Starting phenix.real_space_refine
on Wed Jun  4 14:28:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7swn_25476/06_2025/7swn_25476_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7swn_25476/06_2025/7swn_25476.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7swn_25476/06_2025/7swn_25476.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7swn_25476/06_2025/7swn_25476.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7swn_25476/06_2025/7swn_25476_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7swn_25476/06_2025/7swn_25476_neut.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.001
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      17      5.16       5
     C    2080      2.51       5
     N     554      2.21       5
     O     632      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3283
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    Chain: "H"
      Number of atoms: 924
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 120, 924
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 108, 823
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 100}
  Time building chain proxies: 3.29, per 1000 atoms: 1.00
  Number of scatterers: 3283
  At special positions: 0
  Unit cell: (100.65, 70.95, 75.075, 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      17     16.00
     O     632      8.00
     N     554      7.00
     C    2080      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, 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=2.04
    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  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  97 " - pdb=" SG  CYS H 100B" distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 438.5 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:
      7 helices and 9 sheets defined
      8.3% alpha, 26.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 366 through 371
    Processing helix  chain 'A' and resid 386 through 389
    Processing helix  chain 'A' and resid 405 through 410
    Processing helix  chain 'H' and resid 28 through 31
    Processing helix  chain 'H' and resid 61 through 64
      removed outlier: 4.034A  pdb=" N   GLN H  64 " --> pdb=" O   GLN H  61 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 61 through 64'
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.551A  pdb=" N   THR H  87 " --> pdb=" O   SER H  84 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.319A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.864A  pdb=" N   THR H 107 " --> pdb=" O   TYR H  90 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   VAL H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   TRP H  50 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.864A  pdb=" N   THR H 107 " --> pdb=" O   TYR H  90 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ILE H 102 " --> pdb=" O   ALA H  94 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 97 through 98
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 11
      removed outlier: 6.398A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.816A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 11
    Processing sheet with id=AA9, first strand: chain 'L' and resid 20 through 23

    83 hydrogen bonds defined for protein.
    186 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: 0.87

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1043
        1.34 -     1.46: 862
        1.46 -     1.58: 1442
        1.58 -     1.71: 0
        1.71 -     1.83: 20
  Bond restraints: 3367
  Sorted by residual:
  bond pdb=" N   VAL H  67 "
       pdb=" CA  VAL H  67 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.22e+00
  bond pdb=" N   VAL H  89 "
       pdb=" CA  VAL H  89 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.22e-02 6.72e+03 8.12e+00
  bond pdb=" N   VAL L 104 "
       pdb=" CA  VAL L 104 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.22e-02 6.72e+03 7.79e+00
  bond pdb=" N   ARG H  71 "
       pdb=" CA  ARG H  71 "
    ideal  model  delta    sigma   weight residual
    1.454  1.490 -0.035 1.29e-02 6.01e+03 7.54e+00
  bond pdb=" N   ASN A 450 "
       pdb=" CA  ASN A 450 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.32e-02 5.74e+03 7.12e+00
  ... (remaining 3362 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 4286
        2.01 -     4.02: 250
        4.02 -     6.02: 34
        6.02 -     8.03: 4
        8.03 -    10.04: 3
  Bond angle restraints: 4577
  Sorted by residual:
  angle pdb=" N   VAL H  89 "
        pdb=" CA  VAL H  89 "
        pdb=" C   VAL H  89 "
      ideal   model   delta    sigma   weight residual
     106.88   97.68    9.20 1.52e+00 4.33e-01 3.66e+01
  angle pdb=" N   PRO L  59 "
        pdb=" CA  PRO L  59 "
        pdb=" C   PRO L  59 "
      ideal   model   delta    sigma   weight residual
     111.15  118.00   -6.85 1.58e+00 4.01e-01 1.88e+01
  angle pdb=" C   ILE L  58 "
        pdb=" N   PRO L  59 "
        pdb=" CA  PRO L  59 "
      ideal   model   delta    sigma   weight residual
     119.90  124.22   -4.32 1.02e+00 9.61e-01 1.80e+01
  angle pdb=" N   SER H  74 "
        pdb=" CA  SER H  74 "
        pdb=" C   SER H  74 "
      ideal   model   delta    sigma   weight residual
     112.68  107.38    5.30 1.33e+00 5.65e-01 1.59e+01
  angle pdb=" N   ARG L  61 "
        pdb=" CA  ARG L  61 "
        pdb=" C   ARG L  61 "
      ideal   model   delta    sigma   weight residual
     113.31  105.45    7.86 2.04e+00 2.40e-01 1.48e+01
  ... (remaining 4572 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.34: 1754
       16.34 -    32.68: 182
       32.68 -    49.01: 42
       49.01 -    65.35: 8
       65.35 -    81.69: 4
  Dihedral angle restraints: 1990
    sinusoidal: 771
      harmonic: 1219
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  92 "
           pdb=" CB  CYS H  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -127.47   41.47     1      1.00e+01 1.00e-02 2.41e+01
  dihedral pdb=" CA  VAL A 401 "
           pdb=" C   VAL A 401 "
           pdb=" N   ILE A 402 "
           pdb=" CA  ILE A 402 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.37  -19.63     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  ALA A 522 "
           pdb=" C   ALA A 522 "
           pdb=" N   THR A 523 "
           pdb=" CA  THR A 523 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.19  -18.81     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 1987 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 407
       0.072 -    0.144: 78
       0.144 -    0.216: 6
       0.216 -    0.288: 0
       0.288 -    0.360: 1
  Chirality restraints: 492
  Sorted by residual:
  chirality pdb=" CA  VAL H  89 "
            pdb=" N   VAL H  89 "
            pdb=" C   VAL H  89 "
            pdb=" CB  VAL H  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.80   -0.36 2.00e-01 2.50e+01 3.25e+00
  chirality pdb=" CA  VAL L 104 "
            pdb=" N   VAL L 104 "
            pdb=" C   VAL L 104 "
            pdb=" CB  VAL L 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CB  VAL A 407 "
            pdb=" CA  VAL A 407 "
            pdb=" CG1 VAL A 407 "
            pdb=" CG2 VAL A 407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 489 not shown)

  Planarity restraints: 592
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H 100F"    0.023 2.00e-02 2.50e+03   2.63e-02 1.21e+01
        pdb=" CG  PHE H 100F"   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE H 100F"    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE H 100F"    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE H 100F"   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE H 100F"    0.016 2.00e-02 2.50e+03
        pdb=" CZ  PHE H 100F"   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H  50 "    0.016 2.00e-02 2.50e+03   1.63e-02 6.64e+00
        pdb=" CG  TRP H  50 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TRP H  50 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP H  50 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP H  50 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP H  50 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP H  50 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H  50 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H  50 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP H  50 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 425 "    0.039 5.00e-02 4.00e+02   5.83e-02 5.44e+00
        pdb=" N   PRO A 426 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 426 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 426 "    0.032 5.00e-02 4.00e+02
  ... (remaining 589 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 478
        2.74 -     3.28: 3571
        3.28 -     3.82: 5496
        3.82 -     4.36: 6691
        4.36 -     4.90: 10807
  Nonbonded interactions: 27043
  Sorted by model distance:
  nonbonded pdb=" O   LEU L   4 "
            pdb=" NE2 GLN L 100 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OH  TYR A 451 "
            pdb=" O   PHE A 497 "
     model   vdw
     2.205 3.040
  nonbonded pdb=" O   LYS H  12 "
            pdb=" N   SER H 112 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" O   PHE H  63 "
            pdb=" CG1 VAL H  67 "
     model   vdw
     2.238 3.460
  nonbonded pdb=" O   LYS H  62 "
            pdb=" NH2 ARG H  66 "
     model   vdw
     2.241 3.120
  ... (remaining 27038 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:             1.980
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.670
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6976
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      :  0.007   0.069   3374  Z= 0.369
  Angle     :  1.068  10.040   4591  Z= 0.609
  Chirality :  0.058   0.360    492
  Planarity :  0.007   0.058    592
  Dihedral  : 14.582  81.689   1195
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 41.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 21.88 %
    Favored  : 78.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.82 (0.35), residues: 416
  helix: -4.85 (0.38), residues: 30
  sheet: -2.02 (0.52), residues: 102
  loop : -3.75 (0.30), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.005   TRP H  50 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.059   0.005   PHE H 100F
 TYR   0.038   0.003   TYR L  91 
 ARG   0.012   0.001   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18755 (   76)
  hydrogen bonds       : angle      11.65780 (  186)
  SS BOND              : bond        0.00740 (    7)
  SS BOND              : angle       1.92999 (   14)
  covalent geometry    : bond        0.00724 ( 3367)
  covalent geometry    : angle       1.06390 ( 4577)

*********************** 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
  100 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.7819 (tt0) cc_final: 0.7602 (tt0)
REVERT: A  424 LYS cc_start: 0.9304 (tttm) cc_final: 0.9070 (tmtt)
REVERT: A  436 TRP cc_start: 0.7984 (p-90) cc_final: 0.7682 (p-90)
REVERT: H   20 VAL cc_start: 0.8821 (t) cc_final: 0.7589 (t)
REVERT: H   35 GLN cc_start: 0.8075 (pt0) cc_final: 0.7730 (pt0)
REVERT: H   50 TRP cc_start: 0.7631 (p-90) cc_final: 0.7377 (p-90)
REVERT: H   52 VAL cc_start: 0.8910 (t) cc_final: 0.8666 (t)
REVERT: H   83 ARG cc_start: 0.8258 (ttp-110) cc_final: 0.7959 (tpm170)
REVERT: L   77 ARG cc_start: 0.6410 (mmm160) cc_final: 0.4600 (mmt180)
REVERT: L   89 GLN cc_start: 0.8116 (tt0) cc_final: 0.7912 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.2225
  time to fit residues: 25.5303
Evaluate side-chains
  72 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    0.0470
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.5684

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

Flipped N/Q/H residues before XYZ refinement:
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.091674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.077945 restraints weight = 14241.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.080510 restraints weight = 9042.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.082345 restraints weight = 6321.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3593
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3593 r_free = 0.3593    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3593
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7023
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3374  Z= 0.162
  Angle     :  0.792  11.794   4591  Z= 0.406
  Chirality :  0.047   0.155    492
  Planarity :  0.006   0.050    592
  Dihedral  :  6.547  20.054    466
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 21.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.06 %
    Favored  : 88.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.21 (0.36), residues: 416
  helix: -4.57 (0.48), residues: 24
  sheet: -1.70 (0.49), residues: 103
  loop : -3.30 (0.32), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 353 
 HIS   0.001   0.001   HIS H 100C
 PHE   0.027   0.003   PHE H 100F
 TYR   0.014   0.002   TYR A 495 
 ARG   0.006   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04047 (   76)
  hydrogen bonds       : angle       9.51066 (  186)
  SS BOND              : bond        0.00543 (    7)
  SS BOND              : angle       1.19248 (   14)
  covalent geometry    : bond        0.00363 ( 3367)
  covalent geometry    : angle       0.79016 ( 4577)

*********************** 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
  106 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  406 GLU cc_start: 0.8267 (tt0) cc_final: 0.7880 (tt0)
REVERT: A  424 LYS cc_start: 0.9425 (tttm) cc_final: 0.9007 (tmtt)
REVERT: A  454 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8622 (tpp80)
REVERT: H   35 GLN cc_start: 0.8811 (pt0) cc_final: 0.8357 (pt0)
REVERT: H   50 TRP cc_start: 0.8031 (p-90) cc_final: 0.7814 (p-90)
REVERT: H   71 ARG cc_start: 0.8699 (ptt-90) cc_final: 0.8424 (ptt-90)
REVERT: H   80 MET cc_start: 0.8276 (ppp) cc_final: 0.7707 (ppp)
REVERT: H   83 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7874 (tpm170)
REVERT: L   42 GLN cc_start: 0.8833 (mp10) cc_final: 0.8383 (mp10)
REVERT: L   77 ARG cc_start: 0.7076 (mmm160) cc_final: 0.5199 (mpt180)
REVERT: L   89 GLN cc_start: 0.8638 (tt0) cc_final: 0.8052 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2182
  time to fit residues: 26.7005
Evaluate side-chains
  77 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 14 optimal weight:    0.1980
   chunk 36 optimal weight:    0.0470
   chunk 32 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   chunk 19 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.4278

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

Flipped N/Q/H residues before XYZ refinement:
A 394 ASN
A 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.094832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.081395 restraints weight = 14336.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.083908 restraints weight = 9163.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.085802 restraints weight = 6434.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3675 r_free = 0.3675    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3374  Z= 0.127
  Angle     :  0.721   9.187   4591  Z= 0.363
  Chirality :  0.046   0.156    492
  Planarity :  0.006   0.048    592
  Dihedral  :  5.602  17.973    466
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.74 %
    Favored  : 94.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.98 (0.36), residues: 416
  helix: -4.38 (0.48), residues: 30
  sheet: -1.65 (0.49), residues: 104
  loop : -3.04 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 436 
 HIS   0.002   0.001   HIS H 100C
 PHE   0.018   0.002   PHE A 342 
 TYR   0.022   0.002   TYR L  91 
 ARG   0.008   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03178 (   76)
  hydrogen bonds       : angle       8.45293 (  186)
  SS BOND              : bond        0.00418 (    7)
  SS BOND              : angle       0.88267 (   14)
  covalent geometry    : bond        0.00289 ( 3367)
  covalent geometry    : angle       0.72075 ( 4577)

*********************** 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
  109 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 ILE cc_start: 0.9397 (mm) cc_final: 0.9087 (mm)
REVERT: A  423 TYR cc_start: 0.6023 (t80) cc_final: 0.5588 (t80)
REVERT: A  424 LYS cc_start: 0.9488 (tttm) cc_final: 0.9213 (tmtt)
REVERT: A  425 LEU cc_start: 0.9218 (mp) cc_final: 0.8835 (mt)
REVERT: A  444 LYS cc_start: 0.8791 (tmmt) cc_final: 0.8466 (tptt)
REVERT: H   20 VAL cc_start: 0.8996 (t) cc_final: 0.8735 (t)
REVERT: H   35 GLN cc_start: 0.8873 (pt0) cc_final: 0.8478 (pt0)
REVERT: H   67 VAL cc_start: 0.7285 (p) cc_final: 0.7038 (p)
REVERT: H   83 ARG cc_start: 0.8186 (ttp-110) cc_final: 0.7914 (tpm170)
REVERT: H  105 GLN cc_start: 0.8119 (pm20) cc_final: 0.7832 (tp-100)
REVERT: L   42 GLN cc_start: 0.8746 (mp10) cc_final: 0.8446 (mp10)
REVERT: L   77 ARG cc_start: 0.6890 (mmm160) cc_final: 0.5779 (mpt180)
  outliers start: 1
  outliers final: 1
  residues processed: 109
  average time/residue: 0.2312
  time to fit residues: 29.2111
Evaluate side-chains
  78 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 38 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 20 optimal weight:    0.3980
   chunk 1 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0980
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 437 ASN
A 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.090799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.077681 restraints weight = 14651.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.080168 restraints weight = 9251.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.082065 restraints weight = 6439.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3613 r_free = 0.3613    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3613 r_free = 0.3613    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3613
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3374  Z= 0.162
  Angle     :  0.744   9.037   4591  Z= 0.378
  Chirality :  0.047   0.255    492
  Planarity :  0.006   0.057    592
  Dihedral  :  5.797  19.701    466
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 19.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  4.74 %
    Favored  : 94.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.91 (0.37), residues: 416
  helix: -4.19 (0.56), residues: 30
  sheet: -1.55 (0.49), residues: 102
  loop : -3.02 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 353 
 HIS   0.000   0.000   HIS H 100C
 PHE   0.017   0.002   PHE A 342 
 TYR   0.032   0.002   TYR L  91 
 ARG   0.006   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03596 (   76)
  hydrogen bonds       : angle       8.32201 (  186)
  SS BOND              : bond        0.00509 (    7)
  SS BOND              : angle       1.32697 (   14)
  covalent geometry    : bond        0.00357 ( 3367)
  covalent geometry    : angle       0.74141 ( 4577)

*********************** 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
  106 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.6181 (t80) cc_final: 0.5879 (t80)
REVERT: A  424 LYS cc_start: 0.9519 (tttm) cc_final: 0.9202 (tmtt)
REVERT: A  425 LEU cc_start: 0.9285 (mp) cc_final: 0.8974 (mm)
REVERT: A  444 LYS cc_start: 0.8987 (tmmt) cc_final: 0.8772 (tptt)
REVERT: A  471 GLU cc_start: 0.7499 (mp0) cc_final: 0.7229 (mp0)
REVERT: H   10 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8633 (mt-10)
REVERT: H   20 VAL cc_start: 0.9088 (t) cc_final: 0.8807 (t)
REVERT: H   35 GLN cc_start: 0.8879 (pt0) cc_final: 0.8407 (pt0)
REVERT: H   83 ARG cc_start: 0.8334 (ttp-110) cc_final: 0.7962 (tpm170)
REVERT: H  105 GLN cc_start: 0.8088 (pm20) cc_final: 0.7772 (tp-100)
REVERT: H  108 MET cc_start: 0.8545 (mtt) cc_final: 0.8328 (mtp)
REVERT: L   42 GLN cc_start: 0.8685 (mp10) cc_final: 0.8308 (mp10)
REVERT: L   71 PHE cc_start: 0.8567 (m-80) cc_final: 0.8290 (m-80)
REVERT: L   77 ARG cc_start: 0.6802 (mmm160) cc_final: 0.5526 (mmt180)
  outliers start: 1
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1676
  time to fit residues: 20.8881
Evaluate side-chains
  81 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0870
   chunk 34 optimal weight:    9.9990
   chunk 33 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 40 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0060
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.5974

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.093978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.081141 restraints weight = 14794.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.083696 restraints weight = 9404.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.085558 restraints weight = 6504.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3677
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3677 r_free = 0.3677    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3677 r_free = 0.3677    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3677
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.4930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3374  Z= 0.122
  Angle     :  0.729  12.416   4591  Z= 0.360
  Chirality :  0.047   0.295    492
  Planarity :  0.006   0.056    592
  Dihedral  :  5.322  16.282    466
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 15.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.77 (0.37), residues: 416
  helix: -4.05 (0.58), residues: 30
  sheet: -1.68 (0.47), residues: 110
  loop : -2.84 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 436 
 HIS   0.001   0.000   HIS H 100C
 PHE   0.015   0.002   PHE A 486 
 TYR   0.026   0.002   TYR H  59 
 ARG   0.007   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03140 (   76)
  hydrogen bonds       : angle       7.83795 (  186)
  SS BOND              : bond        0.00491 (    7)
  SS BOND              : angle       1.10618 (   14)
  covalent geometry    : bond        0.00271 ( 3367)
  covalent geometry    : angle       0.72720 ( 4577)

*********************** 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
  108 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.500 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.5834 (t80) cc_final: 0.5606 (t80)
REVERT: A  424 LYS cc_start: 0.9484 (tttm) cc_final: 0.9233 (tmtt)
REVERT: A  425 LEU cc_start: 0.9214 (mp) cc_final: 0.8942 (mm)
REVERT: A  471 GLU cc_start: 0.7593 (mp0) cc_final: 0.7262 (mp0)
REVERT: A  492 LEU cc_start: 0.8912 (mm) cc_final: 0.8706 (mm)
REVERT: A  516 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8215 (mp0)
REVERT: H   35 GLN cc_start: 0.8768 (pt0) cc_final: 0.8416 (pt0)
REVERT: H   83 ARG cc_start: 0.8225 (ttp-110) cc_final: 0.7933 (tpm170)
REVERT: H   85 GLU cc_start: 0.8408 (tt0) cc_final: 0.8092 (mt-10)
REVERT: H  105 GLN cc_start: 0.8040 (pm20) cc_final: 0.7777 (tp-100)
REVERT: H  108 MET cc_start: 0.8574 (mtt) cc_final: 0.8374 (mtp)
REVERT: L   49 TYR cc_start: 0.8285 (p90) cc_final: 0.7991 (p90)
REVERT: L   77 ARG cc_start: 0.6686 (mmm160) cc_final: 0.5523 (mpt180)
REVERT: L   82 ASP cc_start: 0.4648 (m-30) cc_final: 0.4331 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.2376
  time to fit residues: 30.8243
Evaluate side-chains
  82 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 19 optimal weight:    8.9990
   chunk 26 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   chunk 39 optimal weight:    0.0770
   chunk 10 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    2.4146

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

Flipped N/Q/H residues before XYZ refinement:
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 GLN
A 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.088473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.075310 restraints weight = 15249.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.077813 restraints weight = 9518.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.079633 restraints weight = 6585.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3562
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3562 r_free = 0.3562    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3562
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7096
moved from start:          0.4645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3374  Z= 0.184
  Angle     :  0.759   8.767   4591  Z= 0.384
  Chirality :  0.046   0.223    492
  Planarity :  0.006   0.056    592
  Dihedral  :  5.777  17.945    466
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 20.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.66 (0.37), residues: 416
  helix: -4.13 (0.58), residues: 30
  sheet: -1.53 (0.48), residues: 106
  loop : -2.77 (0.34), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 353 
 HIS   0.001   0.000   HIS H 100C
 PHE   0.018   0.002   PHE A 342 
 TYR   0.023   0.003   TYR H  59 
 ARG   0.006   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03608 (   76)
  hydrogen bonds       : angle       8.29882 (  186)
  SS BOND              : bond        0.00488 (    7)
  SS BOND              : angle       1.07958 (   14)
  covalent geometry    : bond        0.00398 ( 3367)
  covalent geometry    : angle       0.75758 ( 4577)

*********************** 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
  98 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 ARG cc_start: 0.8328 (ttt-90) cc_final: 0.8046 (tmt170)
REVERT: A  424 LYS cc_start: 0.9535 (tttm) cc_final: 0.9181 (tmtt)
REVERT: A  471 GLU cc_start: 0.7611 (mp0) cc_final: 0.7281 (mp0)
REVERT: A  498 GLN cc_start: 0.8077 (pt0) cc_final: 0.7745 (pt0)
REVERT: A  516 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8046 (mp0)
REVERT: H   20 VAL cc_start: 0.9073 (t) cc_final: 0.8850 (t)
REVERT: H   35 GLN cc_start: 0.8839 (pt0) cc_final: 0.8334 (pt0)
REVERT: H   36 TRP cc_start: 0.7816 (m100) cc_final: 0.6776 (m100)
REVERT: H   83 ARG cc_start: 0.8508 (ttp-110) cc_final: 0.7987 (tpm170)
REVERT: H  105 GLN cc_start: 0.7949 (pm20) cc_final: 0.7736 (tp-100)
REVERT: H  108 MET cc_start: 0.8550 (mtt) cc_final: 0.8310 (mtp)
REVERT: L   35 TRP cc_start: 0.7147 (m100) cc_final: 0.6557 (m100)
REVERT: L   42 GLN cc_start: 0.8650 (mp10) cc_final: 0.8248 (mp10)
REVERT: L   49 TYR cc_start: 0.8497 (p90) cc_final: 0.8177 (p90)
REVERT: L   77 ARG cc_start: 0.6914 (mmm160) cc_final: 0.5562 (mpt180)
REVERT: L   88 CYS cc_start: 0.5054 (t) cc_final: 0.4451 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1759
  time to fit residues: 20.4820
Evaluate side-chains
  79 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 39 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9980
   chunk 3 optimal weight:    9.9990
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 25 optimal weight:    0.4980
   chunk 21 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.092835 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.079624 restraints weight = 14528.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.082199 restraints weight = 9100.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.084055 restraints weight = 6269.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3651
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3651 r_free = 0.3651    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3651 r_free = 0.3651    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3651
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6983
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3374  Z= 0.123
  Angle     :  0.717   8.719   4591  Z= 0.358
  Chirality :  0.046   0.170    492
  Planarity :  0.006   0.062    592
  Dihedral  :  5.205  15.910    466
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.38), residues: 416
  helix: -4.18 (0.57), residues: 24
  sheet: -1.32 (0.49), residues: 104
  loop : -2.55 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 436 
 HIS   0.003   0.001   HIS H 100C
 PHE   0.014   0.001   PHE A 342 
 TYR   0.027   0.002   TYR L  91 
 ARG   0.007   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03060 (   76)
  hydrogen bonds       : angle       7.79660 (  186)
  SS BOND              : bond        0.00518 (    7)
  SS BOND              : angle       1.44699 (   14)
  covalent geometry    : bond        0.00274 ( 3367)
  covalent geometry    : angle       0.71404 ( 4577)

*********************** 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
  108 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 ARG cc_start: 0.8362 (ttt-90) cc_final: 0.8055 (tmt170)
REVERT: A  424 LYS cc_start: 0.9474 (tttm) cc_final: 0.9176 (tptt)
REVERT: A  466 ARG cc_start: 0.7511 (ttp80) cc_final: 0.6925 (ttp80)
REVERT: A  471 GLU cc_start: 0.7617 (mp0) cc_final: 0.7209 (mp0)
REVERT: H   35 GLN cc_start: 0.8884 (pt0) cc_final: 0.8455 (pt0)
REVERT: H   83 ARG cc_start: 0.8372 (ttp-110) cc_final: 0.7995 (tpm170)
REVERT: H  108 MET cc_start: 0.8518 (mtt) cc_final: 0.8299 (mtp)
REVERT: L   49 TYR cc_start: 0.8394 (p90) cc_final: 0.8111 (p90)
REVERT: L   77 ARG cc_start: 0.6917 (mmm160) cc_final: 0.5818 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1742
  time to fit residues: 22.4586
Evaluate side-chains
  83 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.0870
   chunk 5 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 18 optimal weight:    6.9990
   chunk 28 optimal weight:    0.9980
   chunk 4 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   overall best weight:    1.1360

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 105 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.092505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.079376 restraints weight = 14877.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.082023 restraints weight = 9330.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.083893 restraints weight = 6409.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3638
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3638 r_free = 0.3638    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3638 r_free = 0.3638    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3638
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.5498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3374  Z= 0.133
  Angle     :  0.726   8.721   4591  Z= 0.363
  Chirality :  0.045   0.155    492
  Planarity :  0.006   0.069    592
  Dihedral  :  5.334  21.575    466
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 19.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  0.56 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.37 (0.38), residues: 416
  helix: -4.62 (0.39), residues: 18
  sheet: -1.77 (0.45), residues: 116
  loop : -2.42 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 353 
 HIS   0.000   0.000   HIS A 519 
 PHE   0.017   0.002   PHE A 486 
 TYR   0.016   0.002   TYR L  91 
 ARG   0.007   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03161 (   76)
  hydrogen bonds       : angle       7.67330 (  186)
  SS BOND              : bond        0.00453 (    7)
  SS BOND              : angle       1.33998 (   14)
  covalent geometry    : bond        0.00301 ( 3367)
  covalent geometry    : angle       0.72302 ( 4577)

*********************** 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
  103 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 ILE cc_start: 0.9287 (mm) cc_final: 0.9085 (mm)
REVERT: A  424 LYS cc_start: 0.9498 (tttm) cc_final: 0.9202 (tmtt)
REVERT: A  425 LEU cc_start: 0.9202 (mp) cc_final: 0.8881 (mm)
REVERT: A  471 GLU cc_start: 0.7514 (mp0) cc_final: 0.7146 (mp0)
REVERT: H   35 GLN cc_start: 0.8884 (pt0) cc_final: 0.8326 (pt0)
REVERT: H   83 ARG cc_start: 0.8402 (ttp-110) cc_final: 0.8011 (tpm170)
REVERT: H  100 PHE cc_start: 0.7965 (m-80) cc_final: 0.7682 (m-80)
REVERT: H  105 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8006 (pm20)
REVERT: H  108 MET cc_start: 0.8496 (mtt) cc_final: 0.8272 (mtp)
REVERT: L   49 TYR cc_start: 0.8421 (p90) cc_final: 0.8043 (p90)
REVERT: L   71 PHE cc_start: 0.8317 (m-80) cc_final: 0.8015 (m-80)
REVERT: L   77 ARG cc_start: 0.6902 (mmm160) cc_final: 0.5993 (mpt180)
  outliers start: 1
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1668
  time to fit residues: 20.2905
Evaluate side-chains
  81 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 80
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 22 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    1.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.092720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.079424 restraints weight = 15015.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.082033 restraints weight = 9475.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.083931 restraints weight = 6543.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3639 r_free = 0.3639    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.5571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3374  Z= 0.130
  Angle     :  0.719   8.608   4591  Z= 0.358
  Chirality :  0.045   0.153    492
  Planarity :  0.006   0.071    592
  Dihedral  :  5.215  15.453    466
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 18.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.38), residues: 416
  helix: -4.72 (0.35), residues: 18
  sheet: -1.66 (0.45), residues: 124
  loop : -2.43 (0.35), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 353 
 HIS   0.001   0.000   HIS H 100C
 PHE   0.017   0.002   PHE A 486 
 TYR   0.018   0.002   TYR L  91 
 ARG   0.007   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03088 (   76)
  hydrogen bonds       : angle       7.66633 (  186)
  SS BOND              : bond        0.00451 (    7)
  SS BOND              : angle       1.29377 (   14)
  covalent geometry    : bond        0.00294 ( 3367)
  covalent geometry    : angle       0.71688 ( 4577)

*********************** 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
  102 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 ILE cc_start: 0.9337 (mm) cc_final: 0.9126 (mm)
REVERT: A  424 LYS cc_start: 0.9495 (tttm) cc_final: 0.9174 (tmtt)
REVERT: A  471 GLU cc_start: 0.7551 (mp0) cc_final: 0.7165 (mp0)
REVERT: H   20 VAL cc_start: 0.9057 (t) cc_final: 0.8841 (t)
REVERT: H   35 GLN cc_start: 0.8889 (pt0) cc_final: 0.8401 (pt0)
REVERT: H   83 ARG cc_start: 0.8402 (ttp-110) cc_final: 0.8007 (tpm170)
REVERT: H  105 GLN cc_start: 0.8624 (tp40) cc_final: 0.8209 (pm20)
REVERT: L   35 TRP cc_start: 0.7114 (m100) cc_final: 0.6632 (m100)
REVERT: L   42 GLN cc_start: 0.8490 (mp10) cc_final: 0.8135 (mp10)
REVERT: L   49 TYR cc_start: 0.8362 (p90) cc_final: 0.8035 (p90)
REVERT: L   71 PHE cc_start: 0.8255 (m-80) cc_final: 0.7971 (m-10)
REVERT: L   77 ARG cc_start: 0.6872 (mmm160) cc_final: 0.5952 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1858
  time to fit residues: 22.5417
Evaluate side-chains
  78 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    9.9990
   chunk 29 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 39 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.089121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.075974 restraints weight = 14912.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.078514 restraints weight = 9545.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.080281 restraints weight = 6671.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3570
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3570 r_free = 0.3570    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3570
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.5318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3374  Z= 0.171
  Angle     :  0.747   8.866   4591  Z= 0.377
  Chirality :  0.045   0.149    492
  Planarity :  0.006   0.076    592
  Dihedral  :  5.653  16.072    466
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 22.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.06 %
    Favored  : 88.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.34 (0.38), residues: 416
  helix: -4.52 (0.39), residues: 30
  sheet: -1.03 (0.49), residues: 108
  loop : -2.60 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 353 
 HIS   0.002   0.001   HIS H 100C
 PHE   0.016   0.002   PHE A 342 
 TYR   0.015   0.002   TYR H  59 
 ARG   0.006   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03293 (   76)
  hydrogen bonds       : angle       8.05318 (  186)
  SS BOND              : bond        0.00465 (    7)
  SS BOND              : angle       1.36428 (   14)
  covalent geometry    : bond        0.00380 ( 3367)
  covalent geometry    : angle       0.74394 ( 4577)

********************** 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
  95 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 ILE cc_start: 0.9383 (mm) cc_final: 0.9113 (pt)
REVERT: A  424 LYS cc_start: 0.9524 (tttm) cc_final: 0.9199 (tmtt)
REVERT: A  471 GLU cc_start: 0.7575 (mp0) cc_final: 0.7212 (mp0)
REVERT: A  498 GLN cc_start: 0.8047 (pt0) cc_final: 0.7763 (pt0)
REVERT: H   20 VAL cc_start: 0.9120 (t) cc_final: 0.8889 (t)
REVERT: H   35 GLN cc_start: 0.8860 (pt0) cc_final: 0.8355 (pt0)
REVERT: H   83 ARG cc_start: 0.8528 (ttp-110) cc_final: 0.8042 (tpm170)
REVERT: H  105 GLN cc_start: 0.8661 (tp40) cc_final: 0.8135 (pm20)
REVERT: L   35 TRP cc_start: 0.7166 (m100) cc_final: 0.6761 (m100)
REVERT: L   42 GLN cc_start: 0.8520 (mp10) cc_final: 0.8049 (mp10)
REVERT: L   49 TYR cc_start: 0.8409 (p90) cc_final: 0.8048 (p90)
REVERT: L   71 PHE cc_start: 0.8338 (m-80) cc_final: 0.8126 (m-80)
REVERT: L   77 ARG cc_start: 0.6841 (mmm160) cc_final: 0.5916 (mpt180)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1825
  time to fit residues: 20.4430
Evaluate side-chains
  72 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 30 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0870
   chunk 16 optimal weight:    0.0470
   chunk 15 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 7 optimal weight:    8.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.5656

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.093649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.080764 restraints weight = 14789.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.083333 restraints weight = 9238.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.085137 restraints weight = 6344.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3658 r_free = 0.3658    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3658 r_free = 0.3658    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.5789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3374  Z= 0.120
  Angle     :  0.711   8.429   4591  Z= 0.353
  Chirality :  0.045   0.154    492
  Planarity :  0.006   0.083    592
  Dihedral  :  5.097  15.337    466
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 16.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.38), residues: 416
  helix: -4.73 (0.37), residues: 18
  sheet: -1.45 (0.48), residues: 110
  loop : -2.31 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 353 
 HIS   0.000   0.000   HIS H 100C
 PHE   0.019   0.002   PHE A 486 
 TYR   0.019   0.001   TYR L  91 
 ARG   0.008   0.001   ARG A 466 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02999 (   76)
  hydrogen bonds       : angle       7.62069 (  186)
  SS BOND              : bond        0.00408 (    7)
  SS BOND              : angle       1.23870 (   14)
  covalent geometry    : bond        0.00274 ( 3367)
  covalent geometry    : angle       0.70910 ( 4577)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1722.64 seconds
wall clock time: 30 minutes 34.88 seconds (1834.88 seconds total)