Starting phenix.real_space_refine
on Wed Sep 17 04:32:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9h76_51912/09_2025/9h76_51912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9h76_51912/09_2025/9h76_51912.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9h76_51912/09_2025/9h76_51912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9h76_51912/09_2025/9h76_51912.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9h76_51912/09_2025/9h76_51912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9h76_51912/09_2025/9h76_51912.map"
  }
  resolution = 2.9
  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=   0.002
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    2756      2.51       5
     N     661      2.21       5
     O     724      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4157
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3263
          Classifications: {'peptide': 430}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 406}
    Chain: "B"
      Number of atoms: 888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 888
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 2, 'TRANS': 113}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   LYS A 154 " occ=0.82
      ... (7 atoms not shown)
      pdb=" NZ  LYS A 154 " occ=0.82
    residue:
      pdb=" N   ALA A 501 " occ=0.00
      ... (4 atoms not shown)
      pdb=" OXT ALA A 501 " occ=0.00
  Time building chain proxies: 1.33, per 1000 atoms: 0.32
  Number of scatterers: 4157
  At special positions: 0
  Unit cell: (72.93, 75.99, 99.45, 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     724      8.00
     N     661      7.00
     C    2756      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS B  97 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 185.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  976

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 4 sheets defined
      71.1% alpha, 12.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 18
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.728A  pdb=" N   PHE A  24 " --> pdb=" O   ALA A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 33
    Processing helix  chain 'A' and resid 35 through 64
      removed outlier: 3.556A  pdb=" N   LEU A  40 " --> pdb=" O   PRO A  36 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE A  60 " --> pdb=" O   THR A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 78
    Processing helix  chain 'A' and resid 79 through 93
    Processing helix  chain 'A' and resid 93 through 115
    Processing helix  chain 'A' and resid 117 through 119
      No H-bonds generated for 'chain 'A' and resid 117 through 119'
    Processing helix  chain 'A' and resid 120 through 137
    Processing helix  chain 'A' and resid 139 through 154
      removed outlier: 4.248A  pdb=" N   SER A 143 " --> pdb=" O   GLY A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 167
      removed outlier: 3.986A  pdb=" N   LEU A 158 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 177
      removed outlier: 3.623A  pdb=" N   VAL A 177 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 201
      removed outlier: 4.029A  pdb=" N   GLY A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   SER A 192 " --> pdb=" O   THR A 188 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA A 200 " --> pdb=" O   ALA A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 204
      No H-bonds generated for 'chain 'A' and resid 202 through 204'
    Processing helix  chain 'A' and resid 205 through 214
      removed outlier: 4.174A  pdb=" N   THR A 209 " --> pdb=" O   ILE A 205 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   GLY A 212 " --> pdb=" O   GLY A 208 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLU A 213 " --> pdb=" O   THR A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 247
      removed outlier: 4.310A  pdb=" N   LYS A 223 " --> pdb=" O   LYS A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 254
    Processing helix  chain 'A' and resid 257 through 267
    Processing helix  chain 'A' and resid 269 through 304
      removed outlier: 4.351A  pdb=" N   LYS A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A 297 " --> pdb=" O   SER A 293 " (cutoff:3.500A)
      Proline residue:  A 298  - end of helix
      removed outlier: 3.612A  pdb=" N   GLN A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 315
    Processing helix  chain 'A' and resid 324 through 340
    Processing helix  chain 'A' and resid 342 through 372
    Processing helix  chain 'A' and resid 386 through 406
    Processing helix  chain 'A' and resid 406 through 431
      Proline residue:  A 422  - end of helix
    Processing helix  chain 'B' and resid 30 through 34
    Processing helix  chain 'B' and resid 88 through 92
    Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 8
      removed outlier: 3.567A  pdb=" N   LEU B  20 " --> pdb=" O   MET B  84 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 8
      removed outlier: 3.534A  pdb=" N   THR B  79 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 14
      removed outlier: 3.662A  pdb=" N   VAL B  94 " --> pdb=" O   GLN B  41 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   MET B  36 " --> pdb=" O   ARG B  52 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   ARG B  52 " --> pdb=" O   MET B  36 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   TRP B  38 " --> pdb=" O   VAL B  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14

    310 hydrogen bonds defined for protein.
    879 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: 0.61

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 671
        1.33 -     1.45: 1119
        1.45 -     1.57: 2436
        1.57 -     1.69: 0
        1.69 -     1.81: 29
  Bond restraints: 4255
  Sorted by residual:
  bond pdb=" CB  MET B  84 "
       pdb=" CG  MET B  84 "
    ideal  model  delta    sigma   weight residual
    1.520  1.457  0.063 3.00e-02 1.11e+03 4.47e+00
  bond pdb=" SD  MET A 233 "
       pdb=" CE  MET A 233 "
    ideal  model  delta    sigma   weight residual
    1.791  1.748  0.043 2.50e-02 1.60e+03 3.01e+00
  bond pdb=" CA  GLN B  15 "
       pdb=" C   GLN B  15 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.019 1.30e-02 5.92e+03 2.07e+00
  bond pdb=" CD  GLN B  15 "
       pdb=" OE1 GLN B  15 "
    ideal  model  delta    sigma   weight residual
    1.231  1.205  0.026 1.90e-02 2.77e+03 1.82e+00
  bond pdb=" N   GLY A  19 "
       pdb=" CA  GLY A  19 "
    ideal  model  delta    sigma   weight residual
    1.458  1.446  0.012 9.20e-03 1.18e+04 1.59e+00
  ... (remaining 4250 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.13: 5540
        1.13 -     2.26: 186
        2.26 -     3.40: 52
        3.40 -     4.53: 17
        4.53 -     5.66: 11
  Bond angle restraints: 5806
  Sorted by residual:
  angle pdb=" CB  GLU A  75 "
        pdb=" CG  GLU A  75 "
        pdb=" CD  GLU A  75 "
      ideal   model   delta    sigma   weight residual
     112.60  118.26   -5.66 1.70e+00 3.46e-01 1.11e+01
  angle pdb=" CA  GLU A  75 "
        pdb=" CB  GLU A  75 "
        pdb=" CG  GLU A  75 "
      ideal   model   delta    sigma   weight residual
     114.10  119.32   -5.22 2.00e+00 2.50e-01 6.82e+00
  angle pdb=" CB  GLN B   5 "
        pdb=" CG  GLN B   5 "
        pdb=" CD  GLN B   5 "
      ideal   model   delta    sigma   weight residual
     112.60  116.66   -4.06 1.70e+00 3.46e-01 5.71e+00
  angle pdb=" CB  GLU A 376 "
        pdb=" CG  GLU A 376 "
        pdb=" CD  GLU A 376 "
      ideal   model   delta    sigma   weight residual
     112.60  116.52   -3.92 1.70e+00 3.46e-01 5.32e+00
  angle pdb=" CA  GLN B  15 "
        pdb=" CB  GLN B  15 "
        pdb=" CG  GLN B  15 "
      ideal   model   delta    sigma   weight residual
     114.10  118.56   -4.46 2.00e+00 2.50e-01 4.98e+00
  ... (remaining 5801 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 2141
       17.55 -    35.10: 241
       35.10 -    52.64: 61
       52.64 -    70.19: 7
       70.19 -    87.74: 4
  Dihedral angle restraints: 2454
    sinusoidal: 909
      harmonic: 1545
  Sorted by residual:
  dihedral pdb=" N   ASN B 107 "
           pdb=" CA  ASN B 107 "
           pdb=" CB  ASN B 107 "
           pdb=" CG  ASN B 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.54  -59.46     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CG  LYS A  76 "
           pdb=" CD  LYS A  76 "
           pdb=" CE  LYS A  76 "
           pdb=" NZ  LYS A  76 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.33   59.33     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  LYS B  66 "
           pdb=" CB  LYS B  66 "
           pdb=" CG  LYS B  66 "
           pdb=" CD  LYS B  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.79  -57.79     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 2451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 397
       0.028 -    0.056: 179
       0.056 -    0.084: 77
       0.084 -    0.112: 38
       0.112 -    0.140: 7
  Chirality restraints: 698
  Sorted by residual:
  chirality pdb=" CA  VAL B   4 "
            pdb=" N   VAL B   4 "
            pdb=" C   VAL B   4 "
            pdb=" CB  VAL B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.93e-01
  chirality pdb=" CB  VAL B   4 "
            pdb=" CA  VAL B   4 "
            pdb=" CG1 VAL B   4 "
            pdb=" CG2 VAL B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.14 2.00e-01 2.50e+01 4.66e-01
  chirality pdb=" CA  VAL B 102 "
            pdb=" N   VAL B 102 "
            pdb=" C   VAL B 102 "
            pdb=" CB  VAL B 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.32e-01
  ... (remaining 695 not shown)

  Planarity restraints: 710
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 296 "   -0.174 9.50e-02 1.11e+02   7.84e-02 4.76e+00
        pdb=" NE  ARG A 296 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 296 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 296 "    0.007 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 296 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 387 "   -0.027 5.00e-02 4.00e+02   4.07e-02 2.66e+00
        pdb=" N   PRO A 388 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 388 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 388 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 122 "    0.023 5.00e-02 4.00e+02   3.44e-02 1.90e+00
        pdb=" N   PRO A 123 "   -0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO A 123 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 123 "    0.020 5.00e-02 4.00e+02
  ... (remaining 707 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 30
        2.62 -     3.19: 3992
        3.19 -     3.76: 6720
        3.76 -     4.33: 9200
        4.33 -     4.90: 15696
  Nonbonded interactions: 35638
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B  15 "
            pdb=" N   ALA B  16 "
     model   vdw
     2.053 3.120
  nonbonded pdb=" N   GLU B  90 "
            pdb=" OE1 GLU B  90 "
     model   vdw
     2.135 3.120
  nonbonded pdb=" OE2 GLU A  59 "
            pdb=" NH2 ARG A 369 "
     model   vdw
     2.187 3.120
  nonbonded pdb=" N   GLN B  46 "
            pdb=" OE1 GLN B  46 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   PHE B  31 "
            pdb=" NH2 ARG B  73 "
     model   vdw
     2.266 3.120
  ... (remaining 35633 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.170
  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:          0.170
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.980
  Find NCS groups from input model:        0.020
  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:8.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
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      :  0.005   0.063   4256  Z= 0.194
  Angle     :  0.593   5.660   5808  Z= 0.302
  Chirality :  0.042   0.140    698
  Planarity :  0.005   0.078    710
  Dihedral  : 15.748  87.739   1475
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.66 %
    Favored  : 98.34 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 25.28 %
    Favored  : 74.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 aren not related in a simple way.
  whole:  2.14 (0.38), residues: 542
  helix:  2.34 (0.29), residues: 346
  sheet: -2.18 (0.75), residues: 41
  loop :  0.45 (0.52), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 296 
 TYR   0.010   0.001   TYR A 424 
 PHE   0.014   0.001   PHE A 357 
 TRP   0.011   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00461 ( 4255)
  covalent geometry    : angle       0.59300 ( 5806)
  SS BOND              : bond        0.00224 (    1)
  SS BOND              : angle       0.31372 (    2)
  hydrogen bonds       : bond        0.11902 (  299)
  hydrogen bonds       : angle       5.84354 (  879)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  213 GLU cc_start: 0.9109 (mt-10) cc_final: 0.8823 (tm-30)
REVERT: A  315 ARG cc_start: 0.8012 (tpp80) cc_final: 0.7649 (ttm170)
REVERT: B   61 TYR cc_start: 0.9265 (m-80) cc_final: 0.8896 (m-80)
REVERT: B   62 ASP cc_start: 0.8660 (t70) cc_final: 0.8153 (t0)
REVERT: B   88 LYS cc_start: 0.9576 (mttt) cc_final: 0.9083 (mtpp)
REVERT: B   90 GLU cc_start: 0.9064 (pm20) cc_final: 0.8773 (pm20)
REVERT: B   91 ASP cc_start: 0.9508 (m-30) cc_final: 0.8920 (m-30)
  outliers start: 1
  outliers final: 1
  residues processed: 84
  average time/residue: 0.5632
  time to fit residues: 48.9486
Evaluate side-chains
  82 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 81
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.1980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.085024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.065109 restraints weight = 7446.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.2700 rms_B_bonded: 2.70
r_work: 0.2557 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2557
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2568
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2568 r_free = 0.2568    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2568 r_free = 0.2568    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2568
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.0980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4256  Z= 0.175
  Angle     :  0.558   7.319   5808  Z= 0.289
  Chirality :  0.042   0.129    698
  Planarity :  0.004   0.044    710
  Dihedral  :  3.733  17.066    586
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 21.18 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 aren not related in a simple way.
  whole:  2.08 (0.37), residues: 542
  helix:  2.17 (0.28), residues: 350
  sheet: -2.00 (0.70), residues: 44
  loop :  0.71 (0.54), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 296 
 TYR   0.009   0.001   TYR A 426 
 PHE   0.016   0.001   PHE A 357 
 TRP   0.012   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 4255)
  covalent geometry    : angle       0.55850 ( 5806)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       0.13489 (    2)
  hydrogen bonds       : bond        0.04962 (  299)
  hydrogen bonds       : angle       4.80475 (  879)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A    4 VAL cc_start: 0.8087 (OUTLIER) cc_final: 0.7839 (m)
REVERT: A  213 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8609 (tm-30)
REVERT: A  315 ARG cc_start: 0.7477 (tpp80) cc_final: 0.7046 (ttm170)
REVERT: A  342 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7274 (mt0)
REVERT: B   62 ASP cc_start: 0.8358 (t70) cc_final: 0.7896 (t0)
REVERT: B   88 LYS cc_start: 0.9352 (mttt) cc_final: 0.8950 (mtpp)
REVERT: B   90 GLU cc_start: 0.9232 (pm20) cc_final: 0.8995 (pm20)
REVERT: B   91 ASP cc_start: 0.9338 (m-30) cc_final: 0.8735 (m-30)
REVERT: B  106 GLU cc_start: 0.8689 (tt0) cc_final: 0.8444 (tm-30)
REVERT: B  111 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8589 (pm20)
REVERT: B  114 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8647 (tm-30)
  outliers start: 11
  outliers final: 7
  residues processed: 94
  average time/residue: 0.5423
  time to fit residues: 52.8551
Evaluate side-chains
  92 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.086022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.066133 restraints weight = 7466.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.2720 rms_B_bonded: 2.69
r_work: 0.2577 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2577
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2585
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2585 r_free = 0.2585    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2585
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4256  Z= 0.146
  Angle     :  0.542   7.182   5808  Z= 0.277
  Chirality :  0.042   0.144    698
  Planarity :  0.004   0.044    710
  Dihedral  :  3.726  15.440    586
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 22.32 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 aren not related in a simple way.
  whole:  2.09 (0.37), residues: 542
  helix:  2.14 (0.28), residues: 349
  sheet: -1.14 (0.65), residues: 53
  loop :  0.65 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 296 
 TYR   0.013   0.001   TYR B  96 
 PHE   0.013   0.001   PHE A 357 
 TRP   0.013   0.001   TRP A 355 
 HIS   0.001   0.000   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 4255)
  covalent geometry    : angle       0.54158 ( 5806)
  SS BOND              : bond        0.00046 (    1)
  SS BOND              : angle       0.33931 (    2)
  hydrogen bonds       : bond        0.04527 (  299)
  hydrogen bonds       : angle       4.55408 (  879)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.161 
Fit side-chains
REVERT: A  296 ARG cc_start: 0.8395 (ttm110) cc_final: 0.8191 (ttm170)
REVERT: A  315 ARG cc_start: 0.7554 (tpp80) cc_final: 0.7197 (ttm110)
REVERT: A  342 GLN cc_start: 0.7549 (OUTLIER) cc_final: 0.7302 (mt0)
REVERT: B   61 TYR cc_start: 0.9032 (m-80) cc_final: 0.8629 (m-80)
REVERT: B   62 ASP cc_start: 0.8430 (t70) cc_final: 0.7942 (t0)
REVERT: B   74 ASP cc_start: 0.7879 (t0) cc_final: 0.7611 (OUTLIER)
REVERT: B   77 LYS cc_start: 0.9404 (mtpp) cc_final: 0.8964 (ptpp)
REVERT: B   88 LYS cc_start: 0.9370 (mttt) cc_final: 0.8940 (mtpp)
REVERT: B   90 GLU cc_start: 0.9223 (pm20) cc_final: 0.9005 (pm20)
REVERT: B   91 ASP cc_start: 0.9373 (m-30) cc_final: 0.8624 (m-30)
REVERT: B   92 THR cc_start: 0.9053 (t) cc_final: 0.8763 (p)
REVERT: B  106 GLU cc_start: 0.8723 (tt0) cc_final: 0.8434 (tm-30)
REVERT: B  111 GLN cc_start: 0.8978 (OUTLIER) cc_final: 0.8611 (pm20)
  outliers start: 12
  outliers final: 3
  residues processed: 96
  average time/residue: 0.5292
  time to fit residues: 52.7252
Evaluate side-chains
  87 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 83
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 43 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.9386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.084344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.064691 restraints weight = 7370.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.2733 rms_B_bonded: 2.62
r_work: 0.2596 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.2458 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2458
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2473 r_free = 0.2473    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2473 r_free = 0.2473    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   4256  Z= 0.198
  Angle     :  0.568   6.492   5808  Z= 0.290
  Chirality :  0.043   0.129    698
  Planarity :  0.004   0.046    710
  Dihedral  :  3.754  14.356    584
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 23.69 %
    Favored  : 73.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 aren not related in a simple way.
  whole:  1.93 (0.37), residues: 542
  helix:  1.98 (0.28), residues: 350
  sheet: -1.19 (0.63), residues: 56
  loop :  0.73 (0.59), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 296 
 TYR   0.007   0.001   TYR A  30 
 PHE   0.014   0.001   PHE A 357 
 TRP   0.010   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 4255)
  covalent geometry    : angle       0.56784 ( 5806)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       0.30143 (    2)
  hydrogen bonds       : bond        0.04845 (  299)
  hydrogen bonds       : angle       4.58488 (  879)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7260 (tt0)
REVERT: A  315 ARG cc_start: 0.7741 (tpp80) cc_final: 0.7373 (ttm110)
REVERT: A  342 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7506 (mt0)
REVERT: B   46 GLN cc_start: 0.8479 (pm20) cc_final: 0.8245 (pm20)
REVERT: B   62 ASP cc_start: 0.8569 (t70) cc_final: 0.8072 (t0)
REVERT: B   88 LYS cc_start: 0.9378 (mttt) cc_final: 0.8919 (mtpp)
REVERT: B   90 GLU cc_start: 0.9267 (pm20) cc_final: 0.9050 (pm20)
REVERT: B   91 ASP cc_start: 0.9451 (m-30) cc_final: 0.8776 (m-30)
REVERT: B   92 THR cc_start: 0.9137 (t) cc_final: 0.8888 (p)
REVERT: B  106 GLU cc_start: 0.8842 (tt0) cc_final: 0.8607 (tm-30)
REVERT: B  111 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8687 (pm20)
REVERT: B  114 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8592 (tm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 92
  average time/residue: 0.5324
  time to fit residues: 50.8120
Evaluate side-chains
  90 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 6 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.085414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.065533 restraints weight = 7435.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.2744 rms_B_bonded: 2.67
r_work: 0.2603 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2621
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2621 r_free = 0.2621    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2621 r_free = 0.2621    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2621
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4256  Z= 0.163
  Angle     :  0.554   6.315   5808  Z= 0.282
  Chirality :  0.042   0.155    698
  Planarity :  0.004   0.049    710
  Dihedral  :  3.722  14.679    584
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 24.15 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 aren not related in a simple way.
  whole:  2.03 (0.37), residues: 542
  helix:  2.05 (0.28), residues: 349
  sheet: -0.91 (0.63), residues: 56
  loop :  0.67 (0.59), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 296 
 TYR   0.011   0.001   TYR B  96 
 PHE   0.013   0.001   PHE A 357 
 TRP   0.012   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 4255)
  covalent geometry    : angle       0.55417 ( 5806)
  SS BOND              : bond        0.00003 (    1)
  SS BOND              : angle       0.37479 (    2)
  hydrogen bonds       : bond        0.04572 (  299)
  hydrogen bonds       : angle       4.47049 (  879)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7126 (tt0)
REVERT: A  315 ARG cc_start: 0.7725 (tpp80) cc_final: 0.7362 (ttm110)
REVERT: A  342 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7530 (mt0)
REVERT: B   62 ASP cc_start: 0.8566 (t70) cc_final: 0.8054 (t70)
REVERT: B   88 LYS cc_start: 0.9405 (mttt) cc_final: 0.8931 (mttp)
REVERT: B   91 ASP cc_start: 0.9503 (m-30) cc_final: 0.8774 (m-30)
REVERT: B   92 THR cc_start: 0.9120 (t) cc_final: 0.8901 (p)
REVERT: B  106 GLU cc_start: 0.8749 (tt0) cc_final: 0.8545 (tm-30)
REVERT: B  111 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8645 (pm20)
  outliers start: 18
  outliers final: 12
  residues processed: 96
  average time/residue: 0.5323
  time to fit residues: 53.0964
Evaluate side-chains
  97 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue   32 SER
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 26 optimal weight:    0.1980
   chunk 39 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 29 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.085773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.066008 restraints weight = 7556.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.2758 rms_B_bonded: 2.69
r_work: 0.2615 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2632
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2632 r_free = 0.2632    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2632
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4256  Z= 0.156
  Angle     :  0.577   6.368   5808  Z= 0.293
  Chirality :  0.042   0.163    698
  Planarity :  0.005   0.060    710
  Dihedral  :  3.740  14.849    584
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 24.60 %
    Favored  : 72.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 aren not related in a simple way.
  whole:  2.06 (0.37), residues: 542
  helix:  2.05 (0.27), residues: 349
  sheet: -0.69 (0.66), residues: 56
  loop :  0.65 (0.59), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 296 
 TYR   0.006   0.001   TYR A  30 
 PHE   0.013   0.001   PHE A 357 
 TRP   0.013   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4255)
  covalent geometry    : angle       0.57720 ( 5806)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.32406 (    2)
  hydrogen bonds       : bond        0.04475 (  299)
  hydrogen bonds       : angle       4.41193 (  879)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7092 (tt0)
REVERT: A  315 ARG cc_start: 0.7717 (tpp80) cc_final: 0.7353 (ttm110)
REVERT: A  342 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7525 (mt0)
REVERT: B   62 ASP cc_start: 0.8560 (t70) cc_final: 0.8031 (t70)
REVERT: B   74 ASP cc_start: 0.7993 (t0) cc_final: 0.7684 (t0)
REVERT: B   77 LYS cc_start: 0.9423 (mtpp) cc_final: 0.8988 (ptpp)
REVERT: B   88 LYS cc_start: 0.9413 (mttt) cc_final: 0.8921 (mttp)
REVERT: B   91 ASP cc_start: 0.9482 (m-30) cc_final: 0.8833 (m-30)
REVERT: B  111 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8633 (pm20)
REVERT: B  113 THR cc_start: 0.8774 (OUTLIER) cc_final: 0.8194 (p)
  outliers start: 13
  outliers final: 9
  residues processed: 92
  average time/residue: 0.5485
  time to fit residues: 52.2889
Evaluate side-chains
  96 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue  111 GLN
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0570
   chunk 10 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 26 optimal weight:    0.0470
   chunk 52 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.3996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.086983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.067144 restraints weight = 7513.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.2781 rms_B_bonded: 2.73
r_work: 0.2639 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4256  Z= 0.142
  Angle     :  0.585   6.569   5808  Z= 0.298
  Chirality :  0.041   0.166    698
  Planarity :  0.005   0.067    710
  Dihedral  :  3.732  15.154    584
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 25.06 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 aren not related in a simple way.
  whole:  2.14 (0.37), residues: 542
  helix:  2.12 (0.27), residues: 349
  sheet: -0.60 (0.68), residues: 56
  loop :  0.63 (0.59), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 296 
 TYR   0.009   0.001   TYR B  96 
 PHE   0.013   0.001   PHE A 199 
 TRP   0.014   0.001   TRP A 355 
 HIS   0.001   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4255)
  covalent geometry    : angle       0.58512 ( 5806)
  SS BOND              : bond        0.00068 (    1)
  SS BOND              : angle       0.37176 (    2)
  hydrogen bonds       : bond        0.04221 (  299)
  hydrogen bonds       : angle       4.35785 (  879)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7006 (tt0)
REVERT: A  220 MET cc_start: 0.8137 (tpt) cc_final: 0.7887 (tpp)
REVERT: A  315 ARG cc_start: 0.7712 (tpp80) cc_final: 0.7346 (ttm110)
REVERT: A  342 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7515 (mt0)
REVERT: B   21 ARG cc_start: 0.9074 (ptm160) cc_final: 0.8663 (ptm160)
REVERT: B   62 ASP cc_start: 0.8530 (t70) cc_final: 0.8019 (t70)
REVERT: B   74 ASP cc_start: 0.8001 (t0) cc_final: 0.7692 (t0)
REVERT: B   77 LYS cc_start: 0.9412 (mtpp) cc_final: 0.9010 (ptpp)
REVERT: B   88 LYS cc_start: 0.9394 (mttt) cc_final: 0.8855 (mttp)
REVERT: B   91 ASP cc_start: 0.9480 (m-30) cc_final: 0.8925 (m-30)
REVERT: B  106 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8301 (tm-30)
REVERT: B  113 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8328 (p)
  outliers start: 13
  outliers final: 7
  residues processed: 99
  average time/residue: 0.5240
  time to fit residues: 53.8005
Evaluate side-chains
  97 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.085947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.066163 restraints weight = 7444.063|
|-----------------------------------------------------------------------------|
r_work (start): 0.2762 rms_B_bonded: 2.70
r_work: 0.2626 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2638
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2638 r_free = 0.2638    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2638 r_free = 0.2638    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2638
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4256  Z= 0.164
  Angle     :  0.603   7.141   5808  Z= 0.304
  Chirality :  0.042   0.171    698
  Planarity :  0.005   0.066    710
  Dihedral  :  3.767  14.846    584
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 25.28 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 aren not related in a simple way.
  whole:  2.13 (0.37), residues: 542
  helix:  2.12 (0.27), residues: 349
  sheet: -0.44 (0.65), residues: 63
  loop :  0.59 (0.61), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 296 
 TYR   0.018   0.001   TYR B  96 
 PHE   0.012   0.001   PHE A 199 
 TRP   0.012   0.001   TRP A 355 
 HIS   0.002   0.001   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4255)
  covalent geometry    : angle       0.60300 ( 5806)
  SS BOND              : bond        0.00122 (    1)
  SS BOND              : angle       0.42664 (    2)
  hydrogen bonds       : bond        0.04440 (  299)
  hydrogen bonds       : angle       4.39598 (  879)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.158 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7011 (tt0)
REVERT: A   75 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8481 (tm-30)
REVERT: A  220 MET cc_start: 0.8104 (tpt) cc_final: 0.7857 (tpp)
REVERT: A  315 ARG cc_start: 0.7677 (tpp80) cc_final: 0.7306 (ttm110)
REVERT: A  342 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7450 (mt0)
REVERT: B   62 ASP cc_start: 0.8502 (t70) cc_final: 0.7973 (t70)
REVERT: B   74 ASP cc_start: 0.7996 (t0) cc_final: 0.7676 (t0)
REVERT: B   77 LYS cc_start: 0.9407 (mtpp) cc_final: 0.9010 (ptpp)
REVERT: B   88 LYS cc_start: 0.9432 (mttt) cc_final: 0.8902 (mttp)
REVERT: B   91 ASP cc_start: 0.9489 (m-30) cc_final: 0.8945 (m-30)
REVERT: B   92 THR cc_start: 0.9210 (t) cc_final: 0.8996 (p)
REVERT: B  106 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8341 (tm-30)
REVERT: B  113 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8324 (p)
  outliers start: 15
  outliers final: 9
  residues processed: 97
  average time/residue: 0.5459
  time to fit residues: 54.9820
Evaluate side-chains
  101 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 46 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 53 optimal weight:    2.9990
   chunk 9 optimal weight:    0.1980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.086683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.066982 restraints weight = 7463.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.2777 rms_B_bonded: 2.70
r_work: 0.2633 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2651
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2651 r_free = 0.2651    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2652 r_free = 0.2652    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   4256  Z= 0.153
  Angle     :  0.607   7.141   5808  Z= 0.306
  Chirality :  0.042   0.179    698
  Planarity :  0.005   0.069    710
  Dihedral  :  3.770  14.892    584
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 25.97 %
    Favored  : 71.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 aren not related in a simple way.
  whole:  2.12 (0.37), residues: 542
  helix:  2.13 (0.27), residues: 349
  sheet: -0.82 (0.70), residues: 53
  loop :  0.63 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 296 
 TYR   0.006   0.001   TYR A  95 
 PHE   0.013   0.001   PHE A 199 
 TRP   0.013   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 4255)
  covalent geometry    : angle       0.60706 ( 5806)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.35042 (    2)
  hydrogen bonds       : bond        0.04303 (  299)
  hydrogen bonds       : angle       4.34232 (  879)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7022 (tt0)
REVERT: A   75 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8506 (tm-30)
REVERT: A  220 MET cc_start: 0.8152 (tpt) cc_final: 0.7947 (tpp)
REVERT: A  315 ARG cc_start: 0.7742 (tpp80) cc_final: 0.7380 (ttm110)
REVERT: A  342 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7533 (mt0)
REVERT: A  372 GLN cc_start: 0.8761 (mt0) cc_final: 0.8489 (pt0)
REVERT: B   62 ASP cc_start: 0.8528 (t70) cc_final: 0.7997 (t70)
REVERT: B   74 ASP cc_start: 0.8048 (t0) cc_final: 0.7738 (t0)
REVERT: B   77 LYS cc_start: 0.9410 (mtpp) cc_final: 0.9036 (ptpp)
REVERT: B   88 LYS cc_start: 0.9442 (mttt) cc_final: 0.8932 (mttp)
REVERT: B   91 ASP cc_start: 0.9501 (m-30) cc_final: 0.9010 (m-30)
REVERT: B  106 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8370 (tm-30)
REVERT: B  113 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8385 (p)
  outliers start: 12
  outliers final: 9
  residues processed: 95
  average time/residue: 0.5307
  time to fit residues: 52.3492
Evaluate side-chains
  102 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 53 optimal weight:    0.1980
   chunk 9 optimal weight:    0.6980
   chunk 6 optimal weight:    0.2980
   chunk 28 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.4780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.087169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.067310 restraints weight = 7313.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.2782 rms_B_bonded: 2.70
r_work: 0.2638 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2660 r_free = 0.2660    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2660
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4256  Z= 0.146
  Angle     :  0.599   7.660   5808  Z= 0.303
  Chirality :  0.042   0.174    698
  Planarity :  0.004   0.048    710
  Dihedral  :  3.765  16.279    584
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 26.20 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 aren not related in a simple way.
  whole:  2.14 (0.37), residues: 542
  helix:  2.14 (0.27), residues: 349
  sheet: -0.77 (0.71), residues: 53
  loop :  0.62 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  21 
 TYR   0.014   0.001   TYR B  96 
 PHE   0.013   0.001   PHE A 199 
 TRP   0.014   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4255)
  covalent geometry    : angle       0.59927 ( 5806)
  SS BOND              : bond        0.00044 (    1)
  SS BOND              : angle       0.35681 (    2)
  hydrogen bonds       : bond        0.04230 (  299)
  hydrogen bonds       : angle       4.34396 (  879)

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

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

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1084 Ramachandran restraints generated.
    542 Oldfield, 0 Emsley, 542 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A   59 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.6986 (tt0)
REVERT: A   75 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8493 (tm-30)
REVERT: A  220 MET cc_start: 0.8121 (tpt) cc_final: 0.7847 (tpp)
REVERT: A  296 ARG cc_start: 0.8425 (ttm110) cc_final: 0.8041 (mtt90)
REVERT: A  315 ARG cc_start: 0.7718 (tpp80) cc_final: 0.7357 (ttm110)
REVERT: A  342 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7513 (mt0)
REVERT: A  372 GLN cc_start: 0.8742 (mt0) cc_final: 0.8473 (pt0)
REVERT: B   62 ASP cc_start: 0.8499 (t70) cc_final: 0.8009 (t70)
REVERT: B   74 ASP cc_start: 0.8039 (t0) cc_final: 0.7738 (t0)
REVERT: B   77 LYS cc_start: 0.9409 (mtpp) cc_final: 0.9053 (ptpp)
REVERT: B   88 LYS cc_start: 0.9439 (mttt) cc_final: 0.8902 (mttp)
REVERT: B   91 ASP cc_start: 0.9491 (m-30) cc_final: 0.9026 (m-30)
REVERT: B  106 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8323 (tm-30)
REVERT: B  113 THR cc_start: 0.8910 (OUTLIER) cc_final: 0.8399 (p)
  outliers start: 12
  outliers final: 9
  residues processed: 94
  average time/residue: 0.5198
  time to fit residues: 50.7397
Evaluate side-chains
  101 residues out of total 439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 VAL
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  149 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  342 GLN
Chi-restraints excluded: chain A residue  421 ILE
Chi-restraints excluded: chain B residue    7 VAL
Chi-restraints excluded: chain B residue    9 SER
Chi-restraints excluded: chain B residue  106 GLU
Chi-restraints excluded: chain B residue  113 THR
Chi-restraints excluded: chain B residue  115 VAL
Chi-restraints excluded: chain B residue  116 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 43 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.3980
   chunk 44 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 52 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 32 optimal weight:    0.0040
   overall best weight:    0.4992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.087367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.067441 restraints weight = 7468.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.2786 rms_B_bonded: 2.73
r_work: 0.2651 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2651
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2662
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2662 r_free = 0.2662    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2662
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4256  Z= 0.149
  Angle     :  0.601   7.820   5808  Z= 0.304
  Chirality :  0.042   0.175    698
  Planarity :  0.004   0.048    710
  Dihedral  :  3.763  17.078    584
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 25.97 %
    Favored  : 71.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 aren not related in a simple way.
  whole:  2.14 (0.37), residues: 542
  helix:  2.16 (0.27), residues: 349
  sheet: -0.85 (0.70), residues: 53
  loop :  0.60 (0.57), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  21 
 TYR   0.008   0.001   TYR B  60 
 PHE   0.013   0.001   PHE A 199 
 TRP   0.013   0.001   TRP A 355 
 HIS   0.001   0.000   HIS B  81 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 4255)
  covalent geometry    : angle       0.60072 ( 5806)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.38144 (    2)
  hydrogen bonds       : bond        0.04205 (  299)
  hydrogen bonds       : angle       4.32729 (  879)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1918.44 seconds
wall clock time: 33 minutes 32.87 seconds (2012.87 seconds total)