Starting phenix.real_space_refine
on Wed Jun  3 10:01:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9k8y_62182/06_2026/9k8y_62182.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9k8y_62182/06_2026/9k8y_62182.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9k8y_62182/06_2026/9k8y_62182.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9k8y_62182/06_2026/9k8y_62182.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9k8y_62182/06_2026/9k8y_62182.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9k8y_62182/06_2026/9k8y_62182.map"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    1933      2.51       5
     N     447      2.21       5
     O     484      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2888
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2869
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 361, 2869
          Classifications: {'peptide': 361}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 351}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "A"
      Number of atoms: 19
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 19
          Unusual residues: {'NOS%rna2p': 1}
          Classifications: {'undetermined': 1}
          Modifications used: {'rna2p': 1}
  Time building chain proxies: 0.91, per 1000 atoms: 0.32
  Number of scatterers: 2888
  At special positions: 0
  Unit cell: (77, 55, 74.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O     484      8.00
     N     447      7.00
     C    1933      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 144 " - pdb=" SG  CYS A 375 " distance=2.04

  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: 0.19
  Conformation dependent library (CDL) restraints added in 122.2 milliseconds
  

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  680

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      90.6% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 59
      removed outlier: 3.643A  pdb=" N   LEU A  50 " --> pdb=" O   GLY A  46 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   VAL A  52 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   TRP A  53 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 83
      removed outlier: 3.981A  pdb=" N   ASN A  66 " --> pdb=" O   ASN A  62 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   LEU A  81 " --> pdb=" O   SER A  77 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   PHE A  82 " --> pdb=" O   ILE A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 88
      No H-bonds generated for 'chain 'A' and resid 86 through 88'
    Processing helix  chain 'A' and resid 89 through 111
      removed outlier: 3.588A  pdb=" N   SER A 109 " --> pdb=" O   GLN A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 145
      removed outlier: 3.791A  pdb=" N   ILE A 125 " --> pdb=" O   LEU A 121 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   CYS A 144 " --> pdb=" O   ASN A 140 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   MET A 145 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 175
      removed outlier: 4.277A  pdb=" N   GLY A 161 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   VAL A 162 " --> pdb=" O   GLY A 158 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLN A 173 " --> pdb=" O   LEU A 169 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 210
    Processing helix  chain 'A' and resid 231 through 257
      removed outlier: 5.968A  pdb=" N   LYS A 241 " --> pdb=" O   LYS A 237 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   ALA A 242 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ASN A 250 " --> pdb=" O   MET A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 270
    Processing helix  chain 'A' and resid 272 through 292
      removed outlier: 3.724A  pdb=" N   ARG A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   TYR A 292 " --> pdb=" O   PHE A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 297
      removed outlier: 3.667A  pdb=" N   THR A 297 " --> pdb=" O   PRO A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 306
      removed outlier: 4.541A  pdb=" N   ASN A 304 " --> pdb=" O   ILE A 301 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   THR A 306 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 319
    Processing helix  chain 'A' and resid 321 through 332
      removed outlier: 3.676A  pdb=" N   TRP A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 339
    Processing helix  chain 'A' and resid 339 through 358
    Processing helix  chain 'A' and resid 359 through 368
      removed outlier: 3.630A  pdb=" N   LEU A 363 " --> pdb=" O   THR A 359 " (cutoff:3.500A)
      removed outlier: 5.073A  pdb=" N   VAL A 366 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   LYS A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 400
    Processing helix  chain 'A' and resid 401 through 406
    Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 180

    231 hydrogen bonds defined for protein.
    669 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: 0.43

  Time building geometry restraints manager: 0.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 846
        1.35 -     1.47: 775
        1.47 -     1.59: 1308
        1.59 -     1.71: 0
        1.71 -     1.83: 35
  Bond restraints: 2964
  Sorted by residual:
  bond pdb=" N   VAL A  52 "
       pdb=" CA  VAL A  52 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.034 1.17e-02 7.31e+03 8.41e+00
  bond pdb=" N   ILE A 137 "
       pdb=" CA  ILE A 137 "
    ideal  model  delta    sigma   weight residual
    1.462  1.494 -0.032 1.14e-02 7.69e+03 7.82e+00
  bond pdb=" N   ASN A  51 "
       pdb=" CA  ASN A  51 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.23e-02 6.61e+03 7.06e+00
  bond pdb=" N   ASN A 354 "
       pdb=" CA  ASN A 354 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.23e-02 6.61e+03 6.23e+00
  bond pdb=" N   LEU A  50 "
       pdb=" CA  LEU A  50 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.032 1.31e-02 5.83e+03 6.15e+00
  ... (remaining 2959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 3759
        1.10 -     2.21: 190
        2.21 -     3.31: 47
        3.31 -     4.41: 16
        4.41 -     5.51: 11
  Bond angle restraints: 4023
  Sorted by residual:
  angle pdb=" N   ASN A 250 "
        pdb=" CA  ASN A 250 "
        pdb=" C   ASN A 250 "
      ideal   model   delta    sigma   weight residual
     111.14  105.63    5.51 1.08e+00 8.57e-01 2.61e+01
  angle pdb=" N   ASP A 287 "
        pdb=" CA  ASP A 287 "
        pdb=" C   ASP A 287 "
      ideal   model   delta    sigma   weight residual
     111.07  105.73    5.34 1.07e+00 8.73e-01 2.49e+01
  angle pdb=" C   VAL A 249 "
        pdb=" N   ASN A 250 "
        pdb=" CA  ASN A 250 "
      ideal   model   delta    sigma   weight residual
     120.44  115.25    5.19 1.36e+00 5.41e-01 1.46e+01
  angle pdb=" C   GLN A 135 "
        pdb=" CA  GLN A 135 "
        pdb=" CB  GLN A 135 "
      ideal   model   delta    sigma   weight residual
     110.92  116.20   -5.28 1.59e+00 3.96e-01 1.10e+01
  angle pdb=" O   LEU A 133 "
        pdb=" C   LEU A 133 "
        pdb=" N   ALA A 134 "
      ideal   model   delta    sigma   weight residual
     122.07  125.39   -3.32 1.03e+00 9.43e-01 1.04e+01
  ... (remaining 4018 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.92: 1540
       12.92 -    25.84: 127
       25.84 -    38.76: 43
       38.76 -    51.69: 8
       51.69 -    64.61: 2
  Dihedral angle restraints: 1720
    sinusoidal: 670
      harmonic: 1050
  Sorted by residual:
  dihedral pdb=" CB  CYS A 144 "
           pdb=" SG  CYS A 144 "
           pdb=" SG  CYS A 375 "
           pdb=" CB  CYS A 375 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -128.16   42.16     1      1.00e+01 1.00e-02 2.48e+01
  dihedral pdb=" CD  ARG A 291 "
           pdb=" NE  ARG A 291 "
           pdb=" CZ  ARG A 291 "
           pdb=" NH1 ARG A 291 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -31.93   31.93     1      1.00e+01 1.00e-02 1.45e+01
  dihedral pdb=" CA  PHE A 307 "
           pdb=" C   PHE A 307 "
           pdb=" N   SER A 308 "
           pdb=" CA  SER A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.56   15.44     0      5.00e+00 4.00e-02 9.54e+00
  ... (remaining 1717 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 322
       0.041 -    0.081: 117
       0.081 -    0.122: 33
       0.122 -    0.162: 1
       0.162 -    0.203: 2
  Chirality restraints: 475
  Sorted by residual:
  chirality pdb=" CA  ILE A 137 "
            pdb=" N   ILE A 137 "
            pdb=" C   ILE A 137 "
            pdb=" CB  ILE A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  VAL A  52 "
            pdb=" N   VAL A  52 "
            pdb=" C   VAL A  52 "
            pdb=" CB  VAL A  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.86e-01
  chirality pdb=" CA  ASN A 354 "
            pdb=" N   ASN A 354 "
            pdb=" C   ASN A 354 "
            pdb=" CB  ASN A 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.32e-01
  ... (remaining 472 not shown)

  Planarity restraints: 482
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 291 "   -0.592 9.50e-02 1.11e+02   2.65e-01 4.30e+01
        pdb=" NE  ARG A 291 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 291 "    0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 291 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 291 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 353 "    0.014 2.00e-02 2.50e+03   2.75e-02 7.56e+00
        pdb=" C   THR A 353 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   THR A 353 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ASN A 354 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 249 "   -0.009 2.00e-02 2.50e+03   1.87e-02 3.48e+00
        pdb=" C   VAL A 249 "    0.032 2.00e-02 2.50e+03
        pdb=" O   VAL A 249 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASN A 250 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 479 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 1051
        2.87 -     3.38: 3041
        3.38 -     3.88: 4853
        3.88 -     4.39: 5427
        4.39 -     4.90: 8976
  Nonbonded interactions: 23348
  Sorted by model distance:
  nonbonded pdb=" O   GLY A  46 "
            pdb=" OG  SER A  49 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" OD1 ASP A 172 "
            pdb=" NZ  LYS A 187 "
     model   vdw
     2.378 3.120
  nonbonded pdb=" NZ  LYS A 241 "
            pdb=" OD1 ASN A 310 "
     model   vdw
     2.483 3.120
  nonbonded pdb=" OH  TYR A  65 "
            pdb=" OD1 ASP A 117 "
     model   vdw
     2.527 3.040
  nonbonded pdb=" O   LEU A 133 "
            pdb=" C   ALA A 134 "
     model   vdw
     2.533 3.270
  ... (remaining 23343 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:             1.120
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.600
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5537
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      :  0.004   0.034   2965  Z= 0.259
  Angle     :  0.669   5.515   4025  Z= 0.434
  Chirality :  0.044   0.203    475
  Planarity :  0.013   0.265    482
  Dihedral  : 11.183  64.608   1037
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.77 %
    Favored  : 95.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.43), residues: 357
  helix:  1.55 (0.29), residues: 286
  sheet:  None (None), residues: 0
  loop : -0.22 (0.80), residues: 71

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 319 
 TYR   0.009   0.001   TYR A 119 
 PHE   0.019   0.002   PHE A 394 
 TRP   0.014   0.002   TRP A 398 
 HIS   0.004   0.001   HIS A  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.26 ( 2964)
  covalent geometry    : angle       0.66886 /  0.43 ( 4023)
  SS BOND              : bond        0.00575 /  0.30 (    1)
  SS BOND              : angle       1.30890 /  0.72 (    2)
  hydrogen bonds       : bond        0.14383 /  9.48 (  231)
  hydrogen bonds       : angle       5.71250 /  4.13 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.090 
Fit side-chains
REVERT: A   59 LEU cc_start: 0.6340 (mt) cc_final: 0.5497 (tt)
REVERT: A   67 THR cc_start: 0.7711 (m) cc_final: 0.7509 (p)
REVERT: A  115 GLN cc_start: 0.4352 (mt0) cc_final: 0.3862 (mm-40)
REVERT: A  326 PHE cc_start: 0.8155 (m-80) cc_final: 0.7864 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 117
  average time/residue: 0.0621
  time to fit residues: 8.7732
Evaluate side-chains
  64 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 63
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0270
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0670
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.2776

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 262 HIS
A 316 ASN
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.217851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.191583 restraints weight = 5028.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.197063 restraints weight = 2828.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.201038 restraints weight = 1820.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.203834 restraints weight = 1290.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.205856 restraints weight = 986.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.4549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5835
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   2965  Z= 0.165
  Angle     :  0.627   6.444   4025  Z= 0.328
  Chirality :  0.044   0.181    475
  Planarity :  0.004   0.035    482
  Dihedral  :  5.376  59.179    398
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 14.15 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.44), residues: 357
  helix:  1.99 (0.29), residues: 293
  sheet:  None (None), residues: 0
  loop :  0.59 (0.94), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  60 
 TYR   0.020   0.002   TYR A 181 
 PHE   0.016   0.001   PHE A 104 
 TRP   0.015   0.001   TRP A 356 
 HIS   0.009   0.002   HIS A 262 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.17 ( 2964)
  covalent geometry    : angle       0.62744 /  0.33 ( 4023)
  SS BOND              : bond        0.00155 /  0.08 (    1)
  SS BOND              : angle       0.26622 /  0.14 (    2)
  hydrogen bonds       : bond        0.05625 /  3.73 (  231)
  hydrogen bonds       : angle       4.25141 /  2.97 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 PHE cc_start: 0.7512 (m-80) cc_final: 0.7264 (m-80)
REVERT: A   71 THR cc_start: 0.9119 (OUTLIER) cc_final: 0.8707 (t)
REVERT: A  153 MET cc_start: 0.7235 (tpp) cc_final: 0.6980 (tpp)
REVERT: A  255 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.5893 (tp40)
REVERT: A  398 TRP cc_start: 0.7538 (m100) cc_final: 0.6694 (t-100)
  outliers start: 17
  outliers final: 9
  residues processed: 76
  average time/residue: 0.0504
  time to fit residues: 4.8518
Evaluate side-chains
  68 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  306 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 108 HIS
** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 184 ASN ** 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 = 0.4497 r_free = 0.4497 target = 0.196831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.174119 restraints weight = 5473.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.179205 restraints weight = 2907.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.182575 restraints weight = 1794.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.184861 restraints weight = 1250.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.186493 restraints weight = 948.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.4397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6278
moved from start:          0.5444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   2965  Z= 0.210
  Angle     :  0.730   8.304   4025  Z= 0.386
  Chirality :  0.046   0.159    475
  Planarity :  0.005   0.037    482
  Dihedral  :  5.909  59.780    398
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 18.87 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.43), residues: 357
  helix:  1.36 (0.28), residues: 296
  sheet:  None (None), residues: 0
  loop :  0.19 (0.97), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  60 
 TYR   0.015   0.003   TYR A 181 
 PHE   0.019   0.002   PHE A 288 
 TRP   0.022   0.002   TRP A 356 
 HIS   0.005   0.002   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00471 /  0.21 ( 2964)
  covalent geometry    : angle       0.73006 /  0.39 ( 4023)
  SS BOND              : bond        0.00450 /  0.24 (    1)
  SS BOND              : angle       0.67231 /  0.39 (    2)
  hydrogen bonds       : bond        0.06849 /  4.70 (  231)
  hydrogen bonds       : angle       4.62362 /  3.34 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.144 
Fit side-chains
REVERT: A   71 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.8835 (t)
REVERT: A  153 MET cc_start: 0.7283 (tpp) cc_final: 0.7011 (tpp)
REVERT: A  196 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6621 (mt-10)
REVERT: A  201 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7696 (tp)
REVERT: A  255 GLN cc_start: 0.6873 (OUTLIER) cc_final: 0.5358 (tp40)
REVERT: A  398 TRP cc_start: 0.7387 (m100) cc_final: 0.6642 (t-100)
  outliers start: 19
  outliers final: 9
  residues processed: 77
  average time/residue: 0.0520
  time to fit residues: 5.0551
Evaluate side-chains
  63 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 51
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 ARG
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  297 THR
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  360 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 105 GLN
A 115 GLN
A 184 ASN
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.193796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.171458 restraints weight = 5398.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.176357 restraints weight = 2914.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.179738 restraints weight = 1819.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.181930 restraints weight = 1259.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.183518 restraints weight = 959.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.4386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6344
moved from start:          0.6206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2965  Z= 0.164
  Angle     :  0.637   7.412   4025  Z= 0.335
  Chirality :  0.044   0.165    475
  Planarity :  0.004   0.035    482
  Dihedral  :  5.734  54.105    398
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 19.50 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.44), residues: 357
  helix:  1.61 (0.29), residues: 295
  sheet:  None (None), residues: 0
  loop : -0.14 (0.95), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 319 
 TYR   0.017   0.002   TYR A 403 
 PHE   0.012   0.001   PHE A 104 
 TRP   0.016   0.002   TRP A 356 
 HIS   0.004   0.001   HIS A 108 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 ( 2964)
  covalent geometry    : angle       0.63737 /  0.34 ( 4023)
  SS BOND              : bond        0.00142 /  0.07 (    1)
  SS BOND              : angle       0.30358 /  0.18 (    2)
  hydrogen bonds       : bond        0.05753 /  3.86 (  231)
  hydrogen bonds       : angle       4.34746 /  3.14 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.133 
Fit side-chains
REVERT: A   71 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.8900 (t)
REVERT: A  119 TYR cc_start: 0.5957 (t80) cc_final: 0.5735 (t80)
REVERT: A  153 MET cc_start: 0.7270 (tpp) cc_final: 0.6882 (tpp)
REVERT: A  201 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7685 (tp)
REVERT: A  255 GLN cc_start: 0.6780 (OUTLIER) cc_final: 0.6353 (tp40)
REVERT: A  398 TRP cc_start: 0.7192 (m100) cc_final: 0.6441 (t-100)
  outliers start: 19
  outliers final: 14
  residues processed: 73
  average time/residue: 0.0519
  time to fit residues: 4.8428
Evaluate side-chains
  71 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   60 ARG
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  274 TYR
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  403 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
A 115 GLN
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.208093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.185058 restraints weight = 4534.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.189317 restraints weight = 2558.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.192390 restraints weight = 1685.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.194322 restraints weight = 1220.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.195876 restraints weight = 970.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.4624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6452
moved from start:          0.6946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2965  Z= 0.169
  Angle     :  0.645   9.243   4025  Z= 0.336
  Chirality :  0.044   0.147    475
  Planarity :  0.004   0.038    482
  Dihedral  :  5.858  56.259    398
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 22.33 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.89 (0.43), residues: 357
  helix:  1.70 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -0.57 (0.81), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.012   0.002   TYR A 181 
 PHE   0.021   0.002   PHE A 326 
 TRP   0.015   0.002   TRP A 356 
 HIS   0.006   0.002   HIS A 180 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.17 ( 2964)
  covalent geometry    : angle       0.64540 /  0.34 ( 4023)
  SS BOND              : bond        0.00145 /  0.08 (    1)
  SS BOND              : angle       0.24715 /  0.15 (    2)
  hydrogen bonds       : bond        0.05796 /  3.91 (  231)
  hydrogen bonds       : angle       4.41496 /  3.21 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   60 ARG cc_start: 0.7334 (mmm160) cc_final: 0.6486 (ptt-90)
REVERT: A   71 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.8905 (t)
REVERT: A  119 TYR cc_start: 0.5901 (t80) cc_final: 0.5659 (t80)
REVERT: A  153 MET cc_start: 0.7509 (tpp) cc_final: 0.7170 (tpp)
REVERT: A  201 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7824 (tp)
REVERT: A  255 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6609 (tp40)
REVERT: A  398 TRP cc_start: 0.7118 (m100) cc_final: 0.6358 (t-100)
  outliers start: 18
  outliers final: 13
  residues processed: 68
  average time/residue: 0.0436
  time to fit residues: 3.8960
Evaluate side-chains
  68 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 52
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  164 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  191 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  256 LEU
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  403 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 209 ASN
** A 342 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 = 0.4539 r_free = 0.4539 target = 0.195281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.172082 restraints weight = 5396.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.176207 restraints weight = 2975.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.179154 restraints weight = 1986.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.181010 restraints weight = 1461.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.182578 restraints weight = 1184.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.4546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6443
moved from start:          0.7375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2965  Z= 0.146
  Angle     :  0.609   7.480   4025  Z= 0.317
  Chirality :  0.043   0.150    475
  Planarity :  0.004   0.039    482
  Dihedral  :  5.808  55.239    398
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.12 %
    Favored  : 98.88 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 23.27 %
    Favored  : 69.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.44), residues: 357
  helix:  1.86 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -0.75 (0.80), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 319 
 TYR   0.007   0.002   TYR A 152 
 PHE   0.018   0.001   PHE A 326 
 TRP   0.012   0.002   TRP A 356 
 HIS   0.004   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.15 ( 2964)
  covalent geometry    : angle       0.60895 /  0.32 ( 4023)
  SS BOND              : bond        0.00135 /  0.07 (    1)
  SS BOND              : angle       0.28398 /  0.17 (    2)
  hydrogen bonds       : bond        0.05247 /  3.54 (  231)
  hydrogen bonds       : angle       4.30947 /  3.14 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 59
  time to evaluate  : 0.110 
Fit side-chains
REVERT: A   60 ARG cc_start: 0.7274 (mmm160) cc_final: 0.6541 (ptt-90)
REVERT: A   71 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.8891 (t)
REVERT: A  119 TYR cc_start: 0.6227 (t80) cc_final: 0.6003 (t80)
REVERT: A  145 MET cc_start: 0.7090 (tmm) cc_final: 0.6838 (tmm)
REVERT: A  153 MET cc_start: 0.7534 (tpp) cc_final: 0.7140 (tpp)
REVERT: A  201 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7774 (tp)
REVERT: A  232 TYR cc_start: 0.7733 (m-80) cc_final: 0.7384 (m-10)
REVERT: A  233 MET cc_start: 0.5515 (ptp) cc_final: 0.5276 (ptp)
REVERT: A  255 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6649 (tp40)
REVERT: A  329 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8063 (m-40)
REVERT: A  398 TRP cc_start: 0.7009 (m100) cc_final: 0.6320 (t-100)
  outliers start: 22
  outliers final: 15
  residues processed: 74
  average time/residue: 0.0449
  time to fit residues: 4.3582
Evaluate side-chains
  69 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 50
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  274 TYR
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  405 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 209 ASN
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 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 = 0.4526 r_free = 0.4526 target = 0.194694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.172122 restraints weight = 5395.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.176313 restraints weight = 2958.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.179201 restraints weight = 1940.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.181106 restraints weight = 1427.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.182532 restraints weight = 1147.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.4583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.7658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2965  Z= 0.141
  Angle     :  0.630  10.030   4025  Z= 0.320
  Chirality :  0.042   0.147    475
  Planarity :  0.004   0.039    482
  Dihedral  :  5.849  55.965    398
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 24.84 %
    Favored  : 68.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.44), residues: 357
  helix:  1.86 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -0.93 (0.80), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.011   0.002   TYR A 152 
 PHE   0.018   0.001   PHE A 326 
 TRP   0.011   0.001   TRP A 251 
 HIS   0.003   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.14 ( 2964)
  covalent geometry    : angle       0.63026 /  0.32 ( 4023)
  SS BOND              : bond        0.00065 /  0.03 (    1)
  SS BOND              : angle       0.26971 /  0.16 (    2)
  hydrogen bonds       : bond        0.05101 /  3.43 (  231)
  hydrogen bonds       : angle       4.29282 /  3.13 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 57
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 THR cc_start: 0.9304 (OUTLIER) cc_final: 0.8893 (t)
REVERT: A  145 MET cc_start: 0.7124 (tmm) cc_final: 0.6868 (tmm)
REVERT: A  153 MET cc_start: 0.7481 (tpp) cc_final: 0.7127 (tpp)
REVERT: A  201 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7801 (tp)
REVERT: A  255 GLN cc_start: 0.7241 (OUTLIER) cc_final: 0.6934 (tp40)
REVERT: A  329 ASN cc_start: 0.8325 (OUTLIER) cc_final: 0.7945 (m-40)
REVERT: A  398 TRP cc_start: 0.6901 (m100) cc_final: 0.6308 (t-100)
  outliers start: 22
  outliers final: 13
  residues processed: 72
  average time/residue: 0.0424
  time to fit residues: 4.0812
Evaluate side-chains
  69 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 52
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  209 ASN
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  360 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.190268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.167677 restraints weight = 5540.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.171753 restraints weight = 3056.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.174653 restraints weight = 2011.890|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.176652 restraints weight = 1474.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.177943 restraints weight = 1175.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.4538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6507
moved from start:          0.7914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2965  Z= 0.153
  Angle     :  0.652   8.907   4025  Z= 0.341
  Chirality :  0.044   0.155    475
  Planarity :  0.004   0.038    482
  Dihedral  :  5.906  55.428    398
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 24.53 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.44), residues: 357
  helix:  1.72 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -1.04 (0.81), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.013   0.002   TYR A 119 
 PHE   0.021   0.002   PHE A 165 
 TRP   0.011   0.002   TRP A 356 
 HIS   0.004   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.15 ( 2964)
  covalent geometry    : angle       0.65257 /  0.34 ( 4023)
  SS BOND              : bond        0.00078 /  0.04 (    1)
  SS BOND              : angle       0.32884 /  0.19 (    2)
  hydrogen bonds       : bond        0.05432 /  3.67 (  231)
  hydrogen bonds       : angle       4.37196 /  3.19 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A   60 ARG cc_start: 0.7170 (mmm160) cc_final: 0.6542 (ptt-90)
REVERT: A   71 THR cc_start: 0.9261 (OUTLIER) cc_final: 0.8881 (t)
REVERT: A  145 MET cc_start: 0.7265 (tmm) cc_final: 0.6962 (tmm)
REVERT: A  153 MET cc_start: 0.7551 (tpp) cc_final: 0.7142 (tpp)
REVERT: A  201 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7770 (tp)
REVERT: A  255 GLN cc_start: 0.7261 (OUTLIER) cc_final: 0.6873 (tp40)
REVERT: A  329 ASN cc_start: 0.8363 (OUTLIER) cc_final: 0.8019 (m-40)
REVERT: A  398 TRP cc_start: 0.6991 (m100) cc_final: 0.6199 (t-100)
  outliers start: 22
  outliers final: 16
  residues processed: 73
  average time/residue: 0.0415
  time to fit residues: 4.0493
Evaluate side-chains
  75 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 55
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 LEU
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  378 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.190108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.167508 restraints weight = 5586.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.171554 restraints weight = 3075.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.174422 restraints weight = 2027.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.176382 restraints weight = 1502.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.177683 restraints weight = 1206.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.4494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6553
moved from start:          0.8269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2965  Z= 0.154
  Angle     :  0.675   9.201   4025  Z= 0.344
  Chirality :  0.044   0.175    475
  Planarity :  0.004   0.037    482
  Dihedral  :  6.038  55.486    398
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  7.55 %
    Allowed  : 24.53 %
    Favored  : 67.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.67 (0.44), residues: 357
  helix:  1.66 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -1.28 (0.79), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.009   0.001   TYR A 403 
 PHE   0.015   0.002   PHE A 326 
 TRP   0.013   0.002   TRP A 251 
 HIS   0.004   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.15 ( 2964)
  covalent geometry    : angle       0.67536 /  0.34 ( 4023)
  SS BOND              : bond        0.00029 /  0.02 (    1)
  SS BOND              : angle       0.48801 /  0.28 (    2)
  hydrogen bonds       : bond        0.05476 /  3.64 (  231)
  hydrogen bonds       : angle       4.41939 /  3.22 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 57
  time to evaluate  : 0.072 
Fit side-chains
REVERT: A   60 ARG cc_start: 0.7208 (mmm160) cc_final: 0.6666 (ptt-90)
REVERT: A   71 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8903 (t)
REVERT: A  153 MET cc_start: 0.7496 (tpp) cc_final: 0.7077 (tpp)
REVERT: A  196 GLU cc_start: 0.6227 (OUTLIER) cc_final: 0.5957 (mp0)
REVERT: A  201 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7778 (tp)
REVERT: A  255 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6868 (tp40)
REVERT: A  329 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7923 (m-40)
REVERT: A  398 TRP cc_start: 0.6856 (m100) cc_final: 0.6212 (t-100)
  outliers start: 24
  outliers final: 16
  residues processed: 73
  average time/residue: 0.0403
  time to fit residues: 3.8298
Evaluate side-chains
  75 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  196 GLU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  231 SER
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  290 SER
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  378 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0980
   chunk 17 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 115 GLN
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 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 = 0.4409 r_free = 0.4409 target = 0.187651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.166979 restraints weight = 5588.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.171626 restraints weight = 2891.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.174788 restraints weight = 1778.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.176888 restraints weight = 1236.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.178280 restraints weight = 941.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6475
moved from start:          0.8459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   2965  Z= 0.146
  Angle     :  0.705  10.195   4025  Z= 0.350
  Chirality :  0.044   0.162    475
  Planarity :  0.004   0.038    482
  Dihedral  :  6.082  55.812    398
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 25.47 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.79 (0.44), residues: 357
  helix:  1.75 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -1.20 (0.79), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.008   0.001   TYR A 403 
 PHE   0.015   0.001   PHE A 326 
 TRP   0.012   0.002   TRP A 251 
 HIS   0.003   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.15 ( 2964)
  covalent geometry    : angle       0.70544 /  0.35 ( 4023)
  SS BOND              : bond        0.00006 /  0.00 (    1)
  SS BOND              : angle       0.27883 /  0.16 (    2)
  hydrogen bonds       : bond        0.05083 /  3.39 (  231)
  hydrogen bonds       : angle       4.32674 /  3.16 (  669)

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

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

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  714 Ramachandran restraints generated.
    357 Oldfield, 0 Emsley, 357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 0.101 
Fit side-chains
REVERT: A   60 ARG cc_start: 0.7133 (mmm160) cc_final: 0.6658 (ptt-90)
REVERT: A   71 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8889 (t)
REVERT: A  153 MET cc_start: 0.7238 (tpp) cc_final: 0.6879 (tpp)
REVERT: A  201 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7861 (tp)
REVERT: A  255 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6694 (tp40)
REVERT: A  329 ASN cc_start: 0.8217 (OUTLIER) cc_final: 0.7856 (m-40)
REVERT: A  398 TRP cc_start: 0.6891 (m100) cc_final: 0.6166 (t-100)
  outliers start: 19
  outliers final: 13
  residues processed: 67
  average time/residue: 0.0447
  time to fit residues: 3.8552
Evaluate side-chains
  70 residues out of total 322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  183 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  201 LEU
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  255 GLN
Chi-restraints excluded: chain A residue  260 VAL
Chi-restraints excluded: chain A residue  269 HIS
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  329 ASN
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  378 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 6 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0020
   overall best weight:    0.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 209 ASN
** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 342 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 = 0.4410 r_free = 0.4410 target = 0.187703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.167485 restraints weight = 5486.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.172016 restraints weight = 2848.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.174909 restraints weight = 1786.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.177070 restraints weight = 1271.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.178258 restraints weight = 959.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.4361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6492
moved from start:          0.8574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   2965  Z= 0.149
  Angle     :  0.740  10.261   4025  Z= 0.369
  Chirality :  0.044   0.179    475
  Planarity :  0.004   0.037    482
  Dihedral  :  6.081  55.873    398
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 25.16 %
    Favored  : 68.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.44), residues: 357
  helix:  1.74 (0.29), residues: 289
  sheet:  None (None), residues: 0
  loop : -1.16 (0.78), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 291 
 TYR   0.011   0.001   TYR A 119 
 PHE   0.013   0.001   PHE A 326 
 TRP   0.012   0.002   TRP A 251 
 HIS   0.003   0.001   HIS A 298 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.15 ( 2964)
  covalent geometry    : angle       0.73980 /  0.37 ( 4023)
  SS BOND              : bond        0.00207 /  0.11 (    1)
  SS BOND              : angle       0.43833 /  0.23 (    2)
  hydrogen bonds       : bond        0.05111 /  3.42 (  231)
  hydrogen bonds       : angle       4.33805 /  3.16 (  669)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 710.07 seconds
wall clock time: 12 minutes 56.40 seconds (776.40 seconds total)