Starting phenix.real_space_refine
on Wed Sep 17 04:53:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rfb_19117/09_2025/8rfb_19117_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rfb_19117/09_2025/8rfb_19117.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rfb_19117/09_2025/8rfb_19117.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rfb_19117/09_2025/8rfb_19117.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rfb_19117/09_2025/8rfb_19117_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rfb_19117/09_2025/8rfb_19117_neut.cif"
  }
  resolution = 4.01
  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=   0.013
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      24      5.16       5
     C    2979      2.51       5
     N     765      2.21       5
     O     864      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4632
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4632
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 597, 4632
          Classifications: {'peptide': 597}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'PTRANS': 32, 'TRANS': 564}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 221
          Unresolved non-hydrogen dihedrals: 151
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 15, 'ARG:plan': 6, 'ASP:plan': 7, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 118
  Time building chain proxies: 1.33, per 1000 atoms: 0.29
  Number of scatterers: 4632
  At special positions: 0
  Unit cell: (69.39, 74.9412, 103.622, 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      24     16.00
     O     864      8.00
     N     765      7.00
     C    2979      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 507 " - pdb=" SG  CYS A 538 " distance=2.67

  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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 203.9 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1132

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 9 sheets defined
      22.9% alpha, 30.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 149 through 152
    Processing helix  chain 'A' and resid 333 through 337
    Processing helix  chain 'A' and resid 436 through 440
    Processing helix  chain 'A' and resid 491 through 501
    Processing helix  chain 'A' and resid 516 through 522
      removed outlier: 3.816A  pdb=" N   HIS A 520 " --> pdb=" O   GLY A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 546
      removed outlier: 4.175A  pdb=" N   GLY A 531 " --> pdb=" O   LYS A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 551
      No H-bonds generated for 'chain 'A' and resid 549 through 551'
    Processing helix  chain 'A' and resid 561 through 572
    Processing helix  chain 'A' and resid 573 through 576
    Processing helix  chain 'A' and resid 587 through 593
    Processing helix  chain 'A' and resid 600 through 605
    Processing helix  chain 'A' and resid 613 through 624
    Processing helix  chain 'A' and resid 649 through 672
      removed outlier: 3.593A  pdb=" N   ILE A 653 " --> pdb=" O   PRO A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 695 through 711
    Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 117
      removed outlier: 6.584A  pdb=" N   LEU A 129 " --> pdb=" O   LEU A 145 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 163
      removed outlier: 6.515A  pdb=" N   LYS A 173 " --> pdb=" O   ASP A 159 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   ILE A 161 " --> pdb=" O   ALA A 171 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   ALA A 171 " --> pdb=" O   ILE A 161 " (cutoff:3.500A)
      removed outlier: 5.349A  pdb=" N   VAL A 163 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   TYR A 169 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   LYS A 188 " --> pdb=" O   MET A 195 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   MET A 195 " --> pdb=" O   LYS A 188 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 202 through 209
      removed outlier: 7.554A  pdb=" N   VAL A 202 " --> pdb=" O   GLN A 222 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   GLN A 222 " --> pdb=" O   VAL A 202 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   SER A 204 " --> pdb=" O   THR A 220 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   CYS A 227 " --> pdb=" O   ARG A 223 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   HIS A 228 " --> pdb=" O   THR A 246 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   THR A 246 " --> pdb=" O   HIS A 228 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL A 230 " --> pdb=" O   PHE A 244 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 253 through 258
      removed outlier: 7.476A  pdb=" N   VAL A 277 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 301 through 305
      removed outlier: 5.882A  pdb=" N   ARG A 326 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   LEU A 339 " --> pdb=" O   ARG A 326 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 354
      removed outlier: 6.958A  pdb=" N   PHE A 362 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU A 352 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   VAL A 360 " --> pdb=" O   LEU A 352 " (cutoff:3.500A)
      removed outlier: 5.238A  pdb=" N   MET A 354 " --> pdb=" O   HIS A 358 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   HIS A 358 " --> pdb=" O   MET A 354 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 395
      removed outlier: 3.524A  pdb=" N   CYS A 409 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   SER A 410 " --> pdb=" O   PRO A 414 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 441 through 445
      removed outlier: 6.257A  pdb=" N   LEU A 475 " --> pdb=" O   ALA A 505 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   CYS A 507 " --> pdb=" O   LEU A 475 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   HIS A 477 " --> pdb=" O   CYS A 507 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   LEU A 474 " --> pdb=" O   THR A 554 " (cutoff:3.500A)
      removed outlier: 7.311A  pdb=" N   THR A 556 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   VAL A 476 " --> pdb=" O   THR A 556 " (cutoff:3.500A)
      removed outlier: 8.394A  pdb=" N   PHE A 558 " --> pdb=" O   VAL A 476 " (cutoff:3.500A)
      removed outlier: 8.053A  pdb=" N   VAL A 478 " --> pdb=" O   PHE A 558 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   THR A 553 " --> pdb=" O   ALA A 578 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   THR A 580 " --> pdb=" O   THR A 553 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   LEU A 555 " --> pdb=" O   THR A 580 " (cutoff:3.500A)
      removed outlier: 8.138A  pdb=" N   GLU A 582 " --> pdb=" O   LEU A 555 " (cutoff:3.500A)
      removed outlier: 6.993A  pdb=" N   ALA A 557 " --> pdb=" O   GLU A 582 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 449

    193 hydrogen bonds defined for protein.
    528 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: 0.89

  Time building geometry restraints manager: 0.60 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 881
        1.32 -     1.45: 1301
        1.45 -     1.57: 2530
        1.57 -     1.70: 3
        1.70 -     1.83: 34
  Bond restraints: 4749
  Sorted by residual:
  bond pdb=" CA  GLY A 513 "
       pdb=" C   GLY A 513 "
    ideal  model  delta    sigma   weight residual
    1.511  1.553 -0.042 1.03e-02 9.43e+03 1.67e+01
  bond pdb=" CA  ALA A 583 "
       pdb=" C   ALA A 583 "
    ideal  model  delta    sigma   weight residual
    1.534  1.496  0.038 9.50e-03 1.11e+04 1.58e+01
  bond pdb=" N   PRO A 584 "
       pdb=" CA  PRO A 584 "
    ideal  model  delta    sigma   weight residual
    1.466  1.418  0.047 1.19e-02 7.06e+03 1.58e+01
  bond pdb=" CB  HIS A 638 "
       pdb=" CG  HIS A 638 "
    ideal  model  delta    sigma   weight residual
    1.497  1.446  0.051 1.40e-02 5.10e+03 1.34e+01
  bond pdb=" C   ASN A 271 "
       pdb=" N   LYS A 272 "
    ideal  model  delta    sigma   weight residual
    1.333  1.278  0.054 1.50e-02 4.44e+03 1.32e+01
  ... (remaining 4744 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.65: 5813
        2.65 -     5.29: 588
        5.29 -     7.94: 62
        7.94 -    10.59: 7
       10.59 -    13.24: 1
  Bond angle restraints: 6471
  Sorted by residual:
  angle pdb=" C   ASP A 249 "
        pdb=" N   PRO A 250 "
        pdb=" CA  PRO A 250 "
      ideal   model   delta    sigma   weight residual
     119.56  127.86   -8.30 1.02e+00 9.61e-01 6.62e+01
  angle pdb=" C   THR A 331 "
        pdb=" N   PRO A 332 "
        pdb=" CA  PRO A 332 "
      ideal   model   delta    sigma   weight residual
     119.56  127.40   -7.84 1.01e+00 9.80e-01 6.02e+01
  angle pdb=" C   ARG A 413 "
        pdb=" N   PRO A 414 "
        pdb=" CA  PRO A 414 "
      ideal   model   delta    sigma   weight residual
     119.66  125.07   -5.41 7.30e-01 1.88e+00 5.50e+01
  angle pdb=" C   PRO A 387 "
        pdb=" N   PRO A 388 "
        pdb=" CA  PRO A 388 "
      ideal   model   delta    sigma   weight residual
     119.56  126.87   -7.31 1.02e+00 9.61e-01 5.14e+01
  angle pdb=" N   ASN A 241 "
        pdb=" CA  ASN A 241 "
        pdb=" C   ASN A 241 "
      ideal   model   delta    sigma   weight residual
     107.98  121.22  -13.24 1.88e+00 2.83e-01 4.96e+01
  ... (remaining 6466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 2686
       17.98 -    35.96: 101
       35.96 -    53.95: 19
       53.95 -    71.93: 14
       71.93 -    89.91: 2
  Dihedral angle restraints: 2822
    sinusoidal: 1069
      harmonic: 1753
  Sorted by residual:
  dihedral pdb=" CA  ARG A 524 "
           pdb=" C   ARG A 524 "
           pdb=" N   LEU A 525 "
           pdb=" CA  LEU A 525 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.50  -20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  ASP A 713 "
           pdb=" CB  ASP A 713 "
           pdb=" CG  ASP A 713 "
           pdb=" OD1 ASP A 713 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.32   57.32     1      2.00e+01 2.50e-03 1.10e+01
  dihedral pdb=" CB  GLU A 276 "
           pdb=" CG  GLU A 276 "
           pdb=" CD  GLU A 276 "
           pdb=" OE1 GLU A 276 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.91  -89.91     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 2819 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 324
       0.056 -    0.112: 222
       0.112 -    0.168: 126
       0.168 -    0.224: 44
       0.224 -    0.280: 16
  Chirality restraints: 732
  Sorted by residual:
  chirality pdb=" CG  LEU A 589 "
            pdb=" CB  LEU A 589 "
            pdb=" CD1 LEU A 589 "
            pdb=" CD2 LEU A 589 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.87    0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  ILE A 269 "
            pdb=" N   ILE A 269 "
            pdb=" C   ILE A 269 "
            pdb=" CB  ILE A 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  LEU A 515 "
            pdb=" N   LEU A 515 "
            pdb=" C   LEU A 515 "
            pdb=" CB  LEU A 515 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.67e+00
  ... (remaining 729 not shown)

  Planarity restraints: 830
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 519 "   -0.048 2.00e-02 2.50e+03   2.78e-02 1.93e+01
        pdb=" CG  TRP A 519 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 519 "    0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 519 "    0.009 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 519 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 519 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 519 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 519 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 519 "    0.025 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 519 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 257 "   -0.041 2.00e-02 2.50e+03   2.39e-02 1.15e+01
        pdb=" CG  TYR A 257 "    0.010 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 257 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 257 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 257 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 257 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 257 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 257 "   -0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 421 "   -0.017 2.00e-02 2.50e+03   3.37e-02 1.14e+01
        pdb=" C   LYS A 421 "    0.058 2.00e-02 2.50e+03
        pdb=" O   LYS A 421 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   PHE A 422 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 827 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 240
        2.70 -     3.25: 4391
        3.25 -     3.80: 7328
        3.80 -     4.35: 9774
        4.35 -     4.90: 15427
  Nonbonded interactions: 37160
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 228 "
            pdb=" OD1 ASP A 229 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   GLU A 603 "
            pdb=" N   GLU A 606 "
     model   vdw
     2.329 3.120
  nonbonded pdb=" OD2 ASP A 396 "
            pdb=" ND2 ASN A 398 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" OD1 ASP A 210 "
            pdb=" OE1 GLU A 211 "
     model   vdw
     2.463 3.040
  nonbonded pdb=" O   LYS A 168 "
            pdb=" N   LEU A 189 "
     model   vdw
     2.463 3.120
  ... (remaining 37155 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:             0.680
  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:             0.020
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.700
  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:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
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      :  0.018   0.637   4751  Z= 1.046
  Angle     :  1.695  20.028   6473  Z= 1.193
  Chirality :  0.096   0.280    732
  Planarity :  0.010   0.099    830
  Dihedral  : 11.236  89.908   1687
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  2.45 %
    Favored  : 95.50 %
  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 aren not related in a simple way.
  whole:  0.42 (0.32), residues: 591
  helix:  0.82 (0.45), residues: 102
  sheet:  1.14 (0.36), residues: 181
  loop : -0.41 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 510 
 TYR   0.042   0.006   TYR A 257 
 PHE   0.027   0.003   PHE A 218 
 TRP   0.048   0.007   TRP A 519 
 HIS   0.008   0.002   HIS A 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.01526 ( 4749)
  covalent geometry    : angle       1.67645 ( 6471)
  SS BOND              : bond        0.63715 (    1)
  SS BOND              : angle      14.27622 (    2)
  hydrogen bonds       : bond        0.17408 (  193)
  hydrogen bonds       : angle       8.22859 (  528)
  Misc. bond           : bond        0.09024 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 215
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
REVERT: A  207 TRP cc_start: 0.8855 (m100) cc_final: 0.8527 (m100)
REVERT: A  278 TRP cc_start: 0.8463 (m100) cc_final: 0.7825 (m100)
REVERT: A  291 LEU cc_start: 0.8252 (tp) cc_final: 0.8008 (tt)
REVERT: A  347 THR cc_start: 0.8325 (p) cc_final: 0.8068 (p)
REVERT: A  357 ASP cc_start: 0.7081 (m-30) cc_final: 0.6702 (m-30)
REVERT: A  427 LEU cc_start: 0.7624 (tp) cc_final: 0.7387 (pt)
REVERT: A  429 GLU cc_start: 0.7842 (mp0) cc_final: 0.7501 (mp0)
REVERT: A  462 HIS cc_start: 0.8286 (p90) cc_final: 0.7906 (p90)
REVERT: A  601 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8487 (tt)
REVERT: A  621 LYS cc_start: 0.8190 (tttt) cc_final: 0.7846 (tppt)
  outliers start: 10
  outliers final: 1
  residues processed: 217
  average time/residue: 0.0745
  time to fit residues: 20.1839
Evaluate side-chains
  116 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 48 optimal weight:    0.1980
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    0.7980
   chunk 58 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 222 GLN
A 346 ASN
A 365 HIS
A 470 GLN
A 616 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.136164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.109220 restraints weight = 8750.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.113457 restraints weight = 4672.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.116358 restraints weight = 3021.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.118272 restraints weight = 2207.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.119786 restraints weight = 1772.075|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4751  Z= 0.161
  Angle     :  0.681   6.463   6473  Z= 0.371
  Chirality :  0.048   0.182    732
  Planarity :  0.004   0.029    830
  Dihedral  :  5.130  20.779    639
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  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 aren not related in a simple way.
  whole:  0.48 (0.33), residues: 591
  helix:  1.27 (0.47), residues: 114
  sheet:  0.77 (0.37), residues: 180
  loop : -0.28 (0.34), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 442 
 TYR   0.027   0.002   TYR A 169 
 PHE   0.011   0.002   PHE A 120 
 TRP   0.010   0.002   TRP A 502 
 HIS   0.003   0.001   HIS A 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 4749)
  covalent geometry    : angle       0.68035 ( 6471)
  SS BOND              : bond        0.00690 (    1)
  SS BOND              : angle       1.24017 (    2)
  hydrogen bonds       : bond        0.05326 (  193)
  hydrogen bonds       : angle       6.21358 (  528)
  Misc. bond           : bond        0.01347 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 ILE cc_start: 0.9139 (mm) cc_final: 0.8889 (mm)
REVERT: A  207 TRP cc_start: 0.8629 (m100) cc_final: 0.8151 (m100)
REVERT: A  223 ARG cc_start: 0.7813 (ptp-110) cc_final: 0.7548 (ptp-110)
REVERT: A  230 VAL cc_start: 0.9223 (t) cc_final: 0.8997 (p)
REVERT: A  261 ASP cc_start: 0.8808 (p0) cc_final: 0.8466 (p0)
REVERT: A  278 TRP cc_start: 0.8158 (m100) cc_final: 0.7630 (m100)
REVERT: A  346 ASN cc_start: 0.8585 (m-40) cc_final: 0.8298 (m-40)
REVERT: A  427 LEU cc_start: 0.8291 (tp) cc_final: 0.7811 (pt)
REVERT: A  558 PHE cc_start: 0.7914 (t80) cc_final: 0.7710 (t80)
REVERT: A  601 LEU cc_start: 0.8963 (pp) cc_final: 0.8610 (tt)
REVERT: A  621 LYS cc_start: 0.8180 (tttt) cc_final: 0.7376 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 154
  average time/residue: 0.0574
  time to fit residues: 11.8393
Evaluate side-chains
  103 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 11 optimal weight:    9.9990
   chunk 10 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 15 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 45 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 117 HIS
A 222 GLN
A 297 HIS
A 358 HIS
** A 477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.120913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.093559 restraints weight = 9294.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.096962 restraints weight = 5391.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.099320 restraints weight = 3710.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.100960 restraints weight = 2866.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.101882 restraints weight = 2379.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.4889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.061   4751  Z= 0.428
  Angle     :  0.978  13.358   6473  Z= 0.501
  Chirality :  0.056   0.191    732
  Planarity :  0.006   0.036    830
  Dihedral  :  6.298  25.642    639
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 15.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  :  5.52 %
    Favored  : 93.87 %
  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 aren not related in a simple way.
  whole: -0.34 (0.33), residues: 591
  helix:  0.62 (0.46), residues: 114
  sheet:  0.38 (0.37), residues: 187
  loop : -0.96 (0.35), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 382 
 TYR   0.018   0.003   TYR A 231 
 PHE   0.029   0.003   PHE A 362 
 TRP   0.014   0.003   TRP A 502 
 HIS   0.010   0.003   HIS A 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00938 ( 4749)
  covalent geometry    : angle       0.97695 ( 6471)
  SS BOND              : bond        0.01537 (    1)
  SS BOND              : angle       3.16811 (    2)
  hydrogen bonds       : bond        0.05760 (  193)
  hydrogen bonds       : angle       6.45932 (  528)
  Misc. bond           : bond        0.00762 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 115
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 TYR cc_start: 0.8141 (t80) cc_final: 0.7748 (t80)
REVERT: A  278 TRP cc_start: 0.8321 (m100) cc_final: 0.7466 (m100)
REVERT: A  370 TYR cc_start: 0.8341 (m-80) cc_final: 0.7987 (m-10)
REVERT: A  427 LEU cc_start: 0.8620 (tp) cc_final: 0.8232 (pt)
REVERT: A  519 TRP cc_start: 0.8835 (m100) cc_final: 0.8470 (m100)
REVERT: A  554 THR cc_start: 0.9429 (m) cc_final: 0.9204 (t)
REVERT: A  601 LEU cc_start: 0.9182 (pp) cc_final: 0.8835 (tt)
REVERT: A  624 CYS cc_start: 0.8911 (t) cc_final: 0.8677 (t)
REVERT: A  709 GLU cc_start: 0.8357 (mp0) cc_final: 0.8128 (mp0)
  outliers start: 3
  outliers final: 2
  residues processed: 118
  average time/residue: 0.0667
  time to fit residues: 10.1770
Evaluate side-chains
  90 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0970
   chunk 45 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0070
   chunk 37 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6200

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

Flipped N/Q/H residues before XYZ refinement:
A 241 ASN
A 407 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.131153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.102937 restraints weight = 8765.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.106840 restraints weight = 4824.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.109533 restraints weight = 3221.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.111405 restraints weight = 2433.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.112645 restraints weight = 1984.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.5181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4751  Z= 0.128
  Angle     :  0.621   6.625   6473  Z= 0.333
  Chirality :  0.046   0.179    732
  Planarity :  0.004   0.045    830
  Dihedral  :  5.144  19.159    639
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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 aren not related in a simple way.
  whole:  0.01 (0.34), residues: 591
  helix:  1.42 (0.49), residues: 112
  sheet:  0.34 (0.40), residues: 176
  loop : -0.72 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 494 
 TYR   0.037   0.002   TYR A 623 
 PHE   0.016   0.002   PHE A 235 
 TRP   0.034   0.003   TRP A 207 
 HIS   0.006   0.001   HIS A 228 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4749)
  covalent geometry    : angle       0.62001 ( 6471)
  SS BOND              : bond        0.00866 (    1)
  SS BOND              : angle       1.75114 (    2)
  hydrogen bonds       : bond        0.04252 (  193)
  hydrogen bonds       : angle       5.42692 (  528)
  Misc. bond           : bond        0.00215 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7433 (t) cc_final: 0.7213 (p)
REVERT: A  173 LYS cc_start: 0.8331 (pttm) cc_final: 0.8065 (ttpp)
REVERT: A  207 TRP cc_start: 0.8636 (m100) cc_final: 0.8323 (m100)
REVERT: A  217 LEU cc_start: 0.9031 (tp) cc_final: 0.8712 (tp)
REVERT: A  223 ARG cc_start: 0.7858 (ptp-170) cc_final: 0.7546 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7775 (m-80) cc_final: 0.7312 (m-10)
REVERT: A  238 ASN cc_start: 0.7876 (m-40) cc_final: 0.7662 (m-40)
REVERT: A  245 TYR cc_start: 0.8241 (t80) cc_final: 0.7873 (t80)
REVERT: A  278 TRP cc_start: 0.8217 (m100) cc_final: 0.7981 (m100)
REVERT: A  427 LEU cc_start: 0.8563 (tp) cc_final: 0.8141 (pt)
REVERT: A  488 MET cc_start: 0.8814 (mmm) cc_final: 0.7878 (mmm)
REVERT: A  490 PHE cc_start: 0.9242 (t80) cc_final: 0.8974 (t80)
REVERT: A  500 ASP cc_start: 0.8741 (t0) cc_final: 0.8457 (t0)
REVERT: A  601 LEU cc_start: 0.9046 (pp) cc_final: 0.8750 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0523
  time to fit residues: 9.5992
Evaluate side-chains
  97 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 0 optimal weight:   50.0000
   chunk 52 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0370
   chunk 44 optimal weight:    0.2980
   chunk 47 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0050
   chunk 12 optimal weight:    8.9990
   overall best weight:    1.2676

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

Flipped N/Q/H residues before XYZ refinement:
A 336 ASN
A 702 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.130698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.101740 restraints weight = 9010.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.105617 restraints weight = 5049.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.108213 restraints weight = 3414.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.110029 restraints weight = 2619.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.111227 restraints weight = 2156.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.5470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4751  Z= 0.144
  Angle     :  0.623   6.723   6473  Z= 0.334
  Chirality :  0.045   0.150    732
  Planarity :  0.004   0.036    830
  Dihedral  :  4.895  16.999    639
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  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 aren not related in a simple way.
  whole: -0.02 (0.34), residues: 591
  helix:  1.27 (0.48), residues: 113
  sheet:  0.38 (0.39), residues: 180
  loop : -0.73 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 494 
 TYR   0.018   0.002   TYR A 301 
 PHE   0.015   0.002   PHE A 705 
 TRP   0.027   0.003   TRP A 519 
 HIS   0.007   0.001   HIS A 462 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 4749)
  covalent geometry    : angle       0.62228 ( 6471)
  SS BOND              : bond        0.00932 (    1)
  SS BOND              : angle       1.58255 (    2)
  hydrogen bonds       : bond        0.04026 (  193)
  hydrogen bonds       : angle       5.36168 (  528)
  Misc. bond           : bond        0.00194 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 TRP cc_start: 0.8616 (m100) cc_final: 0.7694 (m100)
REVERT: A  223 ARG cc_start: 0.7885 (ptp-170) cc_final: 0.7624 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7664 (m-80) cc_final: 0.7156 (m-10)
REVERT: A  238 ASN cc_start: 0.8007 (m-40) cc_final: 0.7744 (m-40)
REVERT: A  245 TYR cc_start: 0.8153 (t80) cc_final: 0.7708 (t80)
REVERT: A  427 LEU cc_start: 0.8590 (tp) cc_final: 0.8195 (pt)
REVERT: A  488 MET cc_start: 0.8813 (mmm) cc_final: 0.7939 (mmm)
REVERT: A  490 PHE cc_start: 0.9248 (t80) cc_final: 0.8919 (t80)
REVERT: A  500 ASP cc_start: 0.8841 (t0) cc_final: 0.8390 (t0)
REVERT: A  601 LEU cc_start: 0.9099 (pp) cc_final: 0.8792 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0539
  time to fit residues: 8.5815
Evaluate side-chains
  92 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   chunk 9 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 33 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 0 optimal weight:   50.0000
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 228 HIS
A 346 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.131681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.102545 restraints weight = 9071.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.106434 restraints weight = 5137.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.109029 restraints weight = 3482.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.110843 restraints weight = 2656.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.112026 restraints weight = 2188.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.5573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4751  Z= 0.123
  Angle     :  0.575   6.132   6473  Z= 0.309
  Chirality :  0.044   0.151    732
  Planarity :  0.004   0.039    830
  Dihedral  :  4.694  16.247    639
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.07 %
    Favored  : 96.52 %
  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 aren not related in a simple way.
  whole:  0.10 (0.34), residues: 591
  helix:  1.54 (0.49), residues: 112
  sheet:  0.45 (0.40), residues: 176
  loop : -0.71 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 494 
 TYR   0.017   0.001   TYR A 623 
 PHE   0.016   0.001   PHE A 705 
 TRP   0.023   0.002   TRP A 389 
 HIS   0.002   0.001   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 4749)
  covalent geometry    : angle       0.57438 ( 6471)
  SS BOND              : bond        0.00719 (    1)
  SS BOND              : angle       1.29416 (    2)
  hydrogen bonds       : bond        0.03822 (  193)
  hydrogen bonds       : angle       5.19400 (  528)
  Misc. bond           : bond        0.00154 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8204 (mt-10)
REVERT: A  189 LEU cc_start: 0.8169 (mt) cc_final: 0.7739 (tp)
REVERT: A  207 TRP cc_start: 0.8580 (m100) cc_final: 0.7638 (m100)
REVERT: A  223 ARG cc_start: 0.7861 (ptp-170) cc_final: 0.7606 (ptp-170)
REVERT: A  231 TYR cc_start: 0.7720 (m-80) cc_final: 0.7233 (m-10)
REVERT: A  238 ASN cc_start: 0.7938 (m-40) cc_final: 0.7701 (m-40)
REVERT: A  245 TYR cc_start: 0.8200 (t80) cc_final: 0.7672 (t80)
REVERT: A  347 THR cc_start: 0.8933 (m) cc_final: 0.8580 (p)
REVERT: A  427 LEU cc_start: 0.8589 (tp) cc_final: 0.8196 (pt)
REVERT: A  488 MET cc_start: 0.8789 (mmm) cc_final: 0.8003 (mmm)
REVERT: A  490 PHE cc_start: 0.9192 (t80) cc_final: 0.8952 (t80)
REVERT: A  500 ASP cc_start: 0.8834 (t0) cc_final: 0.8378 (t0)
REVERT: A  558 PHE cc_start: 0.8348 (t80) cc_final: 0.8002 (t80)
REVERT: A  601 LEU cc_start: 0.9105 (pp) cc_final: 0.8815 (tt)
REVERT: A  621 LYS cc_start: 0.8536 (tttt) cc_final: 0.7920 (tppt)
  outliers start: 2
  outliers final: 2
  residues processed: 120
  average time/residue: 0.0568
  time to fit residues: 9.1865
Evaluate side-chains
  101 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 32 optimal weight:    8.9990
   chunk 53 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 48 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 0 optimal weight:   50.0000
   chunk 24 optimal weight:    0.8980
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.126335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.096568 restraints weight = 9089.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.100180 restraints weight = 5277.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.102625 restraints weight = 3677.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.104360 restraints weight = 2868.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.105478 restraints weight = 2397.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.5909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   4751  Z= 0.258
  Angle     :  0.704   7.763   6473  Z= 0.372
  Chirality :  0.047   0.154    732
  Planarity :  0.004   0.037    830
  Dihedral  :  5.136  19.241    639
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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 aren not related in a simple way.
  whole: -0.26 (0.34), residues: 591
  helix:  1.30 (0.48), residues: 110
  sheet:  0.15 (0.40), residues: 178
  loop : -0.91 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 495 
 TYR   0.014   0.002   TYR A 301 
 PHE   0.023   0.002   PHE A 705 
 TRP   0.027   0.003   TRP A 389 
 HIS   0.007   0.002   HIS A 508 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 4749)
  covalent geometry    : angle       0.70297 ( 6471)
  SS BOND              : bond        0.01017 (    1)
  SS BOND              : angle       2.14617 (    2)
  hydrogen bonds       : bond        0.04393 (  193)
  hydrogen bonds       : angle       5.49665 (  528)
  Misc. bond           : bond        0.00224 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 VAL cc_start: 0.7768 (t) cc_final: 0.7532 (p)
REVERT: A  167 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8384 (mt-10)
REVERT: A  207 TRP cc_start: 0.8659 (m100) cc_final: 0.8002 (m100)
REVERT: A  245 TYR cc_start: 0.8157 (t80) cc_final: 0.7626 (t80)
REVERT: A  427 LEU cc_start: 0.8659 (tp) cc_final: 0.8185 (pt)
REVERT: A  462 HIS cc_start: 0.8799 (p90) cc_final: 0.8566 (p90)
REVERT: A  493 GLU cc_start: 0.8873 (pm20) cc_final: 0.8650 (pm20)
REVERT: A  601 LEU cc_start: 0.9210 (pp) cc_final: 0.8922 (tt)
REVERT: A  621 LYS cc_start: 0.8720 (tttt) cc_final: 0.8068 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0594
  time to fit residues: 8.7712
Evaluate side-chains
  86 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 23 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 6 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.130421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.100790 restraints weight = 9102.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.104517 restraints weight = 5204.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.107114 restraints weight = 3599.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.108971 restraints weight = 2769.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.110171 restraints weight = 2295.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.6016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4751  Z= 0.130
  Angle     :  0.615  10.992   6473  Z= 0.322
  Chirality :  0.046   0.151    732
  Planarity :  0.004   0.037    830
  Dihedral  :  4.791  17.459    639
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.23 %
    Favored  : 98.57 %
  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 aren not related in a simple way.
  whole: -0.15 (0.34), residues: 591
  helix:  1.37 (0.49), residues: 113
  sheet:  0.16 (0.41), residues: 171
  loop : -0.78 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 223 
 TYR   0.017   0.001   TYR A 623 
 PHE   0.011   0.001   PHE A 120 
 TRP   0.031   0.002   TRP A 389 
 HIS   0.004   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4749)
  covalent geometry    : angle       0.61446 ( 6471)
  SS BOND              : bond        0.00786 (    1)
  SS BOND              : angle       1.69989 (    2)
  hydrogen bonds       : bond        0.04002 (  193)
  hydrogen bonds       : angle       5.29323 (  528)
  Misc. bond           : bond        0.00159 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 TRP cc_start: 0.8634 (m100) cc_final: 0.8073 (m100)
REVERT: A  223 ARG cc_start: 0.7819 (ptp-170) cc_final: 0.7479 (ptp-170)
REVERT: A  231 TYR cc_start: 0.8067 (m-80) cc_final: 0.7643 (m-10)
REVERT: A  245 TYR cc_start: 0.8279 (t80) cc_final: 0.7764 (t80)
REVERT: A  327 THR cc_start: 0.7525 (m) cc_final: 0.7032 (m)
REVERT: A  427 LEU cc_start: 0.8569 (tp) cc_final: 0.8105 (pt)
REVERT: A  495 ARG cc_start: 0.8854 (tpt-90) cc_final: 0.8455 (tpt-90)
REVERT: A  558 PHE cc_start: 0.8423 (t80) cc_final: 0.8196 (t80)
REVERT: A  601 LEU cc_start: 0.9188 (pp) cc_final: 0.8901 (tt)
REVERT: A  621 LYS cc_start: 0.8570 (tttt) cc_final: 0.7967 (tppt)
  outliers start: 1
  outliers final: 1
  residues processed: 114
  average time/residue: 0.0586
  time to fit residues: 8.9761
Evaluate side-chains
  90 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   chunk 8 optimal weight:    6.9990
   chunk 42 optimal weight:    2.9990
   chunk 43 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN
A 702 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.131278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.101646 restraints weight = 8836.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.105454 restraints weight = 4983.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.108085 restraints weight = 3401.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.109818 restraints weight = 2605.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.111148 restraints weight = 2173.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.6090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4751  Z= 0.125
  Angle     :  0.589   6.662   6473  Z= 0.313
  Chirality :  0.045   0.151    732
  Planarity :  0.004   0.036    830
  Dihedral  :  4.653  16.290    639
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  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 aren not related in a simple way.
  whole: -0.09 (0.34), residues: 591
  helix:  1.57 (0.50), residues: 112
  sheet:  0.09 (0.41), residues: 173
  loop : -0.74 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 495 
 TYR   0.016   0.001   TYR A 623 
 PHE   0.019   0.001   PHE A 244 
 TRP   0.035   0.002   TRP A 389 
 HIS   0.004   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 4749)
  covalent geometry    : angle       0.58889 ( 6471)
  SS BOND              : bond        0.00790 (    1)
  SS BOND              : angle       1.24875 (    2)
  hydrogen bonds       : bond        0.04018 (  193)
  hydrogen bonds       : angle       5.18070 (  528)
  Misc. bond           : bond        0.00159 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8296 (mt-10)
REVERT: A  207 TRP cc_start: 0.8559 (m100) cc_final: 0.8199 (m100)
REVERT: A  223 ARG cc_start: 0.7897 (ptp-170) cc_final: 0.7586 (ptp-170)
REVERT: A  231 TYR cc_start: 0.8009 (m-80) cc_final: 0.7583 (m-10)
REVERT: A  245 TYR cc_start: 0.8177 (t80) cc_final: 0.7667 (t80)
REVERT: A  327 THR cc_start: 0.7503 (m) cc_final: 0.7008 (m)
REVERT: A  343 MET cc_start: 0.8512 (mtp) cc_final: 0.8268 (mtm)
REVERT: A  347 THR cc_start: 0.8995 (m) cc_final: 0.8619 (p)
REVERT: A  427 LEU cc_start: 0.8624 (tp) cc_final: 0.8210 (pt)
REVERT: A  495 ARG cc_start: 0.8799 (tpt-90) cc_final: 0.8353 (tpt-90)
REVERT: A  500 ASP cc_start: 0.9041 (t0) cc_final: 0.8624 (t0)
REVERT: A  558 PHE cc_start: 0.8437 (t80) cc_final: 0.8230 (t80)
REVERT: A  601 LEU cc_start: 0.9195 (pp) cc_final: 0.8920 (tt)
REVERT: A  621 LYS cc_start: 0.8615 (tttt) cc_final: 0.7917 (tppt)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0560
  time to fit residues: 8.9127
Evaluate side-chains
  92 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0570
   chunk 31 optimal weight:    9.9990
   chunk 42 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 33 optimal weight:    6.9990
   chunk 44 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   overall best weight:    1.3702

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN
A 644 ASN
** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.131111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.101499 restraints weight = 9003.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.105333 restraints weight = 5104.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.107887 restraints weight = 3505.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.109676 restraints weight = 2706.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.110902 restraints weight = 2250.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.6178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4751  Z= 0.143
  Angle     :  0.591   6.129   6473  Z= 0.315
  Chirality :  0.046   0.216    732
  Planarity :  0.004   0.037    830
  Dihedral  :  4.672  15.604    639
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  0.20 %
    Favored  : 99.39 %
  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 aren not related in a simple way.
  whole: -0.10 (0.34), residues: 591
  helix:  1.54 (0.50), residues: 112
  sheet:  0.06 (0.41), residues: 173
  loop : -0.73 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 495 
 TYR   0.013   0.001   TYR A 707 
 PHE   0.020   0.002   PHE A 244 
 TRP   0.031   0.002   TRP A 389 
 HIS   0.008   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 4749)
  covalent geometry    : angle       0.59070 ( 6471)
  SS BOND              : bond        0.00811 (    1)
  SS BOND              : angle       1.37777 (    2)
  hydrogen bonds       : bond        0.04041 (  193)
  hydrogen bonds       : angle       5.07418 (  528)
  Misc. bond           : bond        0.00170 (    1)

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

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

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1182 Ramachandran restraints generated.
    591 Oldfield, 0 Emsley, 591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 114
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8322 (mt-10)
REVERT: A  207 TRP cc_start: 0.8574 (m100) cc_final: 0.8275 (m100)
REVERT: A  223 ARG cc_start: 0.7842 (ptp-170) cc_final: 0.7594 (ptp-170)
REVERT: A  231 TYR cc_start: 0.8028 (m-80) cc_final: 0.7616 (m-10)
REVERT: A  245 TYR cc_start: 0.8087 (t80) cc_final: 0.7601 (t80)
REVERT: A  327 THR cc_start: 0.7504 (m) cc_final: 0.7009 (m)
REVERT: A  427 LEU cc_start: 0.8660 (tp) cc_final: 0.8181 (pt)
REVERT: A  495 ARG cc_start: 0.8829 (tpt-90) cc_final: 0.8427 (tpt-90)
REVERT: A  500 ASP cc_start: 0.9002 (t0) cc_final: 0.8681 (t0)
REVERT: A  514 GLU cc_start: 0.7406 (pm20) cc_final: 0.7171 (pm20)
REVERT: A  558 PHE cc_start: 0.8410 (t80) cc_final: 0.8205 (t80)
REVERT: A  601 LEU cc_start: 0.9186 (pp) cc_final: 0.8926 (tt)
REVERT: A  621 LYS cc_start: 0.8630 (tttt) cc_final: 0.7969 (tppt)
  outliers start: 2
  outliers final: 1
  residues processed: 114
  average time/residue: 0.0612
  time to fit residues: 9.2456
Evaluate side-chains
  93 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 30 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 52 optimal weight:    8.9990
   chunk 40 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    0.2980
   chunk 8 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
A 346 ASN
A 644 ASN
A 679 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.129223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.099154 restraints weight = 9034.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.102946 restraints weight = 5170.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.105448 restraints weight = 3570.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.107251 restraints weight = 2770.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.108513 restraints weight = 2313.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.6273

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   4751  Z= 0.166
  Angle     :  0.604   5.989   6473  Z= 0.325
  Chirality :  0.045   0.173    732
  Planarity :  0.004   0.036    830
  Dihedral  :  4.688  16.924    639
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.41 %
    Favored  : 99.39 %
  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 aren not related in a simple way.
  whole: -0.16 (0.34), residues: 591
  helix:  1.50 (0.50), residues: 112
  sheet:  0.05 (0.41), residues: 173
  loop : -0.78 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 495 
 TYR   0.013   0.001   TYR A 301 
 PHE   0.019   0.002   PHE A 244 
 TRP   0.030   0.002   TRP A 389 
 HIS   0.004   0.001   HIS A 477 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 4749)
  covalent geometry    : angle       0.60338 ( 6471)
  SS BOND              : bond        0.00830 (    1)
  SS BOND              : angle       1.59917 (    2)
  hydrogen bonds       : bond        0.04326 (  193)
  hydrogen bonds       : angle       5.15069 (  528)
  Misc. bond           : bond        0.00178 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 899.95 seconds
wall clock time: 16 minutes 18.87 seconds (978.87 seconds total)