 1403
        1.59 -     1.71: 0
        1.71 -     1.83: 19
  Bond restraints: 3333
  Sorted by residual:
  bond pdb=" C   VAL C 382 "
       pdb=" N   SER C 383 "
    ideal  model  delta    sigma   weight residual
    1.330  1.354 -0.024 1.37e-02 5.33e+03 2.96e+00
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.78e+00
  bond pdb=" C5  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.14e+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 1.04e+00
  bond pdb=" N   CYS C 391 "
       pdb=" CA  CYS C 391 "
    ideal  model  delta    sigma   weight residual
    1.455  1.465 -0.010 1.21e-02 6.83e+03 6.90e-01
  ... (remaining 3328 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.83: 4149
        0.83 -     1.67: 303
        1.67 -     2.50: 51
        2.50 -     3.34: 36
        3.34 -     4.17: 5
  Bond angle restraints: 4544
  Sorted by residual:
  angle pdb=" N   MET A  49 "
        pdb=" CA  MET A  49 "
        pdb=" C   MET A  49 "
      ideal   model   delta    sigma   weight residual
     114.04  110.56    3.48 1.24e+00 6.50e-01 7.89e+00
  angle pdb=" N   CYS C 432 "
        pdb=" CA  CYS C 432 "
        pdb=" C   CYS C 432 "
      ideal   model   delta    sigma   weight residual
     107.88  111.39   -3.51 1.41e+00 5.03e-01 6.18e+00
  angle pdb=" N   SER A  97 "
        pdb=" CA  SER A  97 "
        pdb=" C   SER A  97 "
      ideal   model   delta    sigma   weight residual
     108.34  111.47   -3.13 1.31e+00 5.83e-01 5.70e+00
  angle pdb=" CA  GLY C 504 "
        pdb=" C   GLY C 504 "
        pdb=" N   TYR C 505 "
      ideal   model   delta    sigma   weight residual
     118.95  116.79    2.16 1.06e+00 8.90e-01 4.17e+00
  angle pdb=" C   PHE C 486 "
        pdb=" N   ASN C 487 "
        pdb=" CA  ASN C 487 "
      ideal   model   delta    sigma   weight residual
     121.54  125.16   -3.62 1.91e+00 2.74e-01 3.60e+00
  ... (remaining 4539 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.03: 1763
       15.03 -    30.06: 183
       30.06 -    45.10: 30
       45.10 -    60.13: 6
       60.13 -    75.16: 1
  Dihedral angle restraints: 1983
    sinusoidal: 765
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.66   39.34     1      1.00e+01 1.00e-02 2.18e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  97 "
           pdb=" CB  CYS B  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  123.94  -30.94     1      1.00e+01 1.00e-02 1.37e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -58.76  -27.24     1      1.00e+01 1.00e-02 1.06e+01
  ... (remaining 1980 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 364
       0.038 -    0.075: 103
       0.075 -    0.113: 38
       0.113 -    0.150: 5
       0.150 -    0.188: 1
  Chirality restraints: 511
  Sorted by residual:
  chirality pdb=" CB  ILE C 410 "
            pdb=" CA  ILE C 410 "
            pdb=" CG1 ILE C 410 "
            pdb=" CG2 ILE C 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.80e-01
  chirality pdb=" CB  THR C 500 "
            pdb=" CA  THR C 500 "
            pdb=" OG1 THR C 500 "
            pdb=" CG2 THR C 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.43    0.12 2.00e-01 2.50e+01 3.59e-01
  chirality pdb=" CA  ILE B  39 "
            pdb=" N   ILE B  39 "
            pdb=" C   ILE B  39 "
            pdb=" CB  ILE B  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.41e-01
  ... (remaining 508 not shown)

  Planarity restraints: 581
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 520 "    0.016 5.00e-02 4.00e+02   2.43e-02 9.46e-01
        pdb=" N   PRO C 521 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO C 521 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO C 521 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  45 "   -0.015 5.00e-02 4.00e+02   2.26e-02 8.18e-01
        pdb=" N   PRO A  46 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO A  46 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A  46 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  31 "    0.015 5.00e-02 4.00e+02   2.24e-02 8.03e-01
        pdb=" N   PRO B  32 "   -0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "    0.012 5.00e-02 4.00e+02
  ... (remaining 578 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 546
        2.76 -     3.30: 3043
        3.30 -     3.83: 5332
        3.83 -     4.37: 5987
        4.37 -     4.90: 10409
  Nonbonded interactions: 25317
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 430 "
            pdb=" O   PHE C 515 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OD2 ASP C 398 "
            pdb=" OH  TYR C 423 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ILE B 106 "
            pdb=" OH  TYR A  38 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER A   9 "
            pdb=" O   LYS A 105 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   ARG C 408 "
            pdb=" NE2 GLN C 414 "
     model   vdw
     2.313 3.120
  ... (remaining 25312 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:             4.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.210
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
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   0.027   3340  Z= 0.124
  Angle     :  0.537   4.173   4559  Z= 0.306
  Chirality :  0.040   0.188    511
  Planarity :  0.003   0.024    580
  Dihedral  : 11.752  75.160   1191
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.40 (0.34), residues: 415
  helix: -3.86 (0.99), residues: 13
  sheet: -2.42 (0.44), residues: 126
  loop : -3.32 (0.29), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 408 
 TYR   0.007   0.001   TYR B  96 
 PHE   0.008   0.001   PHE C 338 
 TRP   0.005   0.001   TRP B  55 
 HIS   0.001   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 3333)
  covalent geometry    : angle       0.53502 ( 4544)
  SS BOND              : bond        0.00420 (    6)
  SS BOND              : angle       0.90340 (   12)
  hydrogen bonds       : bond        0.31656 (   58)
  hydrogen bonds       : angle      11.20114 (  171)
  link_NAG-ASN         : bond        0.00202 (    1)
  link_NAG-ASN         : angle       1.03656 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.122 
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: C  358 ILE cc_start: 0.9209 (mm) cc_final: 0.8992 (mt)
REVERT: C  365 TYR cc_start: 0.8446 (m-80) cc_final: 0.8241 (m-80)
REVERT: C  405 ASP cc_start: 0.9094 (m-30) cc_final: 0.8536 (m-30)
REVERT: C  449 TYR cc_start: 0.8758 (m-80) cc_final: 0.8523 (m-10)
REVERT: B   13 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7520 (tmtt)
REVERT: B   49 TRP cc_start: 0.8957 (t60) cc_final: 0.8682 (t60)
REVERT: B   56 ASP cc_start: 0.8641 (m-30) cc_final: 0.8431 (m-30)
REVERT: B  104 ASP cc_start: 0.8474 (t0) cc_final: 0.8229 (t0)
REVERT: A   64 PHE cc_start: 0.8558 (m-80) cc_final: 0.8290 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.0917
  time to fit residues: 11.7925
Evaluate side-chains
  67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.4980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    0.4980
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C 354 ASN
C 448 ASN
B  86 ASN
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  41 HIS
A  62 ASN
A  81 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.085618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.070498 restraints weight = 11982.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.073173 restraints weight = 7069.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.075057 restraints weight = 4862.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.076414 restraints weight = 3671.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.077356 restraints weight = 2949.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3340  Z= 0.186
  Angle     :  0.636   6.493   4559  Z= 0.326
  Chirality :  0.045   0.213    511
  Planarity :  0.004   0.031    580
  Dihedral  :  4.785  40.534    480
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  7.50 %
    Favored  : 91.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.76 (0.36), residues: 415
  helix: -3.63 (0.88), residues: 13
  sheet: -2.02 (0.46), residues: 123
  loop : -2.84 (0.31), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 408 
 TYR   0.014   0.002   TYR C 421 
 PHE   0.010   0.001   PHE C 392 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.000   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 3333)
  covalent geometry    : angle       0.62964 ( 4544)
  SS BOND              : bond        0.00679 (    6)
  SS BOND              : angle       1.66101 (   12)
  hydrogen bonds       : bond        0.04491 (   58)
  hydrogen bonds       : angle       7.55988 (  171)
  link_NAG-ASN         : bond        0.00294 (    1)
  link_NAG-ASN         : angle       1.57466 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 83
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  364 ASP cc_start: 0.8016 (p0) cc_final: 0.7718 (p0)
REVERT: C  398 ASP cc_start: 0.9155 (m-30) cc_final: 0.8737 (m-30)
REVERT: C  405 ASP cc_start: 0.8961 (m-30) cc_final: 0.8578 (p0)
REVERT: C  458 LYS cc_start: 0.8673 (pptt) cc_final: 0.8262 (pttm)
REVERT: C  461 LEU cc_start: 0.7133 (tp) cc_final: 0.6900 (tp)
REVERT: B   13 LYS cc_start: 0.7894 (mmtm) cc_final: 0.7641 (tmtt)
REVERT: B   45 LYS cc_start: 0.9261 (tptp) cc_final: 0.9051 (tptp)
REVERT: B   49 TRP cc_start: 0.8849 (t60) cc_final: 0.8419 (t60)
REVERT: B   57 ASP cc_start: 0.8617 (t0) cc_final: 0.8385 (t0)
REVERT: A   64 PHE cc_start: 0.8204 (m-80) cc_final: 0.7419 (m-10)
  outliers start: 2
  outliers final: 0
  residues processed: 85
  average time/residue: 0.0887
  time to fit residues: 8.7850
Evaluate side-chains
  62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0770
   chunk 39 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
C 360 ASN
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  71 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.082478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.067185 restraints weight = 11651.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.069827 restraints weight = 6780.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.071671 restraints weight = 4648.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.073002 restraints weight = 3515.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.073969 restraints weight = 2840.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.3525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3340  Z= 0.221
  Angle     :  0.662   7.729   4559  Z= 0.339
  Chirality :  0.045   0.199    511
  Planarity :  0.004   0.028    580
  Dihedral  :  5.256  43.177    480
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.12 %
    Favored  : 89.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.38 (0.37), residues: 415
  helix: -2.90 (1.21), residues: 13
  sheet: -1.87 (0.46), residues: 123
  loop : -2.52 (0.33), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 408 
 TYR   0.029   0.002   TYR C 495 
 PHE   0.013   0.002   PHE C 392 
 TRP   0.012   0.002   TRP B  55 
 HIS   0.001   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 3333)
  covalent geometry    : angle       0.65552 ( 4544)
  SS BOND              : bond        0.00734 (    6)
  SS BOND              : angle       1.84738 (   12)
  hydrogen bonds       : bond        0.03789 (   58)
  hydrogen bonds       : angle       6.64629 (  171)
  link_NAG-ASN         : bond        0.00330 (    1)
  link_NAG-ASN         : angle       1.47640 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.126 
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: C  364 ASP cc_start: 0.7995 (p0) cc_final: 0.7699 (p0)
REVERT: C  390 LEU cc_start: 0.8814 (tp) cc_final: 0.8533 (tp)
REVERT: C  394 ASN cc_start: 0.7746 (t0) cc_final: 0.6989 (t0)
REVERT: C  398 ASP cc_start: 0.9149 (m-30) cc_final: 0.8704 (m-30)
REVERT: B   20 LEU cc_start: 0.9155 (tp) cc_final: 0.8953 (tp)
REVERT: B   49 TRP cc_start: 0.9059 (t60) cc_final: 0.8710 (t60)
REVERT: A   49 MET cc_start: 0.7802 (ttm) cc_final: 0.7354 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.0808
  time to fit residues: 7.9857
Evaluate side-chains
  66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    0.0040
   chunk 20 optimal weight:    0.0980
   chunk 17 optimal weight:    0.3980
   chunk 5 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0870
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    0.1980
   chunk 29 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.0970

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
A  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.086839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.071841 restraints weight = 10952.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.074591 restraints weight = 6276.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.076488 restraints weight = 4214.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.077777 restraints weight = 3116.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.078807 restraints weight = 2486.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.3754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3340  Z= 0.115
  Angle     :  0.624   7.474   4559  Z= 0.316
  Chirality :  0.045   0.200    511
  Planarity :  0.004   0.035    580
  Dihedral  :  4.696  36.484    480
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.16 (0.38), residues: 415
  helix: -3.11 (1.06), residues: 13
  sheet: -1.67 (0.48), residues: 126
  loop : -2.38 (0.33), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 408 
 TYR   0.013   0.002   TYR C 453 
 PHE   0.010   0.001   PHE A  64 
 TRP   0.010   0.001   TRP A  37 
 HIS   0.001   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 3333)
  covalent geometry    : angle       0.61731 ( 4544)
  SS BOND              : bond        0.00788 (    6)
  SS BOND              : angle       1.88181 (   12)
  hydrogen bonds       : bond        0.02921 (   58)
  hydrogen bonds       : angle       5.96466 (  171)
  link_NAG-ASN         : bond        0.00264 (    1)
  link_NAG-ASN         : angle       0.77212 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  364 ASP cc_start: 0.7822 (p0) cc_final: 0.7518 (p0)
REVERT: C  390 LEU cc_start: 0.8643 (tp) cc_final: 0.8359 (tp)
REVERT: C  398 ASP cc_start: 0.8915 (m-30) cc_final: 0.8479 (m-30)
REVERT: B   49 TRP cc_start: 0.8717 (t60) cc_final: 0.8339 (t60)
REVERT: B   57 ASP cc_start: 0.8534 (t0) cc_final: 0.8266 (t0)
REVERT: A   52 ASP cc_start: 0.8718 (t0) cc_final: 0.8460 (t0)
REVERT: A   55 LYS cc_start: 0.8662 (mtmm) cc_final: 0.8369 (mtmm)
REVERT: A   62 ASN cc_start: 0.8694 (p0) cc_final: 0.8451 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.0877
  time to fit residues: 8.9378
Evaluate side-chains
  66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0170
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.6618

-------------------------------------------------------------------------------
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 = 0.3407 r_free = 0.3407 target = 0.081969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.066976 restraints weight = 11184.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.069520 restraints weight = 6576.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.071322 restraints weight = 4505.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.072627 restraints weight = 3380.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.073565 restraints weight = 2714.216|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.4095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3340  Z= 0.208
  Angle     :  0.673   7.752   4559  Z= 0.346
  Chirality :  0.045   0.222    511
  Planarity :  0.004   0.035    580
  Dihedral  :  5.273  42.519    480
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.84 %
    Favored  : 89.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  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: -2.94 (0.38), residues: 415
  helix: -2.66 (1.18), residues: 13
  sheet: -1.67 (0.46), residues: 129
  loop : -2.15 (0.34), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  63 
 TYR   0.013   0.002   TYR C 495 
 PHE   0.012   0.002   PHE C 392 
 TRP   0.035   0.003   TRP A  37 
 HIS   0.001   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 3333)
  covalent geometry    : angle       0.66722 ( 4544)
  SS BOND              : bond        0.00679 (    6)
  SS BOND              : angle       1.78981 (   12)
  hydrogen bonds       : bond        0.03642 (   58)
  hydrogen bonds       : angle       6.17528 (  171)
  link_NAG-ASN         : bond        0.00357 (    1)
  link_NAG-ASN         : angle       1.47640 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  364 ASP cc_start: 0.8022 (p0) cc_final: 0.7749 (p0)
REVERT: C  390 LEU cc_start: 0.8882 (tp) cc_final: 0.8661 (tp)
REVERT: C  394 ASN cc_start: 0.7302 (t0) cc_final: 0.6980 (t0)
REVERT: C  398 ASP cc_start: 0.9059 (m-30) cc_final: 0.8621 (m-30)
REVERT: C  405 ASP cc_start: 0.9018 (m-30) cc_final: 0.8513 (p0)
REVERT: B   20 LEU cc_start: 0.9169 (tp) cc_final: 0.8964 (tp)
REVERT: B   49 TRP cc_start: 0.8961 (t60) cc_final: 0.8628 (t60)
REVERT: B  100 LEU cc_start: 0.9041 (tp) cc_final: 0.8840 (tp)
REVERT: A   49 MET cc_start: 0.8147 (ttp) cc_final: 0.7842 (ttt)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0826
  time to fit residues: 7.9686
Evaluate side-chains
  65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 20 optimal weight:    0.1980
   chunk 8 optimal weight:    0.0050
   chunk 39 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0170
   overall best weight:    0.2832

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
A  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.083956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.068697 restraints weight = 11281.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.071316 restraints weight = 6638.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.073176 restraints weight = 4535.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.074502 restraints weight = 3409.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.075411 restraints weight = 2741.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.4242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3340  Z= 0.127
  Angle     :  0.629   6.198   4559  Z= 0.320
  Chirality :  0.045   0.237    511
  Planarity :  0.004   0.036    580
  Dihedral  :  4.946  39.257    480
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.36 %
    Favored  : 89.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.39), residues: 415
  helix: -2.37 (1.21), residues: 13
  sheet: -1.64 (0.47), residues: 126
  loop : -2.06 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 408 
 TYR   0.017   0.002   TYR C 495 
 PHE   0.012   0.001   PHE A  64 
 TRP   0.024   0.002   TRP A  37 
 HIS   0.000   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3333)
  covalent geometry    : angle       0.62190 ( 4544)
  SS BOND              : bond        0.00759 (    6)
  SS BOND              : angle       1.84791 (   12)
  hydrogen bonds       : bond        0.02989 (   58)
  hydrogen bonds       : angle       5.94665 (  171)
  link_NAG-ASN         : bond        0.00082 (    1)
  link_NAG-ASN         : angle       0.93560 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  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: C  364 ASP cc_start: 0.8004 (p0) cc_final: 0.7745 (p0)
REVERT: C  377 PHE cc_start: 0.9251 (t80) cc_final: 0.8935 (t80)
REVERT: C  398 ASP cc_start: 0.8920 (m-30) cc_final: 0.8496 (m-30)
REVERT: C  405 ASP cc_start: 0.8962 (m-30) cc_final: 0.8044 (p0)
REVERT: C  408 ARG cc_start: 0.8659 (pmt170) cc_final: 0.7876 (pmt170)
REVERT: B   40 ARG cc_start: 0.8629 (ttp-170) cc_final: 0.8224 (ttp-170)
REVERT: B   49 TRP cc_start: 0.8822 (t60) cc_final: 0.8428 (t60)
REVERT: B   59 LYS cc_start: 0.9042 (mptt) cc_final: 0.8530 (mptt)
REVERT: B   71 ILE cc_start: 0.9414 (tp) cc_final: 0.8985 (tp)
REVERT: B  100 LEU cc_start: 0.8922 (tp) cc_final: 0.8663 (tp)
REVERT: A   77 ILE cc_start: 0.9261 (mp) cc_final: 0.9031 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0843
  time to fit residues: 8.1210
Evaluate side-chains
  68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3370 r_free = 0.3370 target = 0.080314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.065402 restraints weight = 11517.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.067975 restraints weight = 6747.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.069787 restraints weight = 4602.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.071066 restraints weight = 3451.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.071973 restraints weight = 2769.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.4599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3340  Z= 0.251
  Angle     :  0.727   6.375   4559  Z= 0.373
  Chirality :  0.046   0.246    511
  Planarity :  0.004   0.039    580
  Dihedral  :  5.628  44.270    480
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 17.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.75 (0.39), residues: 415
  helix: -1.81 (1.24), residues: 13
  sheet: -1.62 (0.45), residues: 131
  loop : -2.02 (0.35), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 408 
 TYR   0.018   0.002   TYR A  93 
 PHE   0.010   0.002   PHE C 342 
 TRP   0.015   0.002   TRP B  55 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 ( 3333)
  covalent geometry    : angle       0.71846 ( 4544)
  SS BOND              : bond        0.00866 (    6)
  SS BOND              : angle       2.19247 (   12)
  hydrogen bonds       : bond        0.03678 (   58)
  hydrogen bonds       : angle       6.22195 (  171)
  link_NAG-ASN         : bond        0.00463 (    1)
  link_NAG-ASN         : angle       1.57544 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  364 ASP cc_start: 0.8029 (p0) cc_final: 0.7763 (p0)
REVERT: C  378 LYS cc_start: 0.8785 (pttt) cc_final: 0.8554 (pttm)
REVERT: C  390 LEU cc_start: 0.8803 (tp) cc_final: 0.8553 (tp)
REVERT: C  394 ASN cc_start: 0.7488 (t0) cc_final: 0.7072 (t0)
REVERT: C  398 ASP cc_start: 0.9072 (m-30) cc_final: 0.8601 (m-30)
REVERT: B   20 LEU cc_start: 0.9179 (tp) cc_final: 0.8952 (tp)
REVERT: B  100 LEU cc_start: 0.9085 (tp) cc_final: 0.8838 (tp)
REVERT: A   77 ILE cc_start: 0.9308 (mp) cc_final: 0.9063 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0762
  time to fit residues: 7.0491
Evaluate side-chains
  65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    0.2980
   chunk 15 optimal weight:    0.0980
   chunk 22 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0470
   chunk 26 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 17 optimal weight:    0.2980
   chunk 11 optimal weight:    0.0870
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.1656

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

Flipped N/Q/H residues before XYZ refinement:
C 498 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.083828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.068647 restraints weight = 11281.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.071355 restraints weight = 6431.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.073260 restraints weight = 4311.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.074524 restraints weight = 3199.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.075505 restraints weight = 2568.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.4579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3340  Z= 0.122
  Angle     :  0.669   6.494   4559  Z= 0.341
  Chirality :  0.045   0.254    511
  Planarity :  0.004   0.039    580
  Dihedral  :  4.942  38.011    480
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  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: -2.57 (0.39), residues: 415
  helix: -1.92 (1.19), residues: 13
  sheet: -1.40 (0.47), residues: 123
  loop : -1.93 (0.35), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B   5 
 TYR   0.015   0.002   TYR A  93 
 PHE   0.020   0.002   PHE A  64 
 TRP   0.019   0.001   TRP A  37 
 HIS   0.001   0.000   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3333)
  covalent geometry    : angle       0.66279 ( 4544)
  SS BOND              : bond        0.00735 (    6)
  SS BOND              : angle       1.89659 (   12)
  hydrogen bonds       : bond        0.03532 (   58)
  hydrogen bonds       : angle       5.83380 (  171)
  link_NAG-ASN         : bond        0.00247 (    1)
  link_NAG-ASN         : angle       0.85481 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  364 ASP cc_start: 0.8033 (p0) cc_final: 0.7778 (p0)
REVERT: C  377 PHE cc_start: 0.9194 (t80) cc_final: 0.8939 (t80)
REVERT: C  390 LEU cc_start: 0.8679 (tp) cc_final: 0.8464 (tp)
REVERT: C  394 ASN cc_start: 0.7271 (t0) cc_final: 0.6940 (t0)
REVERT: C  398 ASP cc_start: 0.8882 (m-30) cc_final: 0.8389 (m-30)
REVERT: C  405 ASP cc_start: 0.9023 (m-30) cc_final: 0.8469 (m-30)
REVERT: C  408 ARG cc_start: 0.8749 (pmt170) cc_final: 0.8005 (pmt170)
REVERT: B   49 TRP cc_start: 0.8937 (t60) cc_final: 0.8310 (t60)
REVERT: B  100 LEU cc_start: 0.8881 (tp) cc_final: 0.8637 (tp)
REVERT: A   37 TRP cc_start: 0.8617 (m100) cc_final: 0.8206 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.0684
  time to fit residues: 6.9964
Evaluate side-chains
  63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 39 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 5 optimal weight:    2.9990
   chunk 34 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
A  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.081403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.066364 restraints weight = 11451.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.068913 restraints weight = 6652.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.070678 restraints weight = 4534.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.071907 restraints weight = 3420.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.072843 restraints weight = 2784.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.4731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3340  Z= 0.197
  Angle     :  0.715   9.218   4559  Z= 0.364
  Chirality :  0.046   0.275    511
  Planarity :  0.005   0.046    580
  Dihedral  :  5.330  41.267    480
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 16.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.29 %
    Favored  : 87.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  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: -2.52 (0.39), residues: 415
  helix: -1.48 (1.31), residues: 13
  sheet: -1.38 (0.48), residues: 120
  loop : -1.91 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 408 
 TYR   0.020   0.002   TYR C 495 
 PHE   0.010   0.002   PHE C 392 
 TRP   0.014   0.002   TRP A  37 
 HIS   0.001   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 ( 3333)
  covalent geometry    : angle       0.70824 ( 4544)
  SS BOND              : bond        0.00808 (    6)
  SS BOND              : angle       1.99965 (   12)
  hydrogen bonds       : bond        0.03579 (   58)
  hydrogen bonds       : angle       5.93590 (  171)
  link_NAG-ASN         : bond        0.00267 (    1)
  link_NAG-ASN         : angle       1.40117 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.125 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  364 ASP cc_start: 0.8136 (p0) cc_final: 0.7878 (p0)
REVERT: C  377 PHE cc_start: 0.9283 (t80) cc_final: 0.9079 (t80)
REVERT: C  390 LEU cc_start: 0.8901 (tp) cc_final: 0.8626 (tp)
REVERT: C  394 ASN cc_start: 0.7433 (t0) cc_final: 0.7067 (t0)
REVERT: C  398 ASP cc_start: 0.8932 (m-30) cc_final: 0.8443 (m-30)
REVERT: C  405 ASP cc_start: 0.9157 (m-30) cc_final: 0.8489 (m-30)
REVERT: C  408 ARG cc_start: 0.8792 (pmt170) cc_final: 0.8068 (pmt170)
REVERT: B   20 LEU cc_start: 0.9193 (tp) cc_final: 0.8991 (tp)
REVERT: B   45 LYS cc_start: 0.8983 (tptp) cc_final: 0.8689 (tptp)
REVERT: B   49 TRP cc_start: 0.8875 (t60) cc_final: 0.8432 (t60)
REVERT: B   59 LYS cc_start: 0.9030 (mptt) cc_final: 0.8612 (mptt)
REVERT: B   71 ILE cc_start: 0.9432 (tp) cc_final: 0.8874 (tp)
REVERT: B   87 MET cc_start: 0.7660 (ttm) cc_final: 0.7329 (ttp)
REVERT: B  100 LEU cc_start: 0.8934 (tp) cc_final: 0.8640 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0665
  time to fit residues: 6.2882
Evaluate side-chains
  63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 23 optimal weight:    0.1980
   chunk 29 optimal weight:    0.0770
   chunk 32 optimal weight:    0.4980
   chunk 9 optimal weight:    0.2980
   chunk 21 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0770
   chunk 6 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.2296

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.084269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.068948 restraints weight = 11066.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.071576 restraints weight = 6358.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.073413 restraints weight = 4301.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.074770 restraints weight = 3222.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.075750 restraints weight = 2586.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.4728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3340  Z= 0.132
  Angle     :  0.694   6.913   4559  Z= 0.352
  Chirality :  0.047   0.264    511
  Planarity :  0.004   0.044    580
  Dihedral  :  5.080  38.041    480
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.40 (0.39), residues: 415
  helix: -1.45 (1.30), residues: 13
  sheet: -1.16 (0.49), residues: 116
  loop : -1.89 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B   5 
 TYR   0.009   0.001   TYR A  32 
 PHE   0.012   0.001   PHE C 497 
 TRP   0.024   0.002   TRP A  37 
 HIS   0.000   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3333)
  covalent geometry    : angle       0.68887 ( 4544)
  SS BOND              : bond        0.00784 (    6)
  SS BOND              : angle       1.71895 (   12)
  hydrogen bonds       : bond        0.03100 (   58)
  hydrogen bonds       : angle       5.62408 (  171)
  link_NAG-ASN         : bond        0.00113 (    1)
  link_NAG-ASN         : angle       1.11703 (    3)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.120 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  364 ASP cc_start: 0.8190 (p0) cc_final: 0.7930 (p0)
REVERT: C  377 PHE cc_start: 0.9218 (t80) cc_final: 0.8920 (t80)
REVERT: C  390 LEU cc_start: 0.8811 (tp) cc_final: 0.8517 (tp)
REVERT: C  394 ASN cc_start: 0.7431 (t0) cc_final: 0.7054 (t0)
REVERT: C  398 ASP cc_start: 0.8723 (m-30) cc_final: 0.8271 (m-30)
REVERT: C  405 ASP cc_start: 0.9167 (m-30) cc_final: 0.8959 (m-30)
REVERT: B   45 LYS cc_start: 0.9017 (tptp) cc_final: 0.8714 (tptp)
REVERT: B   49 TRP cc_start: 0.8802 (t60) cc_final: 0.8147 (t60)
REVERT: B   59 LYS cc_start: 0.9049 (mptt) cc_final: 0.8544 (mptt)
REVERT: B   71 ILE cc_start: 0.9467 (tp) cc_final: 0.8936 (tp)
REVERT: B   87 MET cc_start: 0.7605 (ttm) cc_final: 0.7264 (ttp)
REVERT: B  100 LEU cc_start: 0.8857 (tp) cc_final: 0.8595 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.0685
  time to fit residues: 6.4719
Evaluate side-chains
  62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    0.0000
   chunk 31 optimal weight:    0.0470
   chunk 29 optimal weight:    0.0060
   chunk 8 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 4 optimal weight:    0.3980
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.2098

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

Flipped N/Q/H residues before XYZ refinement:
A  39 GLN
A  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.084835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.069481 restraints weight = 11468.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.072142 restraints weight = 6538.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.073995 restraints weight = 4384.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.075280 restraints weight = 3279.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.076226 restraints weight = 2657.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.4777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3340  Z= 0.125
  Angle     :  0.652   6.765   4559  Z= 0.332
  Chirality :  0.046   0.272    511
  Planarity :  0.004   0.043    580
  Dihedral  :  4.923  36.507    480
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.11 %
    Favored  : 98.89 %
  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: -2.27 (0.40), residues: 415
  helix: -1.38 (1.31), residues: 13
  sheet: -0.98 (0.50), residues: 116
  loop : -1.85 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 408 
 TYR   0.012   0.001   TYR A  38 
 PHE   0.012   0.001   PHE C 392 
 TRP   0.029   0.002   TRP A  37 
 HIS   0.001   0.000   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3333)
  covalent geometry    : angle       0.64759 ( 4544)
  SS BOND              : bond        0.00683 (    6)
  SS BOND              : angle       1.57264 (   12)
  hydrogen bonds       : bond        0.03134 (   58)
  hydrogen bonds       : angle       5.55336 (  171)
  link_NAG-ASN         : bond        0.00045 (    1)
  link_NAG-ASN         : angle       1.12925 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 850.56 seconds
wall clock time: 15 minutes 17.31 seconds (917.31 seconds total)