Starting phenix.real_space_refine
on Wed Sep 17 03:58:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kh5_62332/09_2025/9kh5_62332_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kh5_62332/09_2025/9kh5_62332.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kh5_62332/09_2025/9kh5_62332_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kh5_62332/09_2025/9kh5_62332_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kh5_62332/09_2025/9kh5_62332.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kh5_62332/09_2025/9kh5_62332.map"
  }
  resolution = 3.74
  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=   0.003 sd=   0.032
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      19      5.16       5
     C    2353      2.51       5
     N     549      2.21       5
     O     605      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 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: 3526
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3526
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 455, 3526
          Classifications: {'peptide': 455}
          Link IDs: {'PTRANS': 20, 'TRANS': 434}
  Time building chain proxies: 1.01, per 1000 atoms: 0.29
  Number of scatterers: 3526
  At special positions: 0
  Unit cell: (71.82, 87.21, 71.82, 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      19     16.00
     O     605      8.00
     N     549      7.00
     C    2353      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.34
  Conformation dependent library (CDL) restraints added in 139.4 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  846

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      78.2% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 48
      removed outlier: 4.855A  pdb=" N   CYS A  44 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   LEU A  45 " --> pdb=" O   ASN A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 56
    Processing helix  chain 'A' and resid 57 through 67
      removed outlier: 3.790A  pdb=" N   GLY A  61 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL A  62 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   LEU A  63 " --> pdb=" O   PRO A  59 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE A  64 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
      removed outlier: 4.003A  pdb=" N   TYR A  65 " --> pdb=" O   GLY A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 97
      removed outlier: 3.554A  pdb=" N   THR A  95 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 112
    Processing helix  chain 'A' and resid 113 through 126
      removed outlier: 3.982A  pdb=" N   PHE A 117 " --> pdb=" O   GLY A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 145
    Processing helix  chain 'A' and resid 154 through 174
      removed outlier: 3.535A  pdb=" N   SER A 158 " --> pdb=" O   PRO A 154 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   PHE A 171 " --> pdb=" O   CYS A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 209
      removed outlier: 3.788A  pdb=" N   TYR A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   LEU A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   GLY A 209 " --> pdb=" O   ARG A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 240
      removed outlier: 3.850A  pdb=" N   LEU A 230 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER A 238 " --> pdb=" O   SER A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 285
      removed outlier: 3.948A  pdb=" N   LEU A 261 " --> pdb=" O   ARG A 257 " (cutoff:3.500A)
      Proline residue:  A 268  - end of helix
    Processing helix  chain 'A' and resid 286 through 293
    Processing helix  chain 'A' and resid 295 through 305
      removed outlier: 3.530A  pdb=" N   THR A 299 " --> pdb=" O   ALA A 295 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ILE A 304 " --> pdb=" O   PHE A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 340
      removed outlier: 3.946A  pdb=" N   VAL A 329 " --> pdb=" O   ASN A 325 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   ALA A 331 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   SER A 332 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 374
      removed outlier: 3.721A  pdb=" N   TYR A 372 " --> pdb=" O   MET A 368 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   CYS A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 406
      removed outlier: 3.591A  pdb=" N   LEU A 381 " --> pdb=" O   ASP A 377 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   SER A 388 " --> pdb=" O   TYR A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 434
    Processing helix  chain 'A' and resid 439 through 461
      removed outlier: 3.980A  pdb=" N   SER A 443 " --> pdb=" O   ASP A 439 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU A 454 " --> pdb=" O   ALA A 450 " (cutoff:3.500A)
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 466 through 488
    Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 352

    248 hydrogen bonds defined for protein.
    738 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: 0.54

  Time building geometry restraints manager: 0.45 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: 1049
        1.34 -     1.46: 805
        1.46 -     1.57: 1740
        1.57 -     1.69: 0
        1.69 -     1.81: 26
  Bond restraints: 3620
  Sorted by residual:
  bond pdb=" C   TYR A  65 "
       pdb=" N   SER A  66 "
    ideal  model  delta    sigma   weight residual
    1.331  1.299  0.032 1.40e-02 5.10e+03 5.35e+00
  bond pdb=" C   PHE A 148 "
       pdb=" N   PRO A 149 "
    ideal  model  delta    sigma   weight residual
    1.334  1.313  0.021 1.11e-02 8.12e+03 3.55e+00
  bond pdb=" C   ARG A 468 "
       pdb=" O   ARG A 468 "
    ideal  model  delta    sigma   weight residual
    1.244  1.228  0.016 9.80e-03 1.04e+04 2.53e+00
  bond pdb=" C   ALA A 110 "
       pdb=" N   PHE A 111 "
    ideal  model  delta    sigma   weight residual
    1.332  1.311  0.021 1.40e-02 5.10e+03 2.31e+00
  bond pdb=" CA  GLN A 380 "
       pdb=" C   GLN A 380 "
    ideal  model  delta    sigma   weight residual
    1.524  1.506  0.019 1.28e-02 6.10e+03 2.15e+00
  ... (remaining 3615 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.74: 4614
        1.74 -     3.49: 262
        3.49 -     5.23: 50
        5.23 -     6.98: 12
        6.98 -     8.72: 3
  Bond angle restraints: 4941
  Sorted by residual:
  angle pdb=" CA  SER A 217 "
        pdb=" C   SER A 217 "
        pdb=" N   PHE A 218 "
      ideal   model   delta    sigma   weight residual
     119.46  115.85    3.61 6.10e-01 2.69e+00 3.51e+01
  angle pdb=" C   GLU A 256 "
        pdb=" CA  GLU A 256 "
        pdb=" CB  GLU A 256 "
      ideal   model   delta    sigma   weight residual
     116.54  110.18    6.36 1.15e+00 7.56e-01 3.06e+01
  angle pdb=" C   LYS A 467 "
        pdb=" CA  LYS A 467 "
        pdb=" CB  LYS A 467 "
      ideal   model   delta    sigma   weight residual
     115.89  109.49    6.40 1.32e+00 5.74e-01 2.35e+01
  angle pdb=" N   CYS A 174 "
        pdb=" CA  CYS A 174 "
        pdb=" C   CYS A 174 "
      ideal   model   delta    sigma   weight residual
     112.54  106.99    5.55 1.22e+00 6.72e-01 2.07e+01
  angle pdb=" N   PHE A 356 "
        pdb=" CA  PHE A 356 "
        pdb=" C   PHE A 356 "
      ideal   model   delta    sigma   weight residual
     111.90  106.93    4.97 1.32e+00 5.74e-01 1.42e+01
  ... (remaining 4936 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 1784
       16.85 -    33.70: 215
       33.70 -    50.55: 65
       50.55 -    67.40: 22
       67.40 -    84.25: 3
  Dihedral angle restraints: 2089
    sinusoidal: 766
      harmonic: 1323
  Sorted by residual:
  dihedral pdb=" CA  GLN A 303 "
           pdb=" C   GLN A 303 "
           pdb=" N   ILE A 304 "
           pdb=" CA  ILE A 304 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.15  -26.85     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  ILE A 126 "
           pdb=" C   ILE A 126 "
           pdb=" N   ILE A 127 "
           pdb=" CA  ILE A 127 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.52  -23.48     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  LYS A 406 "
           pdb=" C   LYS A 406 "
           pdb=" N   GLU A 407 "
           pdb=" CA  GLU A 407 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.77  -20.23     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 2086 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 351
       0.034 -    0.069: 168
       0.069 -    0.103: 46
       0.103 -    0.137: 17
       0.137 -    0.172: 4
  Chirality restraints: 586
  Sorted by residual:
  chirality pdb=" CB  ILE A 228 "
            pdb=" CA  ILE A 228 "
            pdb=" CG1 ILE A 228 "
            pdb=" CG2 ILE A 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.17 2.00e-01 2.50e+01 7.37e-01
  chirality pdb=" CA  PHE A 218 "
            pdb=" N   PHE A 218 "
            pdb=" C   PHE A 218 "
            pdb=" CB  PHE A 218 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.05e-01
  chirality pdb=" CA  GLU A 128 "
            pdb=" N   GLU A 128 "
            pdb=" C   GLU A 128 "
            pdb=" CB  GLU A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.43e-01
  ... (remaining 583 not shown)

  Planarity restraints: 604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 482 "    0.009 2.00e-02 2.50e+03   1.87e-02 3.50e+00
        pdb=" C   TYR A 482 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   TYR A 482 "    0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 483 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  58 "   -0.029 5.00e-02 4.00e+02   4.42e-02 3.12e+00
        pdb=" N   PRO A  59 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A  59 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  59 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 384 "   -0.013 2.00e-02 2.50e+03   1.22e-02 2.97e+00
        pdb=" CG  TYR A 384 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 384 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 384 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 384 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 384 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 384 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 384 "    0.003 2.00e-02 2.50e+03
  ... (remaining 601 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 979
        2.77 -     3.30: 4288
        3.30 -     3.83: 6402
        3.83 -     4.37: 7474
        4.37 -     4.90: 10943
  Nonbonded interactions: 30086
  Sorted by model distance:
  nonbonded pdb=" O   GLY A  54 "
            pdb=" OG  SER A  58 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   PRO A 358 "
            pdb=" OG  SER A 361 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O   ILE A 449 "
            pdb=" OG  SER A 452 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   VAL A 329 "
            pdb=" OG  SER A 332 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   PHE A  69 "
            pdb=" OG  SER A  72 "
     model   vdw
     2.268 3.040
  ... (remaining 30081 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:             2.000
  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:          0.080
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     5.330
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
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      :  0.008   0.061   3620  Z= 0.390
  Angle     :  0.983   8.722   4941  Z= 0.600
  Chirality :  0.045   0.172    586
  Planarity :  0.005   0.044    604
  Dihedral  : 17.148  84.248   1243
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 28.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.02 %
    Favored  : 86.98 %
  Rotamer:
    Outliers :  8.97 %
    Allowed  : 14.51 %
    Favored  : 76.52 %
  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: -4.34 (0.32), residues: 453
  helix: -2.10 (0.24), residues: 321
  sheet:  None (None), residues: 0
  loop : -4.60 (0.38), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 288 
 TYR   0.030   0.002   TYR A 384 
 PHE   0.015   0.002   PHE A 430 
 TRP   0.010   0.002   TRP A 390 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00754 ( 3620)
  covalent geometry    : angle       0.98253 ( 4941)
  hydrogen bonds       : bond        0.17153 (  248)
  hydrogen bonds       : angle       7.22394 (  738)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 77
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 ARG cc_start: 0.9520 (mmp-170) cc_final: 0.9281 (mmm160)
REVERT: A  167 CYS cc_start: 0.9468 (t) cc_final: 0.8936 (p)
REVERT: A  168 LEU cc_start: 0.9759 (tt) cc_final: 0.9170 (mp)
REVERT: A  223 PHE cc_start: 0.7823 (OUTLIER) cc_final: 0.6790 (t80)
REVERT: A  240 SER cc_start: 0.7013 (p) cc_final: 0.6765 (m)
REVERT: A  247 TYR cc_start: 0.7867 (t80) cc_final: 0.7469 (t80)
  outliers start: 34
  outliers final: 13
  residues processed: 105
  average time/residue: 0.0777
  time to fit residues: 9.7652
Evaluate side-chains
  78 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 TYR
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  289 ASP
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  355 ARG
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  465 GLU
Chi-restraints excluded: chain A residue  474 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:   30.0000
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:   10.0000
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 246 ASN
** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.072335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.057994 restraints weight = 18222.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.059721 restraints weight = 10929.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.060921 restraints weight = 7695.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.061749 restraints weight = 6010.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.062148 restraints weight = 5034.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   3620  Z= 0.242
  Angle     :  0.826   8.050   4941  Z= 0.427
  Chirality :  0.047   0.172    586
  Planarity :  0.006   0.052    604
  Dihedral  : 10.506  59.142    527
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  7.39 %
    Allowed  : 19.79 %
    Favored  : 72.82 %
  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: -2.55 (0.34), residues: 453
  helix: -0.61 (0.25), residues: 325
  sheet:  None (None), residues: 0
  loop : -4.52 (0.35), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 355 
 TYR   0.025   0.002   TYR A 239 
 PHE   0.029   0.002   PHE A 392 
 TRP   0.021   0.002   TRP A 179 
 HIS   0.003   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 3620)
  covalent geometry    : angle       0.82630 ( 4941)
  hydrogen bonds       : bond        0.06597 (  248)
  hydrogen bonds       : angle       5.58280 (  738)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 72
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TRP cc_start: 0.9428 (t-100) cc_final: 0.9139 (t60)
REVERT: A  167 CYS cc_start: 0.9240 (t) cc_final: 0.8850 (p)
REVERT: A  168 LEU cc_start: 0.9725 (tt) cc_final: 0.9200 (mp)
REVERT: A  178 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8150 (pttt)
REVERT: A  223 PHE cc_start: 0.7666 (OUTLIER) cc_final: 0.6620 (t80)
REVERT: A  247 TYR cc_start: 0.7992 (t80) cc_final: 0.7574 (t80)
REVERT: A  252 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7588 (tp)
REVERT: A  472 LEU cc_start: 0.9420 (mt) cc_final: 0.9214 (pp)
  outliers start: 28
  outliers final: 17
  residues processed: 95
  average time/residue: 0.0675
  time to fit residues: 7.8949
Evaluate side-chains
  83 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  138 THR
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  178 LYS
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  252 ILE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  465 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 13 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 5 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 43 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 GLN ** 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 = 0.3526 r_free = 0.3526 target = 0.074886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.060843 restraints weight = 17524.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.062607 restraints weight = 10685.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.063876 restraints weight = 7566.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.064497 restraints weight = 5867.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.065363 restraints weight = 4959.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3620  Z= 0.163
  Angle     :  0.766   7.650   4941  Z= 0.386
  Chirality :  0.044   0.183    586
  Planarity :  0.005   0.055    604
  Dihedral  :  8.829  58.992    513
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 15.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.39 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 24.01 %
    Favored  : 69.92 %
  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: -1.23 (0.38), residues: 453
  helix:  0.43 (0.28), residues: 326
  sheet:  None (None), residues: 0
  loop : -4.24 (0.39), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 340 
 TYR   0.022   0.002   TYR A 155 
 PHE   0.023   0.002   PHE A 392 
 TRP   0.014   0.002   TRP A 390 
 HIS   0.002   0.000   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3620)
  covalent geometry    : angle       0.76619 ( 4941)
  hydrogen bonds       : bond        0.05500 (  248)
  hydrogen bonds       : angle       5.13014 (  738)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TRP cc_start: 0.9401 (t-100) cc_final: 0.9165 (t-100)
REVERT: A  167 CYS cc_start: 0.9229 (t) cc_final: 0.8854 (p)
REVERT: A  168 LEU cc_start: 0.9714 (tt) cc_final: 0.9148 (mp)
REVERT: A  223 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.6367 (t80)
REVERT: A  247 TYR cc_start: 0.7941 (t80) cc_final: 0.7616 (t80)
REVERT: A  305 PHE cc_start: 0.8412 (OUTLIER) cc_final: 0.8056 (m-10)
REVERT: A  378 ILE cc_start: 0.9382 (mp) cc_final: 0.9032 (tp)
REVERT: A  403 LEU cc_start: 0.9678 (tp) cc_final: 0.9431 (pp)
  outliers start: 23
  outliers final: 13
  residues processed: 86
  average time/residue: 0.0714
  time to fit residues: 7.6025
Evaluate side-chains
  79 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  465 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 11 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:    9.9990
   chunk 21 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 41 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    9.9990
   chunk 38 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 GLN ** 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 = 0.3534 r_free = 0.3534 target = 0.075238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.061397 restraints weight = 17210.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.063115 restraints weight = 10552.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.064031 restraints weight = 7457.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.065171 restraints weight = 5945.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.065812 restraints weight = 4863.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.4084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3620  Z= 0.162
  Angle     :  0.743   8.463   4941  Z= 0.377
  Chirality :  0.044   0.175    586
  Planarity :  0.005   0.048    604
  Dihedral  :  8.457  57.701    513
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 16.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 25.33 %
    Favored  : 69.92 %
  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: -0.70 (0.39), residues: 453
  helix:  0.74 (0.28), residues: 324
  sheet:  None (None), residues: 0
  loop : -3.72 (0.45), residues: 129

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 462 
 TYR   0.026   0.002   TYR A  65 
 PHE   0.016   0.001   PHE A 392 
 TRP   0.013   0.001   TRP A 179 
 HIS   0.002   0.001   HIS A 352 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3620)
  covalent geometry    : angle       0.74331 ( 4941)
  hydrogen bonds       : bond        0.05061 (  248)
  hydrogen bonds       : angle       5.03720 (  738)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TRP cc_start: 0.9422 (t-100) cc_final: 0.9206 (t-100)
REVERT: A  167 CYS cc_start: 0.9204 (t) cc_final: 0.8821 (p)
REVERT: A  168 LEU cc_start: 0.9699 (tt) cc_final: 0.9181 (mp)
REVERT: A  223 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6255 (t80)
REVERT: A  247 TYR cc_start: 0.7942 (t80) cc_final: 0.7674 (t80)
REVERT: A  305 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.8224 (m-80)
REVERT: A  350 MET cc_start: 0.8798 (tpp) cc_final: 0.7972 (tpp)
REVERT: A  378 ILE cc_start: 0.9450 (mp) cc_final: 0.9088 (tp)
  outliers start: 18
  outliers final: 12
  residues processed: 80
  average time/residue: 0.0618
  time to fit residues: 6.2063
Evaluate side-chains
  77 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  462 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 8 optimal weight:    7.9990
   chunk 17 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    4.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 484 GLN ** 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 = 0.3466 r_free = 0.3466 target = 0.071697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.057781 restraints weight = 18372.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.059351 restraints weight = 11050.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.060547 restraints weight = 7941.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.061177 restraints weight = 6185.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.061793 restraints weight = 5256.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.4240

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   3620  Z= 0.222
  Angle     :  0.767   9.093   4941  Z= 0.391
  Chirality :  0.044   0.166    586
  Planarity :  0.006   0.047    604
  Dihedral  :  8.391  59.644    509
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 16.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  8.18 %
    Allowed  : 24.27 %
    Favored  : 67.55 %
  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: -0.72 (0.39), residues: 453
  helix:  0.71 (0.28), residues: 326
  sheet:  None (None), residues: 0
  loop : -3.76 (0.45), residues: 127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 410 
 TYR   0.019   0.002   TYR A 155 
 PHE   0.025   0.002   PHE A 392 
 TRP   0.013   0.002   TRP A 179 
 HIS   0.002   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 3620)
  covalent geometry    : angle       0.76713 ( 4941)
  hydrogen bonds       : bond        0.05200 (  248)
  hydrogen bonds       : angle       5.14031 (  738)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 62
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 TRP cc_start: 0.9490 (t-100) cc_final: 0.9280 (t-100)
REVERT: A  167 CYS cc_start: 0.9219 (t) cc_final: 0.8808 (p)
REVERT: A  168 LEU cc_start: 0.9718 (OUTLIER) cc_final: 0.9164 (mp)
REVERT: A  214 PHE cc_start: 0.7610 (OUTLIER) cc_final: 0.7113 (t80)
REVERT: A  223 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6000 (t80)
REVERT: A  227 ASP cc_start: 0.7461 (p0) cc_final: 0.6923 (p0)
REVERT: A  302 ASP cc_start: 0.8727 (p0) cc_final: 0.8401 (p0)
REVERT: A  303 GLN cc_start: 0.9266 (OUTLIER) cc_final: 0.9002 (mm-40)
REVERT: A  305 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8292 (m-80)
REVERT: A  350 MET cc_start: 0.9092 (tpp) cc_final: 0.8347 (tpp)
REVERT: A  378 ILE cc_start: 0.9467 (mp) cc_final: 0.9106 (tp)
  outliers start: 31
  outliers final: 20
  residues processed: 83
  average time/residue: 0.0561
  time to fit residues: 5.9193
Evaluate side-chains
  82 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 57
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  240 SER
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  305 PHE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  375 VAL
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  462 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    0.0670
   chunk 31 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 36 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   overall best weight:    1.6124

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 GLN ** 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 = 0.3498 r_free = 0.3498 target = 0.073694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.060080 restraints weight = 17595.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.061642 restraints weight = 10692.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.062903 restraints weight = 7707.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.063582 restraints weight = 5943.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.064129 restraints weight = 5018.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.4664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   3620  Z= 0.156
  Angle     :  0.762   8.885   4941  Z= 0.378
  Chirality :  0.044   0.210    586
  Planarity :  0.005   0.047    604
  Dihedral  :  8.065  55.921    507
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  6.33 %
    Allowed  : 26.65 %
    Favored  : 67.02 %
  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: -0.37 (0.39), residues: 453
  helix:  1.03 (0.29), residues: 319
  sheet:  None (None), residues: 0
  loop : -3.55 (0.45), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 462 
 TYR   0.019   0.002   TYR A 155 
 PHE   0.020   0.001   PHE A 392 
 TRP   0.017   0.002   TRP A 390 
 HIS   0.001   0.000   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3620)
  covalent geometry    : angle       0.76224 ( 4941)
  hydrogen bonds       : bond        0.04911 (  248)
  hydrogen bonds       : angle       4.96032 (  738)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7457 (mmtt)
REVERT: A  121 TRP cc_start: 0.9422 (t-100) cc_final: 0.9221 (t-100)
REVERT: A  167 CYS cc_start: 0.9218 (t) cc_final: 0.8814 (p)
REVERT: A  168 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9180 (mp)
REVERT: A  223 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.5880 (t80)
REVERT: A  227 ASP cc_start: 0.7435 (p0) cc_final: 0.6914 (p0)
REVERT: A  302 ASP cc_start: 0.8677 (p0) cc_final: 0.8321 (p0)
REVERT: A  303 GLN cc_start: 0.9185 (OUTLIER) cc_final: 0.8974 (mm-40)
REVERT: A  350 MET cc_start: 0.9063 (tpp) cc_final: 0.8299 (tpp)
REVERT: A  378 ILE cc_start: 0.9454 (mp) cc_final: 0.9105 (tp)
  outliers start: 24
  outliers final: 14
  residues processed: 79
  average time/residue: 0.0639
  time to fit residues: 6.4260
Evaluate side-chains
  77 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  462 ARG
Chi-restraints excluded: chain A residue  463 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 44 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 484 GLN ** 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 = 0.3419 r_free = 0.3419 target = 0.069921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.056480 restraints weight = 18823.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.058096 restraints weight = 11118.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.059275 restraints weight = 7823.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.059908 restraints weight = 6036.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.060522 restraints weight = 5113.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.4743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   3620  Z= 0.216
  Angle     :  0.765   6.606   4941  Z= 0.389
  Chirality :  0.044   0.192    586
  Planarity :  0.006   0.061    604
  Dihedral  :  8.056  58.260    507
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  5.80 %
    Allowed  : 26.91 %
    Favored  : 67.28 %
  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: -0.35 (0.40), residues: 453
  helix:  1.06 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -3.56 (0.46), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 119 
 TYR   0.019   0.002   TYR A 247 
 PHE   0.027   0.002   PHE A 392 
 TRP   0.012   0.002   TRP A 179 
 HIS   0.002   0.001   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 3620)
  covalent geometry    : angle       0.76484 ( 4941)
  hydrogen bonds       : bond        0.05167 (  248)
  hydrogen bonds       : angle       5.08653 (  738)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.9486 (tpp) cc_final: 0.9252 (tpp)
REVERT: A  167 CYS cc_start: 0.9228 (t) cc_final: 0.8812 (p)
REVERT: A  168 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9194 (mp)
REVERT: A  378 ILE cc_start: 0.9462 (mp) cc_final: 0.9125 (tt)
  outliers start: 22
  outliers final: 16
  residues processed: 76
  average time/residue: 0.0500
  time to fit residues: 4.9329
Evaluate side-chains
  76 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 59
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  462 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 39 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:   20.0000
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 365 ASN
** A 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.070732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.057156 restraints weight = 18596.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.058874 restraints weight = 11023.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.059842 restraints weight = 7670.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.060806 restraints weight = 6095.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.061195 restraints weight = 5054.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.4936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3620  Z= 0.166
  Angle     :  0.791  12.273   4941  Z= 0.387
  Chirality :  0.044   0.200    586
  Planarity :  0.006   0.052    604
  Dihedral  :  7.925  57.507    507
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 16.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 30.34 %
    Favored  : 64.38 %
  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: -0.22 (0.40), residues: 453
  helix:  1.18 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -3.54 (0.46), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 119 
 TYR   0.017   0.002   TYR A 155 
 PHE   0.023   0.001   PHE A 392 
 TRP   0.022   0.002   TRP A 390 
 HIS   0.001   0.000   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3620)
  covalent geometry    : angle       0.79130 ( 4941)
  hydrogen bonds       : bond        0.04975 (  248)
  hydrogen bonds       : angle       4.91240 (  738)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.8116 (mmmt) cc_final: 0.7661 (mptt)
REVERT: A  167 CYS cc_start: 0.9237 (t) cc_final: 0.8818 (p)
REVERT: A  168 LEU cc_start: 0.9721 (OUTLIER) cc_final: 0.9187 (mp)
REVERT: A  227 ASP cc_start: 0.7425 (p0) cc_final: 0.6953 (p0)
REVERT: A  303 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.9037 (mm-40)
REVERT: A  378 ILE cc_start: 0.9438 (mp) cc_final: 0.9137 (tt)
  outliers start: 20
  outliers final: 16
  residues processed: 75
  average time/residue: 0.0525
  time to fit residues: 5.1009
Evaluate side-chains
  78 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  371 ILE
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  462 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    7.9990
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.072688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.058847 restraints weight = 18022.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.060625 restraints weight = 10760.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.061844 restraints weight = 7538.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.062590 restraints weight = 5820.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.063213 restraints weight = 4901.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.5326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3620  Z= 0.145
  Angle     :  0.792  12.389   4941  Z= 0.382
  Chirality :  0.043   0.196    586
  Planarity :  0.006   0.066    604
  Dihedral  :  7.621  59.177    507
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  4.75 %
    Allowed  : 31.13 %
    Favored  : 64.12 %
  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: -0.05 (0.40), residues: 453
  helix:  1.31 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -3.48 (0.46), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 119 
 TYR   0.016   0.001   TYR A 155 
 PHE   0.019   0.001   PHE A 392 
 TRP   0.031   0.002   TRP A 390 
 HIS   0.001   0.000   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3620)
  covalent geometry    : angle       0.79208 ( 4941)
  hydrogen bonds       : bond        0.04574 (  248)
  hydrogen bonds       : angle       4.72792 (  738)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 67
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7610 (mptt)
REVERT: A  167 CYS cc_start: 0.9249 (t) cc_final: 0.8840 (p)
REVERT: A  168 LEU cc_start: 0.9703 (OUTLIER) cc_final: 0.9163 (mp)
REVERT: A  303 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.9006 (mm-40)
REVERT: A  378 ILE cc_start: 0.9357 (mp) cc_final: 0.9051 (tt)
  outliers start: 18
  outliers final: 15
  residues processed: 78
  average time/residue: 0.0506
  time to fit residues: 5.1547
Evaluate side-chains
  77 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  462 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 18 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 37 optimal weight:    0.4980
   chunk 12 optimal weight:    5.9990
   chunk 31 optimal weight:   20.0000
   chunk 13 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 21 optimal weight:    0.0040
   chunk 0 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.2998

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

Flipped N/Q/H residues before XYZ refinement:
A 365 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.072976 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.059049 restraints weight = 18081.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.060910 restraints weight = 10757.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.062112 restraints weight = 7493.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.062958 restraints weight = 5781.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.063540 restraints weight = 4808.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.5445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3620  Z= 0.147
  Angle     :  0.812  12.015   4941  Z= 0.392
  Chirality :  0.044   0.197    586
  Planarity :  0.006   0.064    604
  Dihedral  :  7.481  58.903    507
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 31.93 %
    Favored  : 63.59 %
  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: -0.03 (0.40), residues: 453
  helix:  1.33 (0.29), residues: 317
  sheet:  None (None), residues: 0
  loop : -3.47 (0.46), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 288 
 TYR   0.015   0.001   TYR A 233 
 PHE   0.020   0.001   PHE A 392 
 TRP   0.030   0.002   TRP A 390 
 HIS   0.001   0.000   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3620)
  covalent geometry    : angle       0.81235 ( 4941)
  hydrogen bonds       : bond        0.04498 (  248)
  hydrogen bonds       : angle       4.75204 (  738)

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

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

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  906 Ramachandran restraints generated.
    453 Oldfield, 0 Emsley, 453 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  167 CYS cc_start: 0.9297 (t) cc_final: 0.8802 (p)
REVERT: A  168 LEU cc_start: 0.9698 (OUTLIER) cc_final: 0.9131 (mp)
REVERT: A  227 ASP cc_start: 0.7386 (p0) cc_final: 0.6896 (p0)
REVERT: A  303 GLN cc_start: 0.9395 (OUTLIER) cc_final: 0.9038 (mm-40)
REVERT: A  350 MET cc_start: 0.9035 (tpp) cc_final: 0.8758 (mmp)
REVERT: A  378 ILE cc_start: 0.9320 (mp) cc_final: 0.9035 (tt)
  outliers start: 17
  outliers final: 15
  residues processed: 77
  average time/residue: 0.0526
  time to fit residues: 5.2708
Evaluate side-chains
  78 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   90 TYR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  179 TRP
Chi-restraints excluded: chain A residue  214 PHE
Chi-restraints excluded: chain A residue  223 PHE
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 LEU
Chi-restraints excluded: chain A residue  261 LEU
Chi-restraints excluded: chain A residue  303 GLN
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain A residue  377 ASP
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  434 VAL
Chi-restraints excluded: chain A residue  437 TYR
Chi-restraints excluded: chain A residue  462 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 20 optimal weight:    8.9990
   chunk 37 optimal weight:    0.0070
   chunk 6 optimal weight:    0.5980
   chunk 27 optimal weight:    5.9990
   chunk 10 optimal weight:    0.4980
   chunk 23 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.6200

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.074152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.060191 restraints weight = 17708.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.061856 restraints weight = 10543.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.063231 restraints weight = 7490.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.064122 restraints weight = 5733.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.064631 restraints weight = 4718.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.5667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3620  Z= 0.149
  Angle     :  0.835  11.767   4941  Z= 0.399
  Chirality :  0.045   0.204    586
  Planarity :  0.006   0.063    604
  Dihedral  :  7.277  57.728    507
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 33.25 %
    Favored  : 62.80 %
  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: -0.07 (0.40), residues: 453
  helix:  1.28 (0.29), residues: 317
  sheet:  None (None), residues: 0
  loop : -3.43 (0.46), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 462 
 TYR   0.014   0.001   TYR A 233 
 PHE   0.018   0.001   PHE A 392 
 TRP   0.028   0.002   TRP A 390 
 HIS   0.001   0.000   HIS A 343 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3620)
  covalent geometry    : angle       0.83471 ( 4941)
  hydrogen bonds       : bond        0.04344 (  248)
  hydrogen bonds       : angle       4.71516 (  738)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 778.68 seconds
wall clock time: 14 minutes 14.83 seconds (854.83 seconds total)