Starting phenix.real_space_refine
on Wed Jul  1 22:04:17 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7y6l_33643/07_2026/7y6l_33643.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7y6l_33643/07_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_33643/07_2026/7y6l_33643.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7y6l_33643/07_2026/7y6l_33643.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7y6l_33643/07_2026/7y6l_33643.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7y6l_33643/07_2026/7y6l_33643.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7y6l_33643/07_2026/7y6l_33643.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7y6l_33643/07_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-6108/lib/python3.11/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 chiralities: 1
  Time building chain proxies: 0.71, per 1000 atoms: 0.21
  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: 0.17
  Conformation dependent library (CDL) restraints added in 118.9 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: 0.09
  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: 0.45

  Time building geometry restraints manager: 0.28 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: 1724
       17.68 -    35.37: 209
       35.37 -    53.05: 42
       53.05 -    70.73: 8
       70.73 -    88.42: 2
  Dihedral angle restraints: 1985
    sinusoidal: 764
      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 1982 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:             0.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.490
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  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:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
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  : 15.573  88.416   1193
  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/Z
  covalent geometry    : bond        0.00361 /  0.16 ( 3397)
  covalent geometry    : angle       0.53994 /  0.29 ( 4618)
  SS BOND              : bond        0.00761 /  0.36 (    6)
  SS BOND              : angle       1.49047 /  1.37 (   12)
  hydrogen bonds       : bond        0.19924 / 12.92 (  106)
  hydrogen bonds       : angle       8.12244 /  5.50 (  261)
  link_NAG-ASN         : bond        0.00371 /  0.20 (    1)
  link_NAG-ASN         : angle       1.84265 /  1.16 (    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  : 0.111 
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: 0.0503
  time to fit residues: 3.2409
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  : 0.068 
-------------------------------------------------------------------------------
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...
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 = 0.3714 r_free = 0.3714 target = 0.163088 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.133423 restraints weight = 3584.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.132537 restraints weight = 3560.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.134424 restraints weight = 3114.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.135153 restraints weight = 2545.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.135298 restraints weight = 2334.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   3404  Z= 0.182
  Angle     :  0.590   9.778   4633  Z= 0.309
  Chirality :  0.047   0.200    499
  Planarity :  0.004   0.042    586
  Dihedral  :  4.668  18.910    467
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 22.25 %
    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: -0.31 (0.41), residues: 416
  helix: -2.80 (0.86), residues: 27
  sheet:  0.92 (0.45), residues: 151
  loop : -0.63 (0.39), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  61 
 TYR   0.016   0.002   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/Z
  covalent geometry    : bond        0.00431 /  0.18 ( 3397)
  covalent geometry    : angle       0.58115 /  0.31 ( 4618)
  SS BOND              : bond        0.00953 /  0.44 (    6)
  SS BOND              : angle       1.75647 /  1.59 (   12)
  hydrogen bonds       : bond        0.03144 /  2.02 (  106)
  hydrogen bonds       : angle       5.66276 /  3.89 (  261)
  link_NAG-ASN         : bond        0.00462 /  0.24 (    1)
  link_NAG-ASN         : angle       2.23490 /  1.31 (    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
  54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 34
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7569 (ttt-90) cc_final: 0.7137 (ttm-80)
REVERT: A  462 LYS cc_start: 0.7235 (OUTLIER) cc_final: 0.6762 (mmtm)
REVERT: H   10 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.5798 (mp0)
  outliers start: 20
  outliers final: 12
  residues processed: 52
  average time/residue: 0.0571
  time to fit residues: 3.6873
Evaluate side-chains
  45 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 31
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
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  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:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 38 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    0.4980
   overall best weight:    2.0986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.161726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.130588 restraints weight = 3619.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.132554 restraints weight = 2943.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.133591 restraints weight = 2564.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.133991 restraints weight = 2361.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.134340 restraints weight = 2268.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1625

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= 0.188
  Angle     :  0.594  10.457   4633  Z= 0.309
  Chirality :  0.047   0.202    499
  Planarity :  0.004   0.039    586
  Dihedral  :  4.661  14.606    465
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  7.32 %
    Allowed  : 22.25 %
    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: -0.41 (0.41), residues: 416
  helix: -2.75 (0.85), residues: 27
  sheet:  0.76 (0.44), residues: 152
  loop : -0.64 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 346 
 TYR   0.015   0.001   TYR L  91 
 PHE   0.011   0.002   PHE A 347 
 TRP   0.009   0.001   TRP H  33 
 HIS   0.003   0.001   HIS H 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00447 /  0.19 ( 3397)
  covalent geometry    : angle       0.58445 /  0.31 ( 4618)
  SS BOND              : bond        0.00961 /  0.44 (    6)
  SS BOND              : angle       1.82828 /  1.66 (   12)
  hydrogen bonds       : bond        0.03111 /  1.97 (  106)
  hydrogen bonds       : angle       5.56654 /  3.80 (  261)
  link_NAG-ASN         : bond        0.00511 /  0.27 (    1)
  link_NAG-ASN         : angle       2.34576 /  1.36 (    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
  60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 34
  time to evaluate  : 0.114 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7588 (ttt-90) cc_final: 0.7151 (ttm-80)
REVERT: A  390 LEU cc_start: 0.5519 (OUTLIER) cc_final: 0.5261 (tp)
REVERT: A  454 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.7300 (ttm-80)
REVERT: A  462 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6975 (mmtt)
REVERT: H   10 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.5785 (mp0)
REVERT: H   39 GLN cc_start: 0.7672 (OUTLIER) cc_final: 0.7314 (tt0)
  outliers start: 26
  outliers final: 18
  residues processed: 57
  average time/residue: 0.0577
  time to fit residues: 4.1630
Evaluate side-chains
  54 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 32
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
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  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   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   33 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:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 32 optimal weight:   20.0000
   chunk 26 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0970
   chunk 34 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.9180

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.165538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.134856 restraints weight = 3495.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.136482 restraints weight = 2838.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.137765 restraints weight = 2491.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.138793 restraints weight = 2269.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.139207 restraints weight = 2148.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3404  Z= 0.115
  Angle     :  0.537   9.183   4633  Z= 0.279
  Chirality :  0.046   0.218    499
  Planarity :  0.003   0.036    586
  Dihedral  :  4.400  15.752    465
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  7.32 %
    Allowed  : 22.25 %
    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: -0.25 (0.41), residues: 416
  helix: -2.34 (0.98), residues: 27
  sheet:  0.90 (0.44), residues: 150
  loop : -0.58 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 454 
 TYR   0.010   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/Z
  covalent geometry    : bond        0.00270 /  0.11 ( 3397)
  covalent geometry    : angle       0.52682 /  0.28 ( 4618)
  SS BOND              : bond        0.00802 /  0.38 (    6)
  SS BOND              : angle       1.57004 /  1.41 (   12)
  hydrogen bonds       : bond        0.02663 /  1.68 (  106)
  hydrogen bonds       : angle       5.42251 /  3.70 (  261)
  link_NAG-ASN         : bond        0.00467 /  0.25 (    1)
  link_NAG-ASN         : angle       3.00693 /  2.34 (    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
  62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 36
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7569 (ttt-90) cc_final: 0.7154 (ttm-80)
REVERT: A  358 ILE cc_start: 0.6476 (OUTLIER) cc_final: 0.6224 (mp)
REVERT: A  382 VAL cc_start: 0.7437 (OUTLIER) cc_final: 0.7155 (p)
REVERT: A  462 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6808 (mmtm)
  outliers start: 26
  outliers final: 17
  residues processed: 60
  average time/residue: 0.0578
  time to fit residues: 4.3079
Evaluate side-chains
  53 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 33
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
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  382 VAL
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  473 TYR
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   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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 30 optimal weight:    7.9990
   chunk 2 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 422 ASN
A 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.165581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.134770 restraints weight = 3516.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.136088 restraints weight = 2896.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.137321 restraints weight = 2555.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.138354 restraints weight = 2332.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.139248 restraints weight = 2191.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3404  Z= 0.120
  Angle     :  0.526   9.179   4633  Z= 0.272
  Chirality :  0.046   0.232    499
  Planarity :  0.004   0.034    586
  Dihedral  :  4.297  15.655    465
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 22.82 %
    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: -0.19 (0.41), residues: 416
  helix: -2.05 (1.04), residues: 25
  sheet:  0.91 (0.43), residues: 151
  loop : -0.59 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 454 
 TYR   0.011   0.001   TYR L  91 
 PHE   0.009   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/Z
  covalent geometry    : bond        0.00282 /  0.12 ( 3397)
  covalent geometry    : angle       0.51692 /  0.27 ( 4618)
  SS BOND              : bond        0.00798 /  0.37 (    6)
  SS BOND              : angle       1.55479 /  1.41 (   12)
  hydrogen bonds       : bond        0.02634 /  1.69 (  106)
  hydrogen bonds       : angle       5.23031 /  3.55 (  261)
  link_NAG-ASN         : bond        0.00602 /  0.32 (    1)
  link_NAG-ASN         : angle       2.36807 /  1.70 (    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
  58 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 31
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7611 (ttt-90) cc_final: 0.7173 (ttm-80)
REVERT: A  382 VAL cc_start: 0.7371 (OUTLIER) cc_final: 0.7079 (p)
REVERT: A  462 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6817 (mmtm)
REVERT: H   10 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.5601 (mp0)
REVERT: H   39 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7252 (tt0)
  outliers start: 27
  outliers final: 18
  residues processed: 55
  average time/residue: 0.0512
  time to fit residues: 3.6871
Evaluate side-chains
  52 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 30
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
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  382 VAL
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  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   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   11 LEU
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   46 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.0570
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   overall best weight:    0.9702

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.166932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.135727 restraints weight = 3524.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.137467 restraints weight = 2857.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.137840 restraints weight = 2485.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.139373 restraints weight = 2374.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.139697 restraints weight = 2207.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.1977

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= 0.112
  Angle     :  0.510   9.007   4633  Z= 0.265
  Chirality :  0.045   0.208    499
  Planarity :  0.003   0.032    586
  Dihedral  :  4.193  15.836    465
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  7.32 %
    Allowed  : 23.10 %
    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:  0.04 (0.42), residues: 416
  helix: -1.41 (1.31), residues: 19
  sheet:  0.97 (0.43), residues: 151
  loop : -0.44 (0.40), residues: 246

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



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.11 ( 3397)
  covalent geometry    : angle       0.50174 /  0.26 ( 4618)
  SS BOND              : bond        0.00775 /  0.36 (    6)
  SS BOND              : angle       1.53248 /  1.38 (   12)
  hydrogen bonds       : bond        0.02575 /  1.63 (  106)
  hydrogen bonds       : angle       5.06351 /  3.45 (  261)
  link_NAG-ASN         : bond        0.00581 /  0.31 (    1)
  link_NAG-ASN         : angle       2.03653 /  1.32 (    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
  59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 33
  time to evaluate  : 0.066 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7614 (ttt-90) cc_final: 0.7151 (ttm-80)
REVERT: A  462 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6841 (mmtm)
REVERT: H   10 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.5641 (mp0)
REVERT: H   39 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.7277 (tt0)
  outliers start: 26
  outliers final: 16
  residues processed: 55
  average time/residue: 0.0344
  time to fit residues: 2.4288
Evaluate side-chains
  50 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 31
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
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  462 LYS
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   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   33 LEU
Chi-restraints excluded: chain L residue   46 VAL
Chi-restraints excluded: chain L residue   75 ILE
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:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    2.0786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.162853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.131340 restraints weight = 3597.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.132992 restraints weight = 2919.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.133630 restraints weight = 2558.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.133630 restraints weight = 2394.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.133630 restraints weight = 2394.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   3404  Z= 0.185
  Angle     :  0.590  10.635   4633  Z= 0.304
  Chirality :  0.047   0.203    499
  Planarity :  0.004   0.033    586
  Dihedral  :  4.525  13.346    465
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 23.38 %
    Favored  : 69.86 %
  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: -0.16 (0.41), residues: 416
  helix: -1.57 (1.25), residues: 19
  sheet:  0.77 (0.43), residues: 153
  loop : -0.55 (0.39), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 454 
 TYR   0.017   0.001   TYR L  91 
 PHE   0.008   0.002   PHE H 109 
 TRP   0.009   0.001   TRP A 353 
 HIS   0.003   0.001   HIS H 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00443 /  0.18 ( 3397)
  covalent geometry    : angle       0.57962 /  0.30 ( 4618)
  SS BOND              : bond        0.00951 /  0.44 (    6)
  SS BOND              : angle       1.85425 /  1.70 (   12)
  hydrogen bonds       : bond        0.02894 /  1.83 (  106)
  hydrogen bonds       : angle       5.21584 /  3.56 (  261)
  link_NAG-ASN         : bond        0.00627 /  0.33 (    1)
  link_NAG-ASN         : angle       2.53920 /  1.73 (    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
  59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 35
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7613 (ttt-90) cc_final: 0.7179 (ttm-80)
REVERT: A  390 LEU cc_start: 0.5378 (OUTLIER) cc_final: 0.5109 (tp)
REVERT: A  462 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7057 (mmtt)
REVERT: H   10 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.5703 (mp0)
REVERT: H   39 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7297 (tt0)
  outliers start: 24
  outliers final: 19
  residues processed: 56
  average time/residue: 0.0362
  time to fit residues: 2.5830
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  : 0.066 
-------------------------------------------------------------------------------
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  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   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   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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 20 optimal weight:    7.9990
   chunk 10 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 25 optimal weight:    0.3980
   chunk 40 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   overall best weight:    2.6786

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.161026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.130318 restraints weight = 3608.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.131807 restraints weight = 2935.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.131812 restraints weight = 2596.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.131813 restraints weight = 2594.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.131813 restraints weight = 2594.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   3404  Z= 0.227
  Angle     :  0.637  11.615   4633  Z= 0.327
  Chirality :  0.049   0.228    499
  Planarity :  0.005   0.037    586
  Dihedral  :  4.806  14.124    465
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  8.17 %
    Allowed  : 21.97 %
    Favored  : 69.86 %
  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: -0.39 (0.41), residues: 416
  helix: -1.83 (1.13), residues: 19
  sheet:  0.62 (0.43), residues: 153
  loop : -0.69 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 454 
 TYR   0.021   0.002   TYR L  91 
 PHE   0.011   0.002   PHE A 347 
 TRP   0.009   0.001   TRP H  33 
 HIS   0.003   0.001   HIS H  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00542 /  0.23 ( 3397)
  covalent geometry    : angle       0.62490 /  0.32 ( 4618)
  SS BOND              : bond        0.01061 /  0.49 (    6)
  SS BOND              : angle       2.11107 /  1.95 (   12)
  hydrogen bonds       : bond        0.03143 /  2.00 (  106)
  hydrogen bonds       : angle       5.40805 /  3.73 (  261)
  link_NAG-ASN         : bond        0.00560 /  0.29 (    1)
  link_NAG-ASN         : angle       2.84864 /  1.95 (    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
  63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 34
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7642 (ttt-90) cc_final: 0.7145 (ttm-80)
REVERT: A  390 LEU cc_start: 0.5403 (OUTLIER) cc_final: 0.5175 (tp)
REVERT: A  462 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7055 (mmtt)
REVERT: H   10 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.5618 (mp0)
REVERT: H   39 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7269 (tt0)
  outliers start: 29
  outliers final: 22
  residues processed: 55
  average time/residue: 0.0375
  time to fit residues: 2.6694
Evaluate side-chains
  60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 34
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
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  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   39 GLN
Chi-restraints excluded: chain H residue   85 SER
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   33 LEU
Chi-restraints excluded: chain L residue   46 VAL
Chi-restraints excluded: chain L residue   50 LYS
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:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 8 optimal weight:    0.4980
   chunk 38 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    1.0982

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.164997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.134373 restraints weight = 3551.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.135900 restraints weight = 2885.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.137193 restraints weight = 2538.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.137326 restraints weight = 2318.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.138548 restraints weight = 2264.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3404  Z= 0.123
  Angle     :  0.544  10.375   4633  Z= 0.280
  Chirality :  0.046   0.208    499
  Planarity :  0.004   0.035    586
  Dihedral  :  4.382  13.510    465
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  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: -0.35 (0.41), residues: 416
  helix: -2.34 (0.92), residues: 25
  sheet:  0.80 (0.43), residues: 151
  loop : -0.68 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 454 
 TYR   0.014   0.001   TYR A 369 
 PHE   0.007   0.001   PHE A 515 
 TRP   0.007   0.001   TRP H  33 
 HIS   0.001   0.000   HIS H 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.12 ( 3397)
  covalent geometry    : angle       0.53577 /  0.28 ( 4618)
  SS BOND              : bond        0.00833 /  0.39 (    6)
  SS BOND              : angle       1.68743 /  1.53 (   12)
  hydrogen bonds       : bond        0.02749 /  1.74 (  106)
  hydrogen bonds       : angle       5.11455 /  3.53 (  261)
  link_NAG-ASN         : bond        0.00624 /  0.33 (    1)
  link_NAG-ASN         : angle       2.00834 /  1.29 (    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
  61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 37
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7626 (ttt-90) cc_final: 0.7186 (ttm-80)
REVERT: A  358 ILE cc_start: 0.6560 (OUTLIER) cc_final: 0.6312 (mp)
REVERT: A  462 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7055 (mmtt)
REVERT: H   10 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.5500 (mp0)
REVERT: H   39 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7286 (tt0)
  outliers start: 24
  outliers final: 19
  residues processed: 57
  average time/residue: 0.0363
  time to fit residues: 2.6675
Evaluate side-chains
  59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 36
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  444 LYS
Chi-restraints excluded: chain A residue  462 LYS
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   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   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:    8.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.9788

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.162592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.131360 restraints weight = 3555.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.133137 restraints weight = 2909.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.134507 restraints weight = 2540.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.134745 restraints weight = 2341.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.135406 restraints weight = 2276.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3404  Z= 0.176
  Angle     :  0.585  10.856   4633  Z= 0.300
  Chirality :  0.047   0.214    499
  Planarity :  0.004   0.034    586
  Dihedral  :  4.557  13.033    465
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 23.94 %
    Favored  : 69.86 %
  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: -0.29 (0.41), residues: 416
  helix: -1.99 (1.10), residues: 19
  sheet:  0.73 (0.43), residues: 151
  loop : -0.63 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 454 
 TYR   0.017   0.002   TYR L  91 
 PHE   0.008   0.001   PHE A 347 
 TRP   0.008   0.001   TRP H  33 
 HIS   0.002   0.001   HIS H 110 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00421 /  0.17 ( 3397)
  covalent geometry    : angle       0.57422 /  0.30 ( 4618)
  SS BOND              : bond        0.00935 /  0.43 (    6)
  SS BOND              : angle       1.91086 /  1.76 (   12)
  hydrogen bonds       : bond        0.02933 /  1.86 (  106)
  hydrogen bonds       : angle       5.19766 /  3.60 (  261)
  link_NAG-ASN         : bond        0.00563 /  0.30 (    1)
  link_NAG-ASN         : angle       2.48273 /  1.62 (    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
  56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 34
  time to evaluate  : 0.080 
Fit side-chains
REVERT: A  357 ARG cc_start: 0.7629 (ttt-90) cc_final: 0.7169 (ttm-80)
REVERT: A  462 LYS cc_start: 0.7447 (OUTLIER) cc_final: 0.7065 (mmtt)
REVERT: H   10 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.5629 (mp0)
REVERT: H   39 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7248 (tt0)
  outliers start: 22
  outliers final: 19
  residues processed: 52
  average time/residue: 0.0348
  time to fit residues: 2.3624
Evaluate side-chains
  56 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 34
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
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  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   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   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:   10.0000
   chunk 34 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 32 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.7184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.166959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.136149 restraints weight = 3566.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.137831 restraints weight = 2889.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.139276 restraints weight = 2510.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.139540 restraints weight = 2290.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.139540 restraints weight = 2219.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045   3404  Z= 0.102
  Angle     :  0.521   9.855   4633  Z= 0.269
  Chirality :  0.045   0.202    499
  Planarity :  0.004   0.032    586
  Dihedral  :  4.227  13.890    465
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 23.66 %
    Favored  : 69.86 %
  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: -0.21 (0.42), residues: 416
  helix: -2.25 (0.94), residues: 25
  sheet:  0.87 (0.44), residues: 151
  loop : -0.55 (0.40), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 454 
 TYR   0.010   0.001   TYR A 369 
 PHE   0.008   0.001   PHE A 515 
 TRP   0.007   0.001   TRP H  33 
 HIS   0.001   0.000   HIS H  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.10 ( 3397)
  covalent geometry    : angle       0.51393 /  0.27 ( 4618)
  SS BOND              : bond        0.00775 /  0.36 (    6)
  SS BOND              : angle       1.56508 /  1.40 (   12)
  hydrogen bonds       : bond        0.02605 /  1.64 (  106)
  hydrogen bonds       : angle       4.94041 /  3.42 (  261)
  link_NAG-ASN         : bond        0.00574 /  0.30 (    1)
  link_NAG-ASN         : angle       1.79219 /  1.10 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 597.15 seconds
wall clock time: 10 minutes 56.84 seconds (656.84 seconds total)