Starting phenix.real_space_refine
on Tue Mar  3 12:25:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sk2_25170/03_2026/7sk2_25170.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sk2_25170/03_2026/7sk2_25170.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.82
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sk2_25170/03_2026/7sk2_25170.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sk2_25170/03_2026/7sk2_25170.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sk2_25170/03_2026/7sk2_25170.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sk2_25170/03_2026/7sk2_25170.map"
  }
  resolution = 3.82
  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=   0.019
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      35      5.16       5
     C    2788      2.51       5
     N     651      2.21       5
     O     703      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4177
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4152
          Classifications: {'peptide': 532}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 22, 'TRANS': 509}
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 2, 'TYR:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'TGI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.05, per 1000 atoms: 0.25
  Number of scatterers: 4177
  At special positions: 0
  Unit cell: (83.739, 73.17, 77.235, 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      35     16.00
     O     703      8.00
     N     651      7.00
     C    2788      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 164 " - pdb=" SG  CYS A 173 " 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: 0.35
  Conformation dependent library (CDL) restraints added in 161.3 milliseconds
  

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  972

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 1 sheets defined
      75.6% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 57
      removed outlier: 3.559A  pdb=" N   MET A  55 " --> pdb=" O   PHE A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 68
    Processing helix  chain 'A' and resid 68 through 78
    Processing helix  chain 'A' and resid 85 through 93
    Processing helix  chain 'A' and resid 93 through 109
    Processing helix  chain 'A' and resid 113 through 118
      removed outlier: 3.927A  pdb=" N   LEU A 118 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 153
      removed outlier: 4.167A  pdb=" N   GLY A 126 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LEU A 151 " --> pdb=" O   ALA A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 196
    Processing helix  chain 'A' and resid 211 through 230
      removed outlier: 3.758A  pdb=" N   CYS A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   TRP A 230 " --> pdb=" O   TYR A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 237
      removed outlier: 3.646A  pdb=" N   TRP A 235 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 245 through 259
      removed outlier: 3.791A  pdb=" N   ILE A 252 " --> pdb=" O   TYR A 248 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   ILE A 253 " --> pdb=" O   ILE A 249 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   LEU A 254 " --> pdb=" O   MET A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 273
      removed outlier: 3.940A  pdb=" N   GLY A 267 " --> pdb=" O   GLY A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 280
      removed outlier: 4.106A  pdb=" N   SER A 280 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 296
      removed outlier: 3.585A  pdb=" N   ILE A 292 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 310
    Processing helix  chain 'A' and resid 315 through 349
      removed outlier: 3.501A  pdb=" N   ASP A 319 " --> pdb=" O   ASN A 315 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ILE A 322 " --> pdb=" O   ARG A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 358
      removed outlier: 3.522A  pdb=" N   VAL A 356 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 362
      No H-bonds generated for 'chain 'A' and resid 360 through 362'
    Processing helix  chain 'A' and resid 363 through 374
      Proline residue:  A 369  - end of helix
    Processing helix  chain 'A' and resid 377 through 410
      removed outlier: 3.919A  pdb=" N   SER A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 418
    Processing helix  chain 'A' and resid 423 through 431
    Processing helix  chain 'A' and resid 431 through 440
      removed outlier: 6.303A  pdb=" N   SER A 437 " --> pdb=" O   LEU A 433 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   ASN A 438 " --> pdb=" O   ILE A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 454
    Processing helix  chain 'A' and resid 457 through 472
    Processing helix  chain 'A' and resid 476 through 489
      removed outlier: 4.423A  pdb=" N   ASP A 482 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 502
    Processing helix  chain 'A' and resid 502 through 518
    Processing helix  chain 'A' and resid 530 through 559
      removed outlier: 3.559A  pdb=" N   SER A 543 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   SER A 544 " --> pdb=" O   MET A 540 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   ILE A 548 " --> pdb=" O   SER A 544 " (cutoff:3.500A)
      Proline residue:  A 549  - end of helix
    Processing helix  chain 'A' and resid 562 through 569
      removed outlier: 4.235A  pdb=" N   ARG A 566 " --> pdb=" O   SER A 562 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   ILE A 567 " --> pdb=" O   LEU A 563 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 523 through 524

    256 hydrogen bonds defined for protein.
    750 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: 0.57

  Time building geometry restraints manager: 0.46 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: 1211
        1.34 -     1.46: 1142
        1.46 -     1.58: 1904
        1.58 -     1.70: 4
        1.70 -     1.82: 52
  Bond restraints: 4313
  Sorted by residual:
  bond pdb=" C03 TGI A 601 "
       pdb=" C07 TGI A 601 "
    ideal  model  delta    sigma   weight residual
    1.468  1.538 -0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" C03 TGI A 601 "
       pdb=" S04 TGI A 601 "
    ideal  model  delta    sigma   weight residual
    1.744  1.690  0.054 2.00e-02 2.50e+03 7.17e+00
  bond pdb=" C07 TGI A 601 "
       pdb=" C20 TGI A 601 "
    ideal  model  delta    sigma   weight residual
    1.480  1.531 -0.051 2.00e-02 2.50e+03 6.49e+00
  bond pdb=" C20 TGI A 601 "
       pdb=" S24 TGI A 601 "
    ideal  model  delta    sigma   weight residual
    1.737  1.687  0.050 2.00e-02 2.50e+03 6.16e+00
  bond pdb=" C14 TGI A 601 "
       pdb=" C15 TGI A 601 "
    ideal  model  delta    sigma   weight residual
    1.539  1.494  0.045 2.00e-02 2.50e+03 4.98e+00
  ... (remaining 4308 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 5608
        2.19 -     4.38: 209
        4.38 -     6.58: 43
        6.58 -     8.77: 16
        8.77 -    10.96: 7
  Bond angle restraints: 5883
  Sorted by residual:
  angle pdb=" C   ILE A 377 "
        pdb=" N   SER A 378 "
        pdb=" CA  SER A 378 "
      ideal   model   delta    sigma   weight residual
     120.58  127.09   -6.51 1.32e+00 5.74e-01 2.43e+01
  angle pdb=" CB  LYS A 350 "
        pdb=" CG  LYS A 350 "
        pdb=" CD  LYS A 350 "
      ideal   model   delta    sigma   weight residual
     111.30  122.26  -10.96 2.30e+00 1.89e-01 2.27e+01
  angle pdb=" CA  VAL A  58 "
        pdb=" CB  VAL A  58 "
        pdb=" CG1 VAL A  58 "
      ideal   model   delta    sigma   weight residual
     110.40  117.16   -6.76 1.70e+00 3.46e-01 1.58e+01
  angle pdb=" C   SER A 302 "
        pdb=" N   LEU A 303 "
        pdb=" CA  LEU A 303 "
      ideal   model   delta    sigma   weight residual
     121.54  129.03   -7.49 1.91e+00 2.74e-01 1.54e+01
  angle pdb=" C   LEU A 416 "
        pdb=" N   ARG A 417 "
        pdb=" CA  ARG A 417 "
      ideal   model   delta    sigma   weight residual
     122.06  115.23    6.83 1.86e+00 2.89e-01 1.35e+01
  ... (remaining 5878 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.93: 2204
       16.93 -    33.86: 179
       33.86 -    50.80: 45
       50.80 -    67.73: 4
       67.73 -    84.66: 4
  Dihedral angle restraints: 2436
    sinusoidal: 906
      harmonic: 1530
  Sorted by residual:
  dihedral pdb=" CA  PHE A 480 "
           pdb=" C   PHE A 480 "
           pdb=" N   TYR A 481 "
           pdb=" CA  TYR A 481 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.99   24.01     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  GLN A 199 "
           pdb=" C   GLN A 199 "
           pdb=" N   MET A 200 "
           pdb=" CA  MET A 200 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.15  -20.85     0      5.00e+00 4.00e-02 1.74e+01
  dihedral pdb=" CA  ALA A 130 "
           pdb=" C   ALA A 130 "
           pdb=" N   VAL A 131 "
           pdb=" CA  VAL A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.94  -20.06     0      5.00e+00 4.00e-02 1.61e+01
  ... (remaining 2433 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 379
       0.039 -    0.079: 170
       0.079 -    0.118: 60
       0.118 -    0.157: 24
       0.157 -    0.197: 9
  Chirality restraints: 642
  Sorted by residual:
  chirality pdb=" CB  VAL A 546 "
            pdb=" CA  VAL A 546 "
            pdb=" CG1 VAL A 546 "
            pdb=" CG2 VAL A 546 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.66e-01
  chirality pdb=" CB  ILE A 341 "
            pdb=" CA  ILE A 341 "
            pdb=" CG1 ILE A 341 "
            pdb=" CG2 ILE A 341 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.43e-01
  chirality pdb=" CA  SER A 378 "
            pdb=" N   SER A 378 "
            pdb=" C   SER A 378 "
            pdb=" CB  SER A 378 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.06e-01
  ... (remaining 639 not shown)

  Planarity restraints: 722
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 137 "   -0.016 2.00e-02 2.50e+03   3.32e-02 1.10e+01
        pdb=" C   ASN A 137 "    0.057 2.00e-02 2.50e+03
        pdb=" O   ASN A 137 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ILE A 138 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 136 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.17e+00
        pdb=" C   LEU A 136 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   LEU A 136 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ASN A 137 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 138 "    0.015 2.00e-02 2.50e+03   3.02e-02 9.09e+00
        pdb=" C   ILE A 138 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   ILE A 138 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TYR A 139 "    0.017 2.00e-02 2.50e+03
  ... (remaining 719 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 815
        2.77 -     3.30: 4247
        3.30 -     3.83: 7327
        3.83 -     4.37: 8299
        4.37 -     4.90: 13716
  Nonbonded interactions: 34404
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 296 "
            pdb=" OG  SER A 328 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   VAL A 142 "
            pdb=" OG  SER A 145 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" O   PHE A  92 "
            pdb=" OG1 THR A 504 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   PHE A 450 "
            pdb=" OG  SER A 454 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   SER A 437 "
            pdb=" OG1 THR A 440 "
     model   vdw
     2.285 3.040
  ... (remaining 34399 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.730
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
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   0.070   4314  Z= 0.251
  Angle     :  1.059  10.959   5885  Z= 0.545
  Chirality :  0.055   0.197    642
  Planarity :  0.006   0.044    722
  Dihedral  : 13.666  84.661   1461
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.59 (0.34), residues: 530
  helix: -1.32 (0.26), residues: 346
  sheet:  None (None), residues: 0
  loop : -2.27 (0.44), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 195 
 TYR   0.039   0.003   TYR A 452 
 PHE   0.037   0.003   PHE A 480 
 TRP   0.027   0.002   TRP A 230 
 HIS   0.001   0.000   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 4313)
  covalent geometry    : angle       1.05876 ( 5883)
  SS BOND              : bond        0.00056 (    1)
  SS BOND              : angle       1.06859 (    2)
  hydrogen bonds       : bond        0.17204 (  256)
  hydrogen bonds       : angle       7.92987 (  750)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  250 MET cc_start: 0.7821 (tmm) cc_final: 0.7527 (tmm)
REVERT: A  283 GLU cc_start: 0.8133 (pp20) cc_final: 0.7926 (pp20)
REVERT: A  292 ILE cc_start: 0.8583 (mm) cc_final: 0.8317 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0591
  time to fit residues: 10.4763
Evaluate side-chains
  110 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 GLN
A 196 ASN
A 483 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.159713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.136751 restraints weight = 9218.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.140756 restraints weight = 5398.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.143128 restraints weight = 3681.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.145346 restraints weight = 2824.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.146618 restraints weight = 2265.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4314  Z= 0.188
  Angle     :  0.729   8.046   5885  Z= 0.380
  Chirality :  0.044   0.141    642
  Planarity :  0.005   0.032    722
  Dihedral  :  6.706  44.766    599
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 11.97 %
    Favored  : 85.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.36), residues: 530
  helix: -0.76 (0.26), residues: 370
  sheet:  None (None), residues: 0
  loop : -1.74 (0.54), residues: 160

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 566 
 TYR   0.025   0.002   TYR A 139 
 PHE   0.017   0.002   PHE A 462 
 TRP   0.018   0.002   TRP A 230 
 HIS   0.008   0.003   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 4313)
  covalent geometry    : angle       0.72873 ( 5883)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.99007 (    2)
  hydrogen bonds       : bond        0.05295 (  256)
  hydrogen bonds       : angle       5.91951 (  750)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASN cc_start: 0.8247 (m-40) cc_final: 0.7713 (m-40)
REVERT: A  174 PHE cc_start: 0.5801 (p90) cc_final: 0.5591 (p90)
REVERT: A  179 MET cc_start: 0.4112 (pmm) cc_final: 0.3905 (pmm)
REVERT: A  283 GLU cc_start: 0.8251 (pp20) cc_final: 0.7466 (pp20)
REVERT: A  287 ASP cc_start: 0.8046 (m-30) cc_final: 0.7401 (m-30)
REVERT: A  321 ILE cc_start: 0.8293 (pt) cc_final: 0.8082 (pt)
REVERT: A  479 ARG cc_start: 0.7610 (ptt180) cc_final: 0.7361 (ptt180)
REVERT: A  527 TYR cc_start: 0.7592 (t80) cc_final: 0.7371 (t80)
REVERT: A  545 MET cc_start: 0.8322 (mmt) cc_final: 0.8104 (mmt)
  outliers start: 11
  outliers final: 10
  residues processed: 132
  average time/residue: 0.0461
  time to fit residues: 8.2531
Evaluate side-chains
  130 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  526 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0870
   chunk 2 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.8962

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.161389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.138333 restraints weight = 9220.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.141871 restraints weight = 5718.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.144534 restraints weight = 4085.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.145982 restraints weight = 3164.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.147343 restraints weight = 2667.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4314  Z= 0.148
  Angle     :  0.682   7.482   5885  Z= 0.351
  Chirality :  0.042   0.187    642
  Planarity :  0.004   0.029    722
  Dihedral  :  6.332  44.079    599
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.61 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.37), residues: 530
  helix: -0.38 (0.27), residues: 365
  sheet:  None (None), residues: 0
  loop : -1.58 (0.53), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 566 
 TYR   0.019   0.002   TYR A 139 
 PHE   0.024   0.002   PHE A 385 
 TRP   0.015   0.002   TRP A 168 
 HIS   0.008   0.003   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 4313)
  covalent geometry    : angle       0.68160 ( 5883)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.79989 (    2)
  hydrogen bonds       : bond        0.04683 (  256)
  hydrogen bonds       : angle       5.52689 (  750)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   77 ASN cc_start: 0.8185 (m110) cc_final: 0.7824 (m-40)
REVERT: A  198 HIS cc_start: 0.7591 (m90) cc_final: 0.6954 (m90)
REVERT: A  283 GLU cc_start: 0.8064 (pp20) cc_final: 0.7409 (pp20)
REVERT: A  287 ASP cc_start: 0.7878 (m-30) cc_final: 0.7459 (m-30)
REVERT: A  321 ILE cc_start: 0.8363 (pt) cc_final: 0.8080 (pt)
REVERT: A  452 TYR cc_start: 0.7938 (t80) cc_final: 0.7571 (t80)
REVERT: A  479 ARG cc_start: 0.7486 (ptt180) cc_final: 0.7214 (ptt180)
  outliers start: 12
  outliers final: 9
  residues processed: 129
  average time/residue: 0.0479
  time to fit residues: 8.3830
Evaluate side-chains
  126 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  523 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0980
   chunk 3 optimal weight:    0.0570
   chunk 29 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 15 optimal weight:    0.0000
   overall best weight:    0.3302

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 438 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.164367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.141789 restraints weight = 9070.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.145457 restraints weight = 5590.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.148097 restraints weight = 3949.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.149624 restraints weight = 3034.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.151117 restraints weight = 2537.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6994
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4314  Z= 0.129
  Angle     :  0.662   7.354   5885  Z= 0.336
  Chirality :  0.041   0.141    642
  Planarity :  0.004   0.039    722
  Dihedral  :  6.081  43.681    599
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.25 %
    Favored  : 78.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.37), residues: 530
  helix:  0.07 (0.28), residues: 354
  sheet:  None (None), residues: 0
  loop : -1.41 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 211 
 TYR   0.019   0.001   TYR A 139 
 PHE   0.022   0.002   PHE A 385 
 TRP   0.013   0.001   TRP A 193 
 HIS   0.008   0.002   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 4313)
  covalent geometry    : angle       0.66222 ( 5883)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       0.70614 (    2)
  hydrogen bonds       : bond        0.04295 (  256)
  hydrogen bonds       : angle       5.29960 (  750)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASN cc_start: 0.8098 (m110) cc_final: 0.7791 (m-40)
REVERT: A  168 TRP cc_start: 0.5783 (p90) cc_final: 0.5512 (p90)
REVERT: A  283 GLU cc_start: 0.8037 (pp20) cc_final: 0.7511 (pp20)
REVERT: A  287 ASP cc_start: 0.7867 (m-30) cc_final: 0.7430 (m-30)
REVERT: A  321 ILE cc_start: 0.8334 (pt) cc_final: 0.8067 (pt)
REVERT: A  450 PHE cc_start: 0.7878 (m-10) cc_final: 0.7399 (m-10)
REVERT: A  452 TYR cc_start: 0.7858 (t80) cc_final: 0.7566 (t80)
REVERT: A  479 ARG cc_start: 0.7425 (ptt180) cc_final: 0.7151 (ptt180)
  outliers start: 10
  outliers final: 8
  residues processed: 128
  average time/residue: 0.0541
  time to fit residues: 9.1155
Evaluate side-chains
  125 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  506 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 52 optimal weight:    0.0060
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0070
   chunk 48 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   overall best weight:    0.5814

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 196 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.164311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.141498 restraints weight = 9098.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.145082 restraints weight = 5681.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.147715 restraints weight = 4055.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.149277 restraints weight = 3140.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.150833 restraints weight = 2629.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7015
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4314  Z= 0.129
  Angle     :  0.672   8.081   5885  Z= 0.340
  Chirality :  0.041   0.140    642
  Planarity :  0.003   0.027    722
  Dihedral  :  5.912  43.725    599
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.77 %
    Favored  : 73.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.37), residues: 530
  helix:  0.22 (0.28), residues: 354
  sheet:  None (None), residues: 0
  loop : -1.29 (0.52), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 211 
 TYR   0.018   0.001   TYR A 139 
 PHE   0.020   0.002   PHE A 385 
 TRP   0.011   0.001   TRP A 193 
 HIS   0.009   0.002   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4313)
  covalent geometry    : angle       0.67204 ( 5883)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       0.66012 (    2)
  hydrogen bonds       : bond        0.04157 (  256)
  hydrogen bonds       : angle       5.23932 (  750)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 124
  time to evaluate  : 0.114 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASN cc_start: 0.8093 (m110) cc_final: 0.7816 (m-40)
REVERT: A  168 TRP cc_start: 0.5674 (p90) cc_final: 0.5453 (p90)
REVERT: A  200 MET cc_start: 0.6518 (tpt) cc_final: 0.6214 (mmm)
REVERT: A  269 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7383 (mm)
REVERT: A  283 GLU cc_start: 0.7983 (pp20) cc_final: 0.7403 (pp20)
REVERT: A  287 ASP cc_start: 0.7872 (m-30) cc_final: 0.7249 (m-30)
REVERT: A  321 ILE cc_start: 0.8345 (pt) cc_final: 0.8078 (pt)
REVERT: A  450 PHE cc_start: 0.7849 (m-10) cc_final: 0.7451 (m-10)
REVERT: A  452 TYR cc_start: 0.7872 (t80) cc_final: 0.7608 (t80)
REVERT: A  479 ARG cc_start: 0.7391 (ptt180) cc_final: 0.7111 (ptt180)
  outliers start: 16
  outliers final: 11
  residues processed: 130
  average time/residue: 0.0565
  time to fit residues: 9.6652
Evaluate side-chains
  132 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  538 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0870
   chunk 44 optimal weight:    0.0770
   chunk 3 optimal weight:    0.0270
   chunk 15 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.4376

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 198 HIS ** 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 = 0.4209 r_free = 0.4209 target = 0.164957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.141718 restraints weight = 9268.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.145533 restraints weight = 5685.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.148243 restraints weight = 4008.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.149998 restraints weight = 3076.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.151445 restraints weight = 2545.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4314  Z= 0.126
  Angle     :  0.679   8.734   5885  Z= 0.342
  Chirality :  0.041   0.148    642
  Planarity :  0.003   0.027    722
  Dihedral  :  5.814  43.520    599
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 23.00 %
    Favored  : 72.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.38), residues: 530
  helix:  0.25 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.26 (0.52), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 566 
 TYR   0.018   0.001   TYR A 139 
 PHE   0.021   0.002   PHE A 385 
 TRP   0.010   0.001   TRP A 193 
 HIS   0.009   0.003   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 4313)
  covalent geometry    : angle       0.67919 ( 5883)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.64118 (    2)
  hydrogen bonds       : bond        0.04095 (  256)
  hydrogen bonds       : angle       5.22709 (  750)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASN cc_start: 0.8094 (m110) cc_final: 0.7847 (m-40)
REVERT: A  121 MET cc_start: 0.8471 (mpp) cc_final: 0.8180 (mpp)
REVERT: A  185 MET cc_start: 0.5886 (ptp) cc_final: 0.5624 (ptp)
REVERT: A  197 MET cc_start: 0.6879 (tmm) cc_final: 0.6646 (tmm)
REVERT: A  200 MET cc_start: 0.6575 (tpt) cc_final: 0.6245 (mmm)
REVERT: A  269 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7376 (mm)
REVERT: A  283 GLU cc_start: 0.8057 (pp20) cc_final: 0.7454 (pp20)
REVERT: A  287 ASP cc_start: 0.7924 (m-30) cc_final: 0.7289 (m-30)
REVERT: A  321 ILE cc_start: 0.8278 (pt) cc_final: 0.8020 (pt)
REVERT: A  450 PHE cc_start: 0.7818 (m-10) cc_final: 0.7442 (m-10)
REVERT: A  452 TYR cc_start: 0.7913 (t80) cc_final: 0.7563 (t80)
REVERT: A  479 ARG cc_start: 0.7487 (ptt180) cc_final: 0.7195 (ptt180)
  outliers start: 18
  outliers final: 12
  residues processed: 130
  average time/residue: 0.0545
  time to fit residues: 9.3689
Evaluate side-chains
  133 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  538 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 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 = 0.4170 r_free = 0.4170 target = 0.161870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.138965 restraints weight = 9358.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.142688 restraints weight = 5770.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.145291 restraints weight = 4078.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.146817 restraints weight = 3138.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.148472 restraints weight = 2617.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7048
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4314  Z= 0.149
  Angle     :  0.707   9.135   5885  Z= 0.356
  Chirality :  0.042   0.157    642
  Planarity :  0.004   0.027    722
  Dihedral  :  5.788  42.368    599
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 15.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 23.47 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.38), residues: 530
  helix:  0.20 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.14 (0.53), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 172 
 TYR   0.019   0.001   TYR A 139 
 PHE   0.020   0.002   PHE A 385 
 TRP   0.010   0.001   TRP A 168 
 HIS   0.008   0.003   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4313)
  covalent geometry    : angle       0.70730 ( 5883)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.57606 (    2)
  hydrogen bonds       : bond        0.04201 (  256)
  hydrogen bonds       : angle       5.26593 (  750)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASN cc_start: 0.8191 (m110) cc_final: 0.7866 (m-40)
REVERT: A  197 MET cc_start: 0.6903 (tmm) cc_final: 0.6454 (tmm)
REVERT: A  198 HIS cc_start: 0.7061 (m-70) cc_final: 0.6342 (m-70)
REVERT: A  269 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7467 (mm)
REVERT: A  283 GLU cc_start: 0.8163 (pp20) cc_final: 0.7532 (pp20)
REVERT: A  287 ASP cc_start: 0.8010 (m-30) cc_final: 0.7316 (m-30)
REVERT: A  321 ILE cc_start: 0.8263 (pt) cc_final: 0.7996 (pt)
REVERT: A  391 MET cc_start: 0.7761 (mtt) cc_final: 0.7506 (mtt)
REVERT: A  452 TYR cc_start: 0.7993 (t80) cc_final: 0.7619 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 130
  average time/residue: 0.0535
  time to fit residues: 9.2833
Evaluate side-chains
  134 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  538 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 40 optimal weight:    0.6980
   chunk 36 optimal weight:    0.3980
   chunk 50 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 15 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 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 = 0.4160 r_free = 0.4160 target = 0.161189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.138707 restraints weight = 9392.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.142335 restraints weight = 5858.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.144497 restraints weight = 4152.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.146655 restraints weight = 3267.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.147674 restraints weight = 2667.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4314  Z= 0.154
  Angle     :  0.724  10.244   5885  Z= 0.365
  Chirality :  0.043   0.150    642
  Planarity :  0.004   0.025    722
  Dihedral  :  5.794  41.258    599
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 23.24 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.49 (0.37), residues: 530
  helix:  0.14 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop : -1.11 (0.53), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 419 
 TYR   0.020   0.001   TYR A 139 
 PHE   0.018   0.002   PHE A 385 
 TRP   0.010   0.001   TRP A 193 
 HIS   0.008   0.003   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 4313)
  covalent geometry    : angle       0.72406 ( 5883)
  SS BOND              : bond        0.00010 (    1)
  SS BOND              : angle       0.72252 (    2)
  hydrogen bonds       : bond        0.04224 (  256)
  hydrogen bonds       : angle       5.32028 (  750)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASN cc_start: 0.8195 (m110) cc_final: 0.7942 (m-40)
REVERT: A  197 MET cc_start: 0.6899 (tmm) cc_final: 0.6396 (tmm)
REVERT: A  198 HIS cc_start: 0.7179 (m-70) cc_final: 0.6460 (m-70)
REVERT: A  269 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7404 (mm)
REVERT: A  283 GLU cc_start: 0.8050 (pp20) cc_final: 0.7521 (pp20)
REVERT: A  287 ASP cc_start: 0.7948 (m-30) cc_final: 0.7305 (m-30)
REVERT: A  321 ILE cc_start: 0.8314 (pt) cc_final: 0.8038 (pt)
REVERT: A  391 MET cc_start: 0.7680 (mtt) cc_final: 0.7424 (mtt)
REVERT: A  452 TYR cc_start: 0.7967 (t80) cc_final: 0.7693 (t80)
REVERT: A  458 MET cc_start: 0.6646 (mmt) cc_final: 0.6144 (mmt)
REVERT: A  479 ARG cc_start: 0.7429 (ptt180) cc_final: 0.7149 (ptt180)
  outliers start: 18
  outliers final: 14
  residues processed: 128
  average time/residue: 0.0545
  time to fit residues: 9.2639
Evaluate side-chains
  132 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  538 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 50 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 11 optimal weight:    0.0870
   chunk 3 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 198 HIS ** 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 = 0.4192 r_free = 0.4192 target = 0.163580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.140535 restraints weight = 9348.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.144383 restraints weight = 5577.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.147178 restraints weight = 3885.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.148756 restraints weight = 2953.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.150480 restraints weight = 2447.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6995
moved from start:          0.3557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4314  Z= 0.134
  Angle     :  0.725  11.007   5885  Z= 0.364
  Chirality :  0.043   0.226    642
  Planarity :  0.004   0.028    722
  Dihedral  :  5.687  40.309    599
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 24.18 %
    Favored  : 72.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.38), residues: 530
  helix:  0.23 (0.28), residues: 353
  sheet:  None (None), residues: 0
  loop : -1.11 (0.52), residues: 177

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 211 
 TYR   0.026   0.002   TYR A 551 
 PHE   0.030   0.002   PHE A 404 
 TRP   0.011   0.001   TRP A 168 
 HIS   0.009   0.003   HIS A 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 4313)
  covalent geometry    : angle       0.72512 ( 5883)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.59363 (    2)
  hydrogen bonds       : bond        0.04114 (  256)
  hydrogen bonds       : angle       5.30197 (  750)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 ASN cc_start: 0.8110 (m110) cc_final: 0.7885 (m-40)
REVERT: A  269 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7446 (mm)
REVERT: A  283 GLU cc_start: 0.8167 (pp20) cc_final: 0.7639 (pp20)
REVERT: A  287 ASP cc_start: 0.7976 (m-30) cc_final: 0.7313 (m-30)
REVERT: A  321 ILE cc_start: 0.8225 (pt) cc_final: 0.7975 (pt)
REVERT: A  391 MET cc_start: 0.7833 (mtt) cc_final: 0.7585 (mtt)
REVERT: A  452 TYR cc_start: 0.8000 (t80) cc_final: 0.7645 (t80)
REVERT: A  458 MET cc_start: 0.6640 (mmt) cc_final: 0.6205 (mmt)
REVERT: A  479 ARG cc_start: 0.7456 (ptt180) cc_final: 0.7163 (ptt180)
  outliers start: 16
  outliers final: 14
  residues processed: 127
  average time/residue: 0.0508
  time to fit residues: 8.6382
Evaluate side-chains
  130 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  538 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 30 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0970
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 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 = 0.4194 r_free = 0.4194 target = 0.163800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.142363 restraints weight = 9157.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.146033 restraints weight = 5564.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.148526 restraints weight = 3883.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.150588 restraints weight = 2973.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.151817 restraints weight = 2392.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   4314  Z= 0.135
  Angle     :  0.743  11.685   5885  Z= 0.372
  Chirality :  0.043   0.241    642
  Planarity :  0.004   0.025    722
  Dihedral  :  5.728  39.924    599
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 15.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 25.59 %
    Favored  : 71.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.37), residues: 530
  helix:  0.23 (0.27), residues: 352
  sheet:  None (None), residues: 0
  loop : -1.08 (0.52), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 419 
 TYR   0.022   0.001   TYR A 527 
 PHE   0.025   0.002   PHE A 294 
 TRP   0.011   0.001   TRP A 168 
 HIS   0.011   0.004   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4313)
  covalent geometry    : angle       0.74349 ( 5883)
  SS BOND              : bond        0.00092 (    1)
  SS BOND              : angle       0.57640 (    2)
  hydrogen bonds       : bond        0.04077 (  256)
  hydrogen bonds       : angle       5.32749 (  750)

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 MET cc_start: 0.6508 (tpt) cc_final: 0.6084 (mmm)
REVERT: A  269 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7359 (mm)
REVERT: A  283 GLU cc_start: 0.8031 (pp20) cc_final: 0.7565 (pp20)
REVERT: A  287 ASP cc_start: 0.7881 (m-30) cc_final: 0.7305 (m-30)
REVERT: A  321 ILE cc_start: 0.8281 (pt) cc_final: 0.8051 (pt)
REVERT: A  391 MET cc_start: 0.7715 (mtt) cc_final: 0.7455 (mtt)
REVERT: A  452 TYR cc_start: 0.7923 (t80) cc_final: 0.7638 (t80)
REVERT: A  458 MET cc_start: 0.6577 (mmt) cc_final: 0.6249 (mmt)
REVERT: A  479 ARG cc_start: 0.7343 (ptt180) cc_final: 0.7037 (ptt180)
  outliers start: 14
  outliers final: 13
  residues processed: 125
  average time/residue: 0.0518
  time to fit residues: 8.7835
Evaluate side-chains
  128 residues out of total 452 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  189 VAL
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  328 SER
Chi-restraints excluded: chain A residue  378 SER
Chi-restraints excluded: chain A residue  417 ARG
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  506 ILE
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  538 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 16 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 34 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 15 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 438 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.160640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.137938 restraints weight = 9308.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.141701 restraints weight = 5670.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.144411 restraints weight = 3977.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.146085 restraints weight = 3026.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.147663 restraints weight = 2490.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   4314  Z= 0.172
  Angle     :  0.795  12.909   5885  Z= 0.396
  Chirality :  0.045   0.237    642
  Planarity :  0.004   0.025    722
  Dihedral  :  5.884  38.752    599
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 18.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 25.82 %
    Favored  : 70.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.37), residues: 530
  helix:  0.16 (0.27), residues: 350
  sheet:  None (None), residues: 0
  loop : -1.25 (0.51), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 195 
 TYR   0.036   0.002   TYR A 551 
 PHE   0.023   0.002   PHE A 294 
 TRP   0.015   0.001   TRP A 193 
 HIS   0.006   0.003   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 4313)
  covalent geometry    : angle       0.79491 ( 5883)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       0.69211 (    2)
  hydrogen bonds       : bond        0.04272 (  256)
  hydrogen bonds       : angle       5.35139 (  750)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 842.32 seconds
wall clock time: 15 minutes 9.57 seconds (909.57 seconds total)