Starting phenix.real_space_refine
on Tue Mar  3 11:30:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7y6l_33643/03_2026/7y6l_33643.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y6l_33643/03_2026/7y6l_33643.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7y6l_33643/03_2026/7y6l_33643.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y6l_33643/03_2026/7y6l_33643.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y6l_33643/03_2026/7y6l_33643.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y6l_33643/03_2026/7y6l_33643.cif"
  }
  resolution = 3.5
  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      16      5.16       5
     C    2115      2.51       5
     N     556      2.21       5
     O     621      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 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: 3308
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1519
          Classifications: {'peptide': 194}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 17
    Chain: "H"
      Number of atoms: 953
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 953
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 4, 'TRANS': 117}
    Chain: "L"
      Number of atoms: 822
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 822
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100}
    Chain: "A"
      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: 0.98, per 1000 atoms: 0.30
  Number of scatterers: 3308
  At special positions: 0
  Unit cell: (101.967, 72.952, 66.32, 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     621      8.00
     N     556      7.00
     C    2115      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  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 A1301 " - " ASN A 343 "
  Time building additional restraints: 0.30
  Conformation dependent library (CDL) restraints added in 121.6 milliseconds
  

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 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:
      6 helices and 7 sheets defined
      8.5% alpha, 31.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 371
      removed outlier: 4.140A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.722A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6
      removed outlier: 4.063A  pdb=" N   LEU H  18 " --> pdb=" O   TRP H  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12
      removed outlier: 4.324A  pdb=" N   TRP H  33 " --> pdb=" O   ILE H  99 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   ILE H  34 " --> pdb=" O   ILE H  50 " (cutoff:3.500A)
      removed outlier: 4.850A  pdb=" N   ILE H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASP H  57 " --> pdb=" O   HIS H  52 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.795A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 112 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   TRP H 112 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ARG H  98 " --> pdb=" O   HIS H 110 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7
    Processing sheet with id=AA7, first strand: chain 'L' and resid 53 through 54
      removed outlier: 6.450A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)

    113 hydrogen bonds defined for protein.
    261 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: 0.52

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1037
        1.35 -     1.48: 969
        1.48 -     1.60: 1371
        1.60 -     1.73: 0
        1.73 -     1.85: 20
  Bond restraints: 3397
  Sorted by residual:
  bond pdb=" CB  CYS A 379 "
       pdb=" SG  CYS A 379 "
    ideal  model  delta    sigma   weight residual
    1.808  1.850 -0.042 3.30e-02 9.18e+02 1.65e+00
  bond pdb=" CB  VAL A 350 "
       pdb=" CG1 VAL A 350 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.34e+00
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.429 -0.023 2.00e-02 2.50e+03 1.34e+00
  bond pdb=" C5  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.12e+00
  bond pdb=" C3  NAG A1301 "
       pdb=" O3  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.63e-01
  ... (remaining 3392 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 4543
        1.74 -     3.48: 67
        3.48 -     5.22: 5
        5.22 -     6.97: 2
        6.97 -     8.71: 1
  Bond angle restraints: 4618
  Sorted by residual:
  angle pdb=" CA  CYS A 432 "
        pdb=" CB  CYS A 432 "
        pdb=" SG  CYS A 432 "
      ideal   model   delta    sigma   weight residual
     114.40  123.11   -8.71 2.30e+00 1.89e-01 1.43e+01
  angle pdb=" C   LYS L  50 "
        pdb=" N   ALA L  51 "
        pdb=" CA  ALA L  51 "
      ideal   model   delta    sigma   weight residual
     121.54  126.98   -5.44 1.91e+00 2.74e-01 8.11e+00
  angle pdb=" C   VAL A 350 "
        pdb=" CA  VAL A 350 "
        pdb=" CB  VAL A 350 "
      ideal   model   delta    sigma   weight residual
     112.26  109.09    3.17 1.62e+00 3.81e-01 3.83e+00
  angle pdb=" N   VAL A 350 "
        pdb=" CA  VAL A 350 "
        pdb=" C   VAL A 350 "
      ideal   model   delta    sigma   weight residual
     111.09  113.30   -2.21 1.25e+00 6.40e-01 3.14e+00
  angle pdb=" CA  TYR L  91 "
        pdb=" CB  TYR L  91 "
        pdb=" CG  TYR L  91 "
      ideal   model   delta    sigma   weight residual
     113.90  117.09   -3.19 1.80e+00 3.09e-01 3.13e+00
  ... (remaining 4613 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 1741
       17.68 -    35.37: 211
       35.37 -    53.05: 44
       53.05 -    70.73: 8
       70.73 -    88.42: 2
  Dihedral angle restraints: 2006
    sinusoidal: 785
      harmonic: 1221
  Sorted by residual:
  dihedral pdb=" CB  CYS A 379 "
           pdb=" SG  CYS A 379 "
           pdb=" SG  CYS A 432 "
           pdb=" CB  CYS A 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   47.13   45.87     1      1.00e+01 1.00e-02 2.92e+01
  dihedral pdb=" CB  CYS A 391 "
           pdb=" SG  CYS A 391 "
           pdb=" SG  CYS A 525 "
           pdb=" CB  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.37   42.63     1      1.00e+01 1.00e-02 2.54e+01
  dihedral pdb=" CA  CYS A 432 "
           pdb=" C   CYS A 432 "
           pdb=" N   VAL A 433 "
           pdb=" CA  VAL A 433 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.73  -16.27     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 2003 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 337
       0.039 -    0.079: 113
       0.079 -    0.118: 46
       0.118 -    0.157: 2
       0.157 -    0.197: 1
  Chirality restraints: 499
  Sorted by residual:
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 9.67e-01
  chirality pdb=" CA  ILE L  48 "
            pdb=" N   ILE L  48 "
            pdb=" C   ILE L  48 "
            pdb=" CB  ILE L  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.82e-01
  chirality pdb=" CA  ILE A 434 "
            pdb=" N   ILE A 434 "
            pdb=" C   ILE A 434 "
            pdb=" CB  ILE A 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  ... (remaining 496 not shown)

  Planarity restraints: 587
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 383 "    0.034 5.00e-02 4.00e+02   5.25e-02 4.41e+00
        pdb=" N   PRO A 384 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 384 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 384 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE H  76 "    0.006 2.00e-02 2.50e+03   1.27e-02 1.62e+00
        pdb=" C   ILE H  76 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   ILE H  76 "    0.008 2.00e-02 2.50e+03
        pdb=" N   THR H  77 "    0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 511 "    0.005 2.00e-02 2.50e+03   1.04e-02 1.08e+00
        pdb=" C   VAL A 511 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   VAL A 511 "    0.007 2.00e-02 2.50e+03
        pdb=" N   VAL A 512 "    0.006 2.00e-02 2.50e+03
  ... (remaining 584 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 255
        2.74 -     3.28: 3095
        3.28 -     3.82: 5294
        3.82 -     4.36: 6181
        4.36 -     4.90: 11199
  Nonbonded interactions: 26024
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 439 "
            pdb=" OG  SER A 443 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OD2 ASP A 398 "
            pdb=" OH  TYR A 423 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" OD1 ASP A 442 "
            pdb=" OH  TYR A 451 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   SER A 443 "
            pdb=" NH1 ARG H  59 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" O   THR A 393 "
            pdb=" OG1 THR A 523 "
     model   vdw
     2.296 3.040
  ... (remaining 26019 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:             0.360
  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:                    0.010
  Process input model:                     5.600
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
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   0.042   3404  Z= 0.158
  Angle     :  0.546   8.708   4633  Z= 0.288
  Chirality :  0.045   0.197    499
  Planarity :  0.004   0.052    586
  Dihedral  : 15.592  88.416   1214
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 24.79 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.30 (0.42), residues: 416
  helix: -3.39 (0.77), residues: 27
  sheet:  0.90 (0.45), residues: 153
  loop : -0.53 (0.40), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 454 
 TYR   0.015   0.001   TYR L  91 
 PHE   0.011   0.001   PHE A 392 
 TRP   0.008   0.001   TRP A 353 
 HIS   0.002   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 3397)
  covalent geometry    : angle       0.53994 ( 4618)
  SS BOND              : bond        0.00761 (    6)
  SS BOND              : angle       1.49047 (   12)
  hydrogen bonds       : bond        0.19924 (  106)
  hydrogen bonds       : angle       8.12244 (  261)
  link_NAG-ASN         : bond        0.00371 (    1)
  link_NAG-ASN         : angle       1.84265 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.093 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7266 (ttt-90) cc_final: 0.6859 (ttm-80)
REVERT: A  403 ARG cc_start: 0.7775 (ttp80) cc_final: 0.7560 (mtp180)
REVERT: A  471 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6402 (mm-30)
REVERT: H   17 SER cc_start: 0.8227 (m) cc_final: 0.7955 (p)
REVERT: H   19 MET cc_start: 0.7052 (ttm) cc_final: 0.6608 (ttp)
REVERT: H   21 SER cc_start: 0.7327 (p) cc_final: 0.7057 (t)
REVERT: L   69 THR cc_start: 0.7509 (p) cc_final: 0.7144 (m)
  outliers start: 2
  outliers final: 2
  residues processed: 52
  average time/residue: 0.0607
  time to fit residues: 3.9429
Evaluate side-chains
  39 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 37
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   85 SER
Chi-restraints excluded: chain H residue  105 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:   20.0000
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    7.9990
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 409 GLN
H  67 HIS
L   6 GLN
L  89 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.162799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.133074 restraints weight = 3594.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.132184 restraints weight = 3363.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.134028 restraints weight = 2985.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.134668 restraints weight = 2491.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.134780 restraints weight = 2313.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3404  Z= 0.182
  Angle     :  0.588   9.617   4633  Z= 0.309
  Chirality :  0.047   0.205    499
  Planarity :  0.004   0.042    586
  Dihedral  :  5.147  36.243    488
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 22.54 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.30 (0.41), residues: 416
  helix: -2.81 (0.85), residues: 27
  sheet:  0.93 (0.45), residues: 151
  loop : -0.63 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 454 
 TYR   0.016   0.001   TYR L  91 
 PHE   0.013   0.002   PHE A 347 
 TRP   0.009   0.001   TRP H  33 
 HIS   0.004   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 3397)
  covalent geometry    : angle       0.57933 ( 4618)
  SS BOND              : bond        0.00953 (    6)
  SS BOND              : angle       1.74582 (   12)
  hydrogen bonds       : bond        0.03168 (  106)
  hydrogen bonds       : angle       5.72694 (  261)
  link_NAG-ASN         : bond        0.00597 (    1)
  link_NAG-ASN         : angle       2.25536 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 36
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7561 (ttt-90) cc_final: 0.7137 (ttm-80)
REVERT: A  462 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6733 (mmtm)
REVERT: H   10 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.5713 (mp0)
REVERT: H   91 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8216 (t)
REVERT: L   69 THR cc_start: 0.8091 (p) cc_final: 0.7745 (m)
  outliers start: 19
  outliers final: 12
  residues processed: 53
  average time/residue: 0.0574
  time to fit residues: 3.8534
Evaluate side-chains
  47 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 32
  time to evaluate  : 0.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  473 TYR
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   89 SER
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  100 THR
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 11 optimal weight:    2.9990
   chunk 38 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 18 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    1.7586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.163462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.132268 restraints weight = 3598.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.134063 restraints weight = 2910.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.135228 restraints weight = 2536.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.136205 restraints weight = 2330.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.136205 restraints weight = 2238.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.1556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   3404  Z= 0.165
  Angle     :  0.563   9.930   4633  Z= 0.295
  Chirality :  0.046   0.205    499
  Planarity :  0.004   0.039    586
  Dihedral  :  5.038  36.184    486
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 21.97 %
    Favored  : 70.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.32 (0.41), residues: 416
  helix: -2.74 (0.85), residues: 27
  sheet:  0.82 (0.45), residues: 152
  loop : -0.58 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 346 
 TYR   0.014   0.001   TYR L  91 
 PHE   0.010   0.001   PHE A 347 
 TRP   0.009   0.001   TRP H  33 
 HIS   0.003   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 3397)
  covalent geometry    : angle       0.55425 ( 4618)
  SS BOND              : bond        0.00923 (    6)
  SS BOND              : angle       1.73478 (   12)
  hydrogen bonds       : bond        0.02996 (  106)
  hydrogen bonds       : angle       5.44244 (  261)
  link_NAG-ASN         : bond        0.00549 (    1)
  link_NAG-ASN         : angle       2.28426 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 34
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7564 (ttt-90) cc_final: 0.7138 (ttm-80)
REVERT: A  390 LEU cc_start: 0.5499 (OUTLIER) cc_final: 0.5235 (tp)
REVERT: A  454 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.8171 (ttm-80)
REVERT: A  462 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6968 (mmtt)
REVERT: A  468 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7938 (mt)
REVERT: H   10 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.5634 (mp0)
REVERT: H   39 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7321 (tt0)
  outliers start: 27
  outliers final: 18
  residues processed: 58
  average time/residue: 0.0603
  time to fit residues: 4.3607
Evaluate side-chains
  55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 32
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  473 TYR
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   89 SER
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  103 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:   20.0000
   chunk 26 optimal weight:    0.5980
   chunk 8 optimal weight:    5.9990
   chunk 35 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0010
   overall best weight:    0.6186

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.167392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.136684 restraints weight = 3477.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.138475 restraints weight = 2825.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.140101 restraints weight = 2453.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.140794 restraints weight = 2239.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.140794 restraints weight = 2103.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.1684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   3404  Z= 0.097
  Angle     :  0.511   8.484   4633  Z= 0.267
  Chirality :  0.045   0.242    499
  Planarity :  0.003   0.035    586
  Dihedral  :  4.857  38.700    486
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 23.38 %
    Favored  : 70.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.13 (0.42), residues: 416
  helix: -2.24 (1.00), residues: 27
  sheet:  0.79 (0.44), residues: 157
  loop : -0.40 (0.40), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 454 
 TYR   0.009   0.001   TYR A 365 
 PHE   0.007   0.001   PHE A 392 
 TRP   0.006   0.001   TRP H 112 
 HIS   0.001   0.000   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 3397)
  covalent geometry    : angle       0.50117 ( 4618)
  SS BOND              : bond        0.00755 (    6)
  SS BOND              : angle       1.47104 (   12)
  hydrogen bonds       : bond        0.02558 (  106)
  hydrogen bonds       : angle       5.33005 (  261)
  link_NAG-ASN         : bond        0.00492 (    1)
  link_NAG-ASN         : angle       2.80550 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 37
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7546 (ttt-90) cc_final: 0.7119 (ttm-80)
REVERT: A  358 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6252 (mp)
REVERT: A  462 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6816 (mmtm)
REVERT: A  468 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7777 (mt)
  outliers start: 22
  outliers final: 13
  residues processed: 57
  average time/residue: 0.0642
  time to fit residues: 4.5229
Evaluate side-chains
  48 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 32
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   89 SER
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   46 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.0050
   chunk 30 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    1.1598

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.165681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.134447 restraints weight = 3510.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.136006 restraints weight = 2870.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.137644 restraints weight = 2529.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.137644 restraints weight = 2329.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.137644 restraints weight = 2329.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3404  Z= 0.125
  Angle     :  0.523   8.968   4633  Z= 0.272
  Chirality :  0.046   0.235    499
  Planarity :  0.003   0.034    586
  Dihedral  :  4.802  37.331    486
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  9.01 %
    Allowed  : 21.69 %
    Favored  : 69.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.02 (0.42), residues: 416
  helix: -1.39 (1.32), residues: 19
  sheet:  0.97 (0.44), residues: 151
  loop : -0.47 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 454 
 TYR   0.012   0.001   TYR L  91 
 PHE   0.008   0.001   PHE A 515 
 TRP   0.007   0.001   TRP H  33 
 HIS   0.002   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 3397)
  covalent geometry    : angle       0.51434 ( 4618)
  SS BOND              : bond        0.00805 (    6)
  SS BOND              : angle       1.57156 (   12)
  hydrogen bonds       : bond        0.02634 (  106)
  hydrogen bonds       : angle       5.18224 (  261)
  link_NAG-ASN         : bond        0.00637 (    1)
  link_NAG-ASN         : angle       2.45097 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 33
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7606 (ttt-90) cc_final: 0.7169 (ttm-80)
REVERT: A  462 LYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6804 (mmtm)
REVERT: A  468 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7676 (mt)
REVERT: H   10 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.5513 (mp0)
REVERT: H   39 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7287 (tt0)
  outliers start: 32
  outliers final: 21
  residues processed: 61
  average time/residue: 0.0535
  time to fit residues: 4.1340
Evaluate side-chains
  56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 31
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  473 TYR
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   89 SER
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   46 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  103 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 40 optimal weight:    5.9990
   chunk 34 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3761 r_free = 0.3761 target = 0.168046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.137120 restraints weight = 3511.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.138879 restraints weight = 2886.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.139513 restraints weight = 2516.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.141090 restraints weight = 2358.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.141452 restraints weight = 2165.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   3404  Z= 0.104
  Angle     :  0.501   8.510   4633  Z= 0.260
  Chirality :  0.045   0.215    499
  Planarity :  0.003   0.032    586
  Dihedral  :  4.649  36.030    486
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  7.32 %
    Allowed  : 23.38 %
    Favored  : 69.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.11 (0.42), residues: 416
  helix: -1.40 (1.31), residues: 19
  sheet:  1.04 (0.43), residues: 151
  loop : -0.42 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 454 
 TYR   0.010   0.001   TYR L  91 
 PHE   0.007   0.001   PHE A 515 
 TRP   0.006   0.001   TRP H  33 
 HIS   0.001   0.000   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3397)
  covalent geometry    : angle       0.49330 ( 4618)
  SS BOND              : bond        0.00752 (    6)
  SS BOND              : angle       1.48032 (   12)
  hydrogen bonds       : bond        0.02494 (  106)
  hydrogen bonds       : angle       5.03946 (  261)
  link_NAG-ASN         : bond        0.00586 (    1)
  link_NAG-ASN         : angle       2.00916 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 30
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7596 (ttt-90) cc_final: 0.7151 (ttm-80)
REVERT: A  462 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6814 (mmtm)
REVERT: A  468 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7666 (mt)
REVERT: H   10 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.5464 (mp0)
  outliers start: 26
  outliers final: 19
  residues processed: 53
  average time/residue: 0.0654
  time to fit residues: 4.3467
Evaluate side-chains
  51 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 29
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  473 TYR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   89 SER
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   46 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   89 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    9.9990
   chunk 6 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 9 optimal weight:    0.4980
   overall best weight:    2.0986

-------------------------------------------------------------------------------
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 = 0.3715 r_free = 0.3715 target = 0.163416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.131845 restraints weight = 3597.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.133385 restraints weight = 2926.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.134968 restraints weight = 2588.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.135565 restraints weight = 2362.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.135564 restraints weight = 2247.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   3404  Z= 0.188
  Angle     :  0.592  10.382   4633  Z= 0.304
  Chirality :  0.048   0.228    499
  Planarity :  0.004   0.032    586
  Dihedral  :  5.036  36.970    486
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 23.10 %
    Favored  : 69.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.10 (0.41), residues: 416
  helix: -1.56 (1.25), residues: 19
  sheet:  0.79 (0.43), residues: 153
  loop : -0.49 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 346 
 TYR   0.015   0.002   TYR L  91 
 PHE   0.009   0.002   PHE A 347 
 TRP   0.009   0.001   TRP A 353 
 HIS   0.002   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 3397)
  covalent geometry    : angle       0.58162 ( 4618)
  SS BOND              : bond        0.00935 (    6)
  SS BOND              : angle       1.87757 (   12)
  hydrogen bonds       : bond        0.02900 (  106)
  hydrogen bonds       : angle       5.21298 (  261)
  link_NAG-ASN         : bond        0.00584 (    1)
  link_NAG-ASN         : angle       2.69323 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 34
  time to evaluate  : 0.109 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7626 (ttt-90) cc_final: 0.7183 (ttm-80)
REVERT: A  462 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.7027 (mmtt)
REVERT: A  468 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7872 (mt)
REVERT: H   10 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.5628 (mp0)
REVERT: H   39 GLN cc_start: 0.7696 (OUTLIER) cc_final: 0.7271 (tt0)
  outliers start: 28
  outliers final: 21
  residues processed: 58
  average time/residue: 0.0420
  time to fit residues: 3.2111
Evaluate side-chains
  58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 33
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  473 TYR
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   89 SER
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  110 HIS
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   46 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  103 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 25 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 23 optimal weight:    7.9990
   overall best weight:    2.9188

-------------------------------------------------------------------------------
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 = 0.3689 r_free = 0.3689 target = 0.160399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.129434 restraints weight = 3610.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.131235 restraints weight = 2967.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.132177 restraints weight = 2595.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.132429 restraints weight = 2404.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.133520 restraints weight = 2334.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063   3404  Z= 0.246
  Angle     :  0.666  11.806   4633  Z= 0.344
  Chirality :  0.050   0.234    499
  Planarity :  0.005   0.035    586
  Dihedral  :  5.414  39.240    486
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 22.54 %
    Favored  : 69.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.51 (0.41), residues: 416
  helix: -2.31 (0.93), residues: 25
  sheet:  0.58 (0.43), residues: 153
  loop : -0.71 (0.40), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 346 
 TYR   0.018   0.002   TYR L  91 
 PHE   0.012   0.002   PHE A 347 
 TRP   0.010   0.002   TRP H  33 
 HIS   0.003   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 ( 3397)
  covalent geometry    : angle       0.65306 ( 4618)
  SS BOND              : bond        0.01103 (    6)
  SS BOND              : angle       2.19885 (   12)
  hydrogen bonds       : bond        0.03185 (  106)
  hydrogen bonds       : angle       5.49280 (  261)
  link_NAG-ASN         : bond        0.00611 (    1)
  link_NAG-ASN         : angle       2.93204 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 33
  time to evaluate  : 0.067 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7631 (ttt-90) cc_final: 0.7140 (ttm-80)
REVERT: A  390 LEU cc_start: 0.5341 (OUTLIER) cc_final: 0.5104 (tp)
REVERT: A  462 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7064 (mmtt)
REVERT: A  468 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7957 (mt)
REVERT: H   10 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.5688 (mp0)
REVERT: H   39 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7257 (tt0)
  outliers start: 28
  outliers final: 21
  residues processed: 55
  average time/residue: 0.0425
  time to fit residues: 3.0424
Evaluate side-chains
  59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 33
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  473 TYR
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   39 GLN
Chi-restraints excluded: chain H residue   89 SER
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   46 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   89 GLN
Chi-restraints excluded: chain L residue  103 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 21 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.166431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.135632 restraints weight = 3530.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.137433 restraints weight = 2885.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.138458 restraints weight = 2522.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.138820 restraints weight = 2323.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.139915 restraints weight = 2236.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3404  Z= 0.113
  Angle     :  0.544   9.828   4633  Z= 0.282
  Chirality :  0.046   0.218    499
  Planarity :  0.004   0.034    586
  Dihedral  :  4.896  37.550    486
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 24.79 %
    Favored  : 68.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.23 (0.42), residues: 416
  helix: -2.34 (0.94), residues: 25
  sheet:  0.82 (0.44), residues: 151
  loop : -0.53 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 454 
 TYR   0.012   0.001   TYR A 369 
 PHE   0.008   0.001   PHE A 515 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.001   0.000   HIS H  67 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 3397)
  covalent geometry    : angle       0.53667 ( 4618)
  SS BOND              : bond        0.00815 (    6)
  SS BOND              : angle       1.60900 (   12)
  hydrogen bonds       : bond        0.02676 (  106)
  hydrogen bonds       : angle       5.18920 (  261)
  link_NAG-ASN         : bond        0.00622 (    1)
  link_NAG-ASN         : angle       2.03159 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 34
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7639 (ttt-90) cc_final: 0.7163 (ttm-80)
REVERT: A  462 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7010 (mmtt)
REVERT: A  468 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7832 (mt)
REVERT: H   10 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.5483 (mp0)
  outliers start: 23
  outliers final: 20
  residues processed: 54
  average time/residue: 0.0482
  time to fit residues: 3.3464
Evaluate side-chains
  56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 33
  time to evaluate  : 0.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  473 TYR
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   89 SER
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   46 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   89 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    9.9990
   chunk 4 optimal weight:    0.8980
   chunk 19 optimal weight:    8.9990
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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 = 0.3731 r_free = 0.3731 target = 0.164574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.133639 restraints weight = 3514.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.135398 restraints weight = 2915.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.136374 restraints weight = 2553.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.136687 restraints weight = 2364.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.137727 restraints weight = 2282.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   3404  Z= 0.151
  Angle     :  0.569  10.186   4633  Z= 0.294
  Chirality :  0.046   0.220    499
  Planarity :  0.004   0.035    586
  Dihedral  :  4.925  36.136    486
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 23.94 %
    Favored  : 69.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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: -0.07 (0.42), residues: 416
  helix: -1.90 (1.13), residues: 19
  sheet:  0.80 (0.43), residues: 151
  loop : -0.41 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 454 
 TYR   0.016   0.001   TYR L  91 
 PHE   0.007   0.001   PHE L  71 
 TRP   0.008   0.001   TRP H  33 
 HIS   0.002   0.001   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 3397)
  covalent geometry    : angle       0.55970 ( 4618)
  SS BOND              : bond        0.00870 (    6)
  SS BOND              : angle       1.78159 (   12)
  hydrogen bonds       : bond        0.02783 (  106)
  hydrogen bonds       : angle       5.27315 (  261)
  link_NAG-ASN         : bond        0.00583 (    1)
  link_NAG-ASN         : angle       2.39913 (    3)

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

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

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  832 Ramachandran restraints generated.
    416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 34
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7633 (ttt-90) cc_final: 0.7166 (ttm-80)
REVERT: A  450 ASN cc_start: 0.7182 (m-40) cc_final: 0.6858 (m110)
REVERT: A  462 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7056 (mmtt)
REVERT: A  468 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7861 (mt)
REVERT: H   10 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.5566 (mp0)
  outliers start: 23
  outliers final: 20
  residues processed: 54
  average time/residue: 0.0570
  time to fit residues: 3.9664
Evaluate side-chains
  56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 33
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  440 ASN
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  473 TYR
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain H residue   10 GLU
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   17 SER
Chi-restraints excluded: chain H residue   89 SER
Chi-restraints excluded: chain H residue  117 LEU
Chi-restraints excluded: chain H residue  119 THR
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   46 VAL
Chi-restraints excluded: chain L residue   75 ILE
Chi-restraints excluded: chain L residue   89 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 37 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 32 optimal weight:   20.0000
   chunk 18 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.166699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.135673 restraints weight = 3554.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.137327 restraints weight = 2897.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.138874 restraints weight = 2530.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.138874 restraints weight = 2295.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.138874 restraints weight = 2295.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   3404  Z= 0.117
  Angle     :  0.536   9.587   4633  Z= 0.278
  Chirality :  0.046   0.213    499
  Planarity :  0.004   0.034    586
  Dihedral  :  4.761  35.622    486
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 23.94 %
    Favored  : 69.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    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:  0.09 (0.42), residues: 416
  helix: -1.76 (1.15), residues: 19
  sheet:  0.91 (0.44), residues: 151
  loop : -0.30 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 454 
 TYR   0.012   0.001   TYR L  91 
 PHE   0.007   0.001   PHE A 392 
 TRP   0.007   0.001   TRP H  33 
 HIS   0.001   0.000   HIS H 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3397)
  covalent geometry    : angle       0.52757 ( 4618)
  SS BOND              : bond        0.00787 (    6)
  SS BOND              : angle       1.60997 (   12)
  hydrogen bonds       : bond        0.02636 (  106)
  hydrogen bonds       : angle       5.03984 (  261)
  link_NAG-ASN         : bond        0.00596 (    1)
  link_NAG-ASN         : angle       2.03603 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 730.01 seconds
wall clock time: 13 minutes 14.51 seconds (794.51 seconds total)