Starting phenix.real_space_refine
on Fri Aug 22 13:46:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hiq_34826/08_2025/8hiq_34826_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hiq_34826/08_2025/8hiq_34826.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hiq_34826/08_2025/8hiq_34826_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hiq_34826/08_2025/8hiq_34826_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hiq_34826/08_2025/8hiq_34826.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hiq_34826/08_2025/8hiq_34826.map"
  }
  resolution = 3.2
  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=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      14      5.16       5
     C    2083      2.51       5
     N     553      2.21       5
     O     621      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3274
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 416, 3226
          Classifications: {'peptide': 416}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 20, 'TRANS': 395}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "A"
      Number of atoms: 48
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 48
          Unusual residues: {'NAP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.10, per 1000 atoms: 0.34
  Number of scatterers: 3274
  At special positions: 0
  Unit cell: (68.034, 71.978, 71.978, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P       3     15.00
     O     621      8.00
     N     553      7.00
     C    2083      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.27
  Conformation dependent library (CDL) restraints added in 130.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  758

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 2 sheets defined
      56.0% alpha, 13.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 19
    Processing helix  chain 'A' and resid 24 through 33
    Processing helix  chain 'A' and resid 79 through 97
      removed outlier: 4.059A  pdb=" N   VAL A  97 " --> pdb=" O   LYS A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 132
    Processing helix  chain 'A' and resid 133 through 135
      No H-bonds generated for 'chain 'A' and resid 133 through 135'
    Processing helix  chain 'A' and resid 149 through 165
    Processing helix  chain 'A' and resid 169 through 174
      removed outlier: 3.812A  pdb=" N   ILE A 174 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 207
    Processing helix  chain 'A' and resid 221 through 236
      removed outlier: 3.686A  pdb=" N   GLY A 236 " --> pdb=" O   LYS A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 280 through 286
      removed outlier: 3.533A  pdb=" N   GLU A 286 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 309
    Processing helix  chain 'A' and resid 323 through 333
    Processing helix  chain 'A' and resid 339 through 344
    Processing helix  chain 'A' and resid 344 through 361
      removed outlier: 4.490A  pdb=" N   VAL A 348 " --> pdb=" O   ASN A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 392
    Processing helix  chain 'A' and resid 394 through 415
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45
      removed outlier: 4.553A  pdb=" N   THR A  55 " --> pdb=" O   ILE A 109 " (cutoff:3.500A)
      removed outlier: 5.509A  pdb=" N   LYS A  69 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   GLY A 106 " --> pdb=" O   LYS A  69 " (cutoff:3.500A)
      removed outlier: 5.754A  pdb=" N   GLY A  71 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   ILE A 108 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ARG A  73 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   THR A  68 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
      removed outlier: 7.951A  pdb=" N   ALA A 143 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   GLY A  70 " --> pdb=" O   ALA A 143 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 279
      removed outlier: 7.479A  pdb=" N   ILE A 215 " --> pdb=" O   VAL A 240 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   VAL A 242 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   VAL A 217 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LYS A 214 " --> pdb=" O   VAL A 291 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   ALA A 293 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   ALA A 216 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   LEU A 292 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   VAL A 314 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)

    184 hydrogen bonds defined for protein.
    531 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: 0.36

  Time building geometry restraints manager: 0.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1062
        1.34 -     1.46: 666
        1.46 -     1.57: 1591
        1.57 -     1.69: 5
        1.69 -     1.81: 27
  Bond restraints: 3351
  Sorted by residual:
  bond pdb=" O2B NAP A 501 "
       pdb=" P2B NAP A 501 "
    ideal  model  delta    sigma   weight residual
    1.736  1.614  0.122 2.00e-02 2.50e+03 3.69e+01
  bond pdb=" C1D NAP A 501 "
       pdb=" O4D NAP A 501 "
    ideal  model  delta    sigma   weight residual
    1.375  1.428 -0.053 2.00e-02 2.50e+03 7.04e+00
  bond pdb=" C5D NAP A 501 "
       pdb=" O5D NAP A 501 "
    ideal  model  delta    sigma   weight residual
    1.403  1.450 -0.047 2.00e-02 2.50e+03 5.54e+00
  bond pdb=" O5D NAP A 501 "
       pdb=" PN  NAP A 501 "
    ideal  model  delta    sigma   weight residual
    1.649  1.604  0.045 2.00e-02 2.50e+03 5.05e+00
  bond pdb=" O3  NAP A 501 "
       pdb=" PA  NAP A 501 "
    ideal  model  delta    sigma   weight residual
    1.647  1.604  0.043 2.00e-02 2.50e+03 4.53e+00
  ... (remaining 3346 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 4403
        1.76 -     3.52: 125
        3.52 -     5.27: 25
        5.27 -     7.03: 5
        7.03 -     8.79: 3
  Bond angle restraints: 4561
  Sorted by residual:
  angle pdb=" CA  MET A 153 "
        pdb=" CB  MET A 153 "
        pdb=" CG  MET A 153 "
      ideal   model   delta    sigma   weight residual
     114.10  107.08    7.02 2.00e+00 2.50e-01 1.23e+01
  angle pdb=" N   GLY A 219 "
        pdb=" CA  GLY A 219 "
        pdb=" C   GLY A 219 "
      ideal   model   delta    sigma   weight residual
     113.18  105.81    7.37 2.37e+00 1.78e-01 9.68e+00
  angle pdb=" C   VAL A 146 "
        pdb=" N   TYR A 147 "
        pdb=" CA  TYR A 147 "
      ideal   model   delta    sigma   weight residual
     123.05  127.73   -4.68 1.57e+00 4.06e-01 8.89e+00
  angle pdb=" N   ARG A 166 "
        pdb=" CA  ARG A 166 "
        pdb=" CB  ARG A 166 "
      ideal   model   delta    sigma   weight residual
     113.65  109.78    3.87 1.47e+00 4.63e-01 6.92e+00
  angle pdb=" C2B NAP A 501 "
        pdb=" O2B NAP A 501 "
        pdb=" P2B NAP A 501 "
      ideal   model   delta    sigma   weight residual
     117.19  109.33    7.86 3.00e+00 1.11e-01 6.87e+00
  ... (remaining 4556 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 1791
       17.85 -    35.71: 175
       35.71 -    53.56: 40
       53.56 -    71.41: 19
       71.41 -    89.27: 7
  Dihedral angle restraints: 2032
    sinusoidal: 843
      harmonic: 1189
  Sorted by residual:
  dihedral pdb=" CA  TYR A 101 "
           pdb=" C   TYR A 101 "
           pdb=" N   GLY A 102 "
           pdb=" CA  GLY A 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.37   18.63     0      5.00e+00 4.00e-02 1.39e+01
  dihedral pdb=" CB  GLU A  45 "
           pdb=" CG  GLU A  45 "
           pdb=" CD  GLU A  45 "
           pdb=" OE1 GLU A  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.75  -88.75     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CA  LYS A 213 "
           pdb=" C   LYS A 213 "
           pdb=" N   LYS A 214 "
           pdb=" CA  LYS A 214 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.96  -16.04     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 2029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 267
       0.025 -    0.050: 126
       0.050 -    0.075: 55
       0.075 -    0.099: 30
       0.099 -    0.124: 23
  Chirality restraints: 501
  Sorted by residual:
  chirality pdb=" CA  ILE A 108 "
            pdb=" N   ILE A 108 "
            pdb=" C   ILE A 108 "
            pdb=" CB  ILE A 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  ILE A 338 "
            pdb=" N   ILE A 338 "
            pdb=" C   ILE A 338 "
            pdb=" CB  ILE A 338 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.71e-01
  chirality pdb=" CA  ILE A 174 "
            pdb=" N   ILE A 174 "
            pdb=" C   ILE A 174 "
            pdb=" CB  ILE A 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.68e-01
  ... (remaining 498 not shown)

  Planarity restraints: 579
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1D NAP A 501 "   -0.021 2.00e-02 2.50e+03   7.61e-02 1.16e+02
        pdb=" C2N NAP A 501 "   -0.071 2.00e-02 2.50e+03
        pdb=" C3N NAP A 501 "   -0.033 2.00e-02 2.50e+03
        pdb=" C4N NAP A 501 "   -0.125 2.00e-02 2.50e+03
        pdb=" C5N NAP A 501 "    0.023 2.00e-02 2.50e+03
        pdb=" C6N NAP A 501 "    0.108 2.00e-02 2.50e+03
        pdb=" C7N NAP A 501 "    0.109 2.00e-02 2.50e+03
        pdb=" N1N NAP A 501 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 141 "    0.034 5.00e-02 4.00e+02   5.11e-02 4.17e+00
        pdb=" N   PRO A 142 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 142 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 142 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 323 "   -0.026 5.00e-02 4.00e+02   4.01e-02 2.57e+00
        pdb=" N   PRO A 324 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 324 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 324 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 576 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 889
        2.81 -     3.33: 3394
        3.33 -     3.85: 5887
        3.85 -     4.38: 6769
        4.38 -     4.90: 11289
  Nonbonded interactions: 28228
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  68 "
            pdb=" OD1 ASP A 140 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" NZ  LYS A 177 "
            pdb=" OD1 ASN A 358 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" O   ASN A 308 "
            pdb=" NZ  LYS A 310 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" OD1 ASN A 319 "
            pdb=" ND2 ASN A 344 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" NE2 GLN A  60 "
            pdb=" O   VAL A 134 "
     model   vdw
     2.328 3.120
  ... (remaining 28223 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.090
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.160
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.020
  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:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.122   3351  Z= 0.234
  Angle     :  0.739   8.787   4561  Z= 0.405
  Chirality :  0.043   0.124    501
  Planarity :  0.006   0.076    579
  Dihedral  : 17.055  89.266   1274
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.43), residues: 414
  helix:  1.97 (0.36), residues: 209
  sheet: -0.06 (0.62), residues: 70
  loop :  0.19 (0.58), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 200 
 TYR   0.010   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 341 
 TRP   0.009   0.001   TRP A  89 
 HIS   0.002   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 3351)
  covalent geometry    : angle       0.73923 ( 4561)
  hydrogen bonds       : bond        0.11605 (  184)
  hydrogen bonds       : angle       5.08940 (  531)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  166 ARG cc_start: 0.5204 (ttt-90) cc_final: 0.4757 (ttt-90)
REVERT: A  388 HIS cc_start: 0.6928 (t70) cc_final: 0.6714 (t-170)
  outliers start: 0
  outliers final: 0
  residues processed: 62
  average time/residue: 0.0963
  time to fit residues: 6.8947
Evaluate side-chains
  52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    9.9990
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 308 ASN
A 357 GLN
A 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.152192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.127404 restraints weight = 7166.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3730 rms_B_bonded: 2.75
r_work: 0.3614 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.111   3351  Z= 0.249
  Angle     :  0.625   8.017   4561  Z= 0.322
  Chirality :  0.045   0.159    501
  Planarity :  0.005   0.051    579
  Dihedral  : 10.548  59.306    517
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  6.67 %
    Favored  : 92.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.42), residues: 414
  helix:  1.85 (0.35), residues: 210
  sheet: -0.18 (0.68), residues: 60
  loop : -0.27 (0.54), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 331 
 TYR   0.009   0.002   TYR A 101 
 PHE   0.011   0.001   PHE A 341 
 TRP   0.010   0.002   TRP A 382 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00600 ( 3351)
  covalent geometry    : angle       0.62513 ( 4561)
  hydrogen bonds       : bond        0.04414 (  184)
  hydrogen bonds       : angle       4.67810 (  531)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A   33 LYS cc_start: 0.4775 (ttpt) cc_final: 0.4470 (ttpt)
REVERT: A  377 MET cc_start: 0.6906 (mmt) cc_final: 0.6555 (mmt)
  outliers start: 3
  outliers final: 3
  residues processed: 57
  average time/residue: 0.0801
  time to fit residues: 5.3314
Evaluate side-chains
  50 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  393 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 27 optimal weight:   20.0000
   chunk 25 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9990
   chunk 16 optimal weight:    4.9990
   chunk 34 optimal weight:    0.6980
   chunk 37 optimal weight:    7.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.156391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.131844 restraints weight = 7054.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 2.75
r_work: 0.3686 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3351  Z= 0.123
  Angle     :  0.504   7.473   4561  Z= 0.263
  Chirality :  0.042   0.130    501
  Planarity :  0.005   0.049    579
  Dihedral  :  9.479  56.256    517
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 11.52 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.31 (0.42), residues: 414
  helix:  2.01 (0.35), residues: 213
  sheet: -0.18 (0.68), residues: 60
  loop : -0.38 (0.55), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 331 
 TYR   0.009   0.001   TYR A 408 
 PHE   0.008   0.001   PHE A 341 
 TRP   0.005   0.001   TRP A  30 
 HIS   0.002   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3351)
  covalent geometry    : angle       0.50443 ( 4561)
  hydrogen bonds       : bond        0.03690 (  184)
  hydrogen bonds       : angle       4.40281 (  531)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  157 MET cc_start: 0.8357 (tmm) cc_final: 0.8085 (tmm)
  outliers start: 1
  outliers final: 1
  residues processed: 52
  average time/residue: 0.0936
  time to fit residues: 5.6875
Evaluate side-chains
  48 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 18 optimal weight:    0.2980
   chunk 17 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    7.9990
   chunk 23 optimal weight:   20.0000
   chunk 8 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 28 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   overall best weight:    1.0182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.157029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.132525 restraints weight = 6980.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3801 rms_B_bonded: 2.74
r_work: 0.3689 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   3351  Z= 0.129
  Angle     :  0.504   7.075   4561  Z= 0.264
  Chirality :  0.042   0.132    501
  Planarity :  0.005   0.047    579
  Dihedral  :  8.832  59.560    517
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.82 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.42), residues: 414
  helix:  2.07 (0.34), residues: 213
  sheet: -0.15 (0.68), residues: 60
  loop : -0.43 (0.55), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 118 
 TYR   0.011   0.001   TYR A 250 
 PHE   0.008   0.001   PHE A 341 
 TRP   0.005   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3351)
  covalent geometry    : angle       0.50432 ( 4561)
  hydrogen bonds       : bond        0.03609 (  184)
  hydrogen bonds       : angle       4.31001 (  531)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.8711 (t0) cc_final: 0.8322 (t0)
REVERT: A  166 ARG cc_start: 0.5844 (ttt-90) cc_final: 0.5410 (ttt-90)
REVERT: A  377 MET cc_start: 0.6964 (mmt) cc_final: 0.6642 (mmt)
  outliers start: 4
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0966
  time to fit residues: 5.9246
Evaluate side-chains
  52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  393 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 39 optimal weight:    1.9990
   chunk 32 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 10 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    1.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.155499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.130906 restraints weight = 7056.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 2.71
r_work: 0.3668 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   3351  Z= 0.166
  Angle     :  0.550   7.336   4561  Z= 0.281
  Chirality :  0.043   0.131    501
  Planarity :  0.005   0.046    579
  Dihedral  :  8.644  59.893    517
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.82 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.42), residues: 414
  helix:  2.04 (0.34), residues: 213
  sheet: -0.25 (0.68), residues: 60
  loop : -0.48 (0.55), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 118 
 TYR   0.009   0.001   TYR A 250 
 PHE   0.009   0.001   PHE A 341 
 TRP   0.006   0.001   TRP A 364 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 3351)
  covalent geometry    : angle       0.54999 ( 4561)
  hydrogen bonds       : bond        0.03757 (  184)
  hydrogen bonds       : angle       4.36105 (  531)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  377 MET cc_start: 0.6994 (mmt) cc_final: 0.6667 (mmt)
  outliers start: 5
  outliers final: 5
  residues processed: 53
  average time/residue: 0.0882
  time to fit residues: 5.4800
Evaluate side-chains
  52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  238 THR
Chi-restraints excluded: chain A residue  393 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 22 optimal weight:    5.9990
   chunk 39 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.159157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.134901 restraints weight = 7067.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3835 rms_B_bonded: 2.72
r_work: 0.3725 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3351  Z= 0.113
  Angle     :  0.522   6.812   4561  Z= 0.268
  Chirality :  0.043   0.132    501
  Planarity :  0.005   0.046    579
  Dihedral  :  8.264  58.873    517
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 13.33 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.42), residues: 414
  helix:  2.07 (0.34), residues: 214
  sheet: -0.07 (0.69), residues: 60
  loop : -0.48 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 118 
 TYR   0.010   0.001   TYR A 147 
 PHE   0.008   0.001   PHE A 341 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.002   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 3351)
  covalent geometry    : angle       0.52199 ( 4561)
  hydrogen bonds       : bond        0.03430 (  184)
  hydrogen bonds       : angle       4.20626 (  531)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.8698 (t0) cc_final: 0.8360 (t0)
  outliers start: 2
  outliers final: 2
  residues processed: 55
  average time/residue: 0.0757
  time to fit residues: 4.8839
Evaluate side-chains
  53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  133 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 31 optimal weight:    9.9990
   chunk 4 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 9 optimal weight:    6.9990
   overall best weight:    1.4786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.156873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.132334 restraints weight = 7135.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3800 rms_B_bonded: 2.73
r_work: 0.3689 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   3351  Z= 0.155
  Angle     :  0.556   7.129   4561  Z= 0.285
  Chirality :  0.043   0.138    501
  Planarity :  0.005   0.048    579
  Dihedral  :  8.272  59.990    517
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 15.45 %
    Favored  : 83.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.42), residues: 414
  helix:  2.08 (0.34), residues: 214
  sheet: -0.04 (0.69), residues: 60
  loop : -0.47 (0.56), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 118 
 TYR   0.010   0.001   TYR A 147 
 PHE   0.009   0.001   PHE A 341 
 TRP   0.010   0.001   TRP A  30 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3351)
  covalent geometry    : angle       0.55570 ( 4561)
  hydrogen bonds       : bond        0.03640 (  184)
  hydrogen bonds       : angle       4.26793 (  531)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 53
  time to evaluate  : 0.129 
Fit side-chains
REVERT: A   39 GLU cc_start: 0.7961 (tt0) cc_final: 0.7592 (pm20)
REVERT: A  111 ASN cc_start: 0.8695 (t0) cc_final: 0.8395 (t0)
REVERT: A  377 MET cc_start: 0.6962 (mmt) cc_final: 0.6605 (mmt)
  outliers start: 3
  outliers final: 2
  residues processed: 56
  average time/residue: 0.0901
  time to fit residues: 5.9235
Evaluate side-chains
  51 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  133 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.159260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.134813 restraints weight = 7200.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 2.79
r_work: 0.3714 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3351  Z= 0.122
  Angle     :  0.544   6.886   4561  Z= 0.280
  Chirality :  0.043   0.138    501
  Planarity :  0.005   0.046    579
  Dihedral  :  8.115  59.962    517
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 16.36 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.42), residues: 414
  helix:  2.08 (0.34), residues: 214
  sheet:  0.11 (0.70), residues: 60
  loop : -0.53 (0.55), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 118 
 TYR   0.018   0.001   TYR A  20 
 PHE   0.008   0.001   PHE A 341 
 TRP   0.008   0.001   TRP A  63 
 HIS   0.002   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 3351)
  covalent geometry    : angle       0.54370 ( 4561)
  hydrogen bonds       : bond        0.03432 (  184)
  hydrogen bonds       : angle       4.18951 (  531)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.8723 (t0) cc_final: 0.8417 (t0)
REVERT: A  114 GLU cc_start: 0.7932 (pm20) cc_final: 0.7689 (pm20)
REVERT: A  400 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.6517 (t80)
  outliers start: 4
  outliers final: 2
  residues processed: 54
  average time/residue: 0.1039
  time to fit residues: 6.5342
Evaluate side-chains
  52 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 49
  time to evaluate  : 0.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  133 ASP
Chi-restraints excluded: chain A residue  400 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 6 optimal weight:    0.1980
   chunk 30 optimal weight:    0.0970
   chunk 34 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    0.0570
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 25 optimal weight:    6.9990
   overall best weight:    0.3496

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

Flipped N/Q/H residues before XYZ refinement:
A 357 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.162705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.138634 restraints weight = 7098.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 2.76
r_work: 0.3769 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.2271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   3351  Z= 0.108
  Angle     :  0.530   6.076   4561  Z= 0.275
  Chirality :  0.043   0.142    501
  Planarity :  0.005   0.046    579
  Dihedral  :  7.794  59.193    517
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.06 %
    Favored  : 82.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.42), residues: 414
  helix:  2.13 (0.35), residues: 215
  sheet:  0.21 (0.72), residues: 58
  loop : -0.69 (0.54), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 118 
 TYR   0.022   0.001   TYR A  20 
 PHE   0.010   0.001   PHE A 197 
 TRP   0.009   0.001   TRP A  63 
 HIS   0.002   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 3351)
  covalent geometry    : angle       0.52952 ( 4561)
  hydrogen bonds       : bond        0.03234 (  184)
  hydrogen bonds       : angle       4.07040 (  531)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.125 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.8709 (t0) cc_final: 0.8382 (t0)
REVERT: A  114 GLU cc_start: 0.7814 (pm20) cc_final: 0.7594 (pm20)
REVERT: A  161 GLU cc_start: 0.8199 (tt0) cc_final: 0.7940 (tp30)
REVERT: A  251 ASN cc_start: 0.7935 (t0) cc_final: 0.7385 (t0)
REVERT: A  400 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.6543 (t80)
  outliers start: 6
  outliers final: 1
  residues processed: 60
  average time/residue: 0.0901
  time to fit residues: 6.3561
Evaluate side-chains
  55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  400 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 28 optimal weight:    8.9990
   chunk 33 optimal weight:    0.8980
   chunk 27 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0070
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
A  19 GLN
A 281 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.161880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.137635 restraints weight = 7024.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 2.78
r_work: 0.3756 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.2341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3351  Z= 0.120
  Angle     :  0.562   6.692   4561  Z= 0.288
  Chirality :  0.043   0.145    501
  Planarity :  0.005   0.053    579
  Dihedral  :  7.733  59.461    517
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 17.58 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.42), residues: 414
  helix:  2.21 (0.34), residues: 215
  sheet:  0.30 (0.72), residues: 58
  loop : -0.73 (0.54), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 118 
 TYR   0.014   0.001   TYR A  20 
 PHE   0.010   0.001   PHE A 197 
 TRP   0.009   0.001   TRP A  63 
 HIS   0.002   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3351)
  covalent geometry    : angle       0.56222 ( 4561)
  hydrogen bonds       : bond        0.03380 (  184)
  hydrogen bonds       : angle       4.12085 (  531)

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  111 ASN cc_start: 0.8742 (t0) cc_final: 0.8401 (t0)
REVERT: A  114 GLU cc_start: 0.7785 (pm20) cc_final: 0.7573 (pm20)
REVERT: A  161 GLU cc_start: 0.8250 (tt0) cc_final: 0.7990 (tp30)
REVERT: A  400 TYR cc_start: 0.7979 (OUTLIER) cc_final: 0.6467 (t80)
  outliers start: 3
  outliers final: 2
  residues processed: 54
  average time/residue: 0.0950
  time to fit residues: 5.9994
Evaluate side-chains
  53 residues out of total 339 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 50
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 VAL
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  400 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 9 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 13 optimal weight:    0.1980
   chunk 17 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 193 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.160522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.136204 restraints weight = 7120.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 2.78
r_work: 0.3735 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3351  Z= 0.129
  Angle     :  0.573   6.988   4561  Z= 0.291
  Chirality :  0.043   0.138    501
  Planarity :  0.005   0.051    579
  Dihedral  :  7.707  59.063    517
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 17.27 %
    Favored  : 81.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.45 (0.42), residues: 414
  helix:  2.17 (0.34), residues: 215
  sheet:  0.33 (0.69), residues: 63
  loop : -0.69 (0.55), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 118 
 TYR   0.031   0.001   TYR A  20 
 PHE   0.009   0.001   PHE A 197 
 TRP   0.006   0.001   TRP A  63 
 HIS   0.002   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3351)
  covalent geometry    : angle       0.57252 ( 4561)
  hydrogen bonds       : bond        0.03441 (  184)
  hydrogen bonds       : angle       4.09839 (  531)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 944.70 seconds
wall clock time: 16 minutes 50.67 seconds (1010.67 seconds total)