Starting phenix.real_space_refine
on Wed Sep 17 04:03:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xd6_38267/09_2025/8xd6_38267_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xd6_38267/09_2025/8xd6_38267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xd6_38267/09_2025/8xd6_38267.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xd6_38267/09_2025/8xd6_38267.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xd6_38267/09_2025/8xd6_38267_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xd6_38267/09_2025/8xd6_38267_neut.cif"
  }
  resolution = 2.79
  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=   0.002
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      15      5.16       5
     C    2131      2.51       5
     N     568      2.21       5
     O     685      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3402
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 419, 3289
          Classifications: {'peptide': 419}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 398}
    Chain: "A"
      Number of atoms: 113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 48, 113
          Unusual residues: {'AKG': 2, 'NDP': 1, 'NH4': 1}
          Classifications: {'undetermined': 4, 'water': 44}
          Link IDs: {None: 47}
  Time building chain proxies: 1.35, per 1000 atoms: 0.40
  Number of scatterers: 3402
  At special positions: 0
  Unit cell: (67.68, 75.952, 69.184, 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      15     16.00
     P       3     15.00
     O     685      8.00
     N     568      7.00
     C    2131      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: 0.35
  Conformation dependent library (CDL) restraints added in 138.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  764

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 3 sheets defined
      55.4% alpha, 18.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 19
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 79 through 97
      removed outlier: 3.814A  pdb=" N   VAL A  97 " --> pdb=" O   LYS A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 115
    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: 3.918A  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 223 through 234
    Processing helix  chain 'A' and resid 256 through 268
    Processing helix  chain 'A' and resid 280 through 286
    Processing helix  chain 'A' and resid 305 through 309
      removed outlier: 3.512A  pdb=" N   ILE A 309 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
    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: 4.427A  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
      removed outlier: 3.762A  pdb=" N   SER A 405 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ARG A 406 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 45
      removed outlier: 6.652A  pdb=" N   GLY A 103 " --> pdb=" O   HIS A  61 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 45
      removed outlier: 6.652A  pdb=" N   GLY A 103 " --> pdb=" O   HIS A  61 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   LYS A  69 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   GLY A 106 " --> pdb=" O   LYS A  69 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   THR A  68 " --> pdb=" O   ILE A 141 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 279
      removed outlier: 6.470A  pdb=" N   ILE A 215 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   ALA A 241 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER A 243 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   LYS A 214 " --> pdb=" O   VAL A 291 " (cutoff:3.500A)
      removed outlier: 7.922A  pdb=" N   ALA A 293 " --> pdb=" O   LYS A 214 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ALA A 216 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU A 292 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   VAL A 314 " --> pdb=" O   ILE A 338 " (cutoff:3.500A)

    199 hydrogen bonds defined for protein.
    570 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: 0.58

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1033
        1.34 -     1.45: 461
        1.45 -     1.57: 1907
        1.57 -     1.69: 2
        1.69 -     1.80: 29
  Bond restraints: 3432
  Sorted by residual:
  bond pdb=" O1N NDP A 501 "
       pdb=" PN  NDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.477  1.549 -0.072 1.00e-02 1.00e+04 5.25e+01
  bond pdb=" O2B NDP A 501 "
       pdb=" P2B NDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.833  1.566  0.267 3.80e-02 6.93e+02 4.93e+01
  bond pdb=" O5D NDP A 501 "
       pdb=" PN  NDP A 501 "
    ideal  model  delta    sigma   weight residual
    1.757  1.558  0.199 3.50e-02 8.16e+02 3.23e+01
  bond pdb=" C1  AKG A 503 "
       pdb=" C2  AKG A 503 "
    ideal  model  delta    sigma   weight residual
    1.559  1.460  0.099 2.00e-02 2.50e+03 2.45e+01
  bond pdb=" C1  AKG A 502 "
       pdb=" C2  AKG A 502 "
    ideal  model  delta    sigma   weight residual
    1.559  1.462  0.097 2.00e-02 2.50e+03 2.37e+01
  ... (remaining 3427 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.43: 4614
        4.43 -     8.86: 27
        8.86 -    13.28: 13
       13.28 -    17.71: 4
       17.71 -    22.14: 1
  Bond angle restraints: 4659
  Sorted by residual:
  angle pdb=" C1D NDP A 501 "
        pdb=" O4D NDP A 501 "
        pdb=" C4D NDP A 501 "
      ideal   model   delta    sigma   weight residual
     105.41  127.55  -22.14 2.71e+00 1.37e-01 6.69e+01
  angle pdb=" C5B NDP A 501 "
        pdb=" O5B NDP A 501 "
        pdb=" PA  NDP A 501 "
      ideal   model   delta    sigma   weight residual
     103.84  119.22  -15.38 1.91e+00 2.73e-01 6.45e+01
  angle pdb=" PA  NDP A 501 "
        pdb=" O3  NDP A 501 "
        pdb=" PN  NDP A 501 "
      ideal   model   delta    sigma   weight residual
     107.74  122.54  -14.80 1.95e+00 2.62e-01 5.74e+01
  angle pdb=" O1X NDP A 501 "
        pdb=" P2B NDP A 501 "
        pdb=" O3X NDP A 501 "
      ideal   model   delta    sigma   weight residual
     117.46  109.41    8.05 1.17e+00 7.36e-01 4.76e+01
  angle pdb=" O2X NDP A 501 "
        pdb=" P2B NDP A 501 "
        pdb=" O3X NDP A 501 "
      ideal   model   delta    sigma   weight residual
     117.33  108.87    8.46 1.48e+00 4.57e-01 3.28e+01
  ... (remaining 4654 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    30.96: 1948
       30.96 -    61.91: 75
       61.91 -    92.86: 9
       92.86 -   123.81: 0
      123.81 -   154.76: 1
  Dihedral angle restraints: 2033
    sinusoidal: 835
      harmonic: 1198
  Sorted by residual:
  dihedral pdb=" C5B NDP A 501 "
           pdb=" O5B NDP A 501 "
           pdb=" PA  NDP A 501 "
           pdb=" O3  NDP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.04   20.28  154.76     1      3.00e+01 1.11e-03 2.03e+01
  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  163.86   16.14     0      5.00e+00 4.00e-02 1.04e+01
  dihedral pdb=" CB  GLU A 371 "
           pdb=" CG  GLU A 371 "
           pdb=" CD  GLU A 371 "
           pdb=" OE1 GLU A 371 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.13   84.13     1      3.00e+01 1.11e-03 9.58e+00
  ... (remaining 2030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 447
       0.079 -    0.159: 50
       0.159 -    0.238: 2
       0.238 -    0.318: 3
       0.318 -    0.397: 3
  Chirality restraints: 505
  Sorted by residual:
  chirality pdb=" C4D NDP A 501 "
            pdb=" C3D NDP A 501 "
            pdb=" C5D NDP A 501 "
            pdb=" O4D NDP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.32   -0.40 2.00e-01 2.50e+01 3.94e+00
  chirality pdb=" C2D NDP A 501 "
            pdb=" C1D NDP A 501 "
            pdb=" C3D NDP A 501 "
            pdb=" O2D NDP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.34   -0.37 2.00e-01 2.50e+01 3.36e+00
  chirality pdb=" C1B NDP A 501 "
            pdb=" C2B NDP A 501 "
            pdb=" N9A NDP A 501 "
            pdb=" O4B NDP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.59    2.24    0.36 2.00e-01 2.50e+01 3.17e+00
  ... (remaining 502 not shown)

  Planarity restraints: 596
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C4N NDP A 501 "   -0.103 2.00e-02 2.50e+03   1.98e-01 3.90e+02
        pdb=" C5N NDP A 501 "    0.255 2.00e-02 2.50e+03
        pdb=" C6N NDP A 501 "   -0.261 2.00e-02 2.50e+03
        pdb=" N1N NDP A 501 "    0.110 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2N NDP A 501 "    0.058 2.00e-02 2.50e+03   1.01e-01 1.26e+02
        pdb=" C3N NDP A 501 "    0.167 2.00e-02 2.50e+03
        pdb=" C4N NDP A 501 "   -0.039 2.00e-02 2.50e+03
        pdb=" C7N NDP A 501 "   -0.106 2.00e-02 2.50e+03
        pdb=" N1N NDP A 501 "   -0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 297 "    0.015 2.00e-02 2.50e+03   2.99e-02 8.94e+00
        pdb=" C   ILE A 297 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   ILE A 297 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLU A 298 "    0.017 2.00e-02 2.50e+03
  ... (remaining 593 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.88: 1239
        2.88 -     3.38: 3313
        3.38 -     3.89: 6137
        3.89 -     4.39: 7345
        4.39 -     4.90: 11813
  Nonbonded interactions: 29847
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  99 "
            pdb=" O   HOH A 601 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" O   VAL A 317 "
            pdb=" ND2 ASN A 344 "
     model   vdw
     2.447 3.120
  nonbonded pdb=" O   GLU A 286 "
            pdb=" NZ  LYS A 310 "
     model   vdw
     2.464 3.120
  nonbonded pdb=" N   ASN A 222 "
            pdb=" O2A NDP A 501 "
     model   vdw
     2.482 3.120
  nonbonded pdb=" NE  ARG A  58 "
            pdb=" OD2 ASP A 140 "
     model   vdw
     2.500 3.120
  ... (remaining 29842 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:                  0.000
  Normalize map: mean=0, sd=1:             1.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.010
  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:6.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
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      :  0.009   0.267   3432  Z= 0.351
  Angle     :  1.123  22.139   4659  Z= 0.569
  Chirality :  0.058   0.397    505
  Planarity :  0.010   0.198    596
  Dihedral  : 16.233 154.763   1269
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  :  2.92 %
    Favored  : 93.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.43), residues: 417
  helix:  1.30 (0.37), residues: 210
  sheet:  0.53 (0.74), residues: 60
  loop : -0.31 (0.55), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  36 
 TYR   0.008   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 341 
 TRP   0.005   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A  61 

Details of bonding type rmsd
  covalent geometry    : bond        0.00907 ( 3432)
  covalent geometry    : angle       1.12305 ( 4659)
  hydrogen bonds       : bond        0.12519 (  184)
  hydrogen bonds       : angle       5.64842 (  570)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.081 
Fit side-chains
  outliers start: 12
  outliers final: 5
  residues processed: 69
  average time/residue: 0.7917
  time to fit residues: 55.7702
Evaluate side-chains
  56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 ILE
Chi-restraints excluded: chain A residue   60 GLN
Chi-restraints excluded: chain A residue  151 LYS
Chi-restraints excluded: chain A residue  351 SER
Chi-restraints excluded: chain A residue  388 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.0000
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 30 optimal weight:    0.5980
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.8988

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

Flipped N/Q/H residues before XYZ refinement:
A  62 ASN
A 337 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.108115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.090649 restraints weight = 4446.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.2728 rms_B_bonded: 1.52
r_work: 0.2625 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2512 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.2512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8978
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3432  Z= 0.112
  Angle     :  0.462   4.412   4659  Z= 0.244
  Chirality :  0.041   0.137    505
  Planarity :  0.004   0.041    596
  Dihedral  : 10.500 151.701    485
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.82 %
    Favored  : 87.43 %
  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:  1.53 (0.44), residues: 417
  helix:  2.01 (0.36), residues: 210
  sheet:  0.54 (0.72), residues: 61
  loop : -0.18 (0.56), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  16 
 TYR   0.009   0.001   TYR A 363 
 PHE   0.008   0.001   PHE A 341 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3432)
  covalent geometry    : angle       0.46229 ( 4659)
  hydrogen bonds       : bond        0.03958 (  184)
  hydrogen bonds       : angle       4.29000 (  570)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.115 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6184 (tpp) cc_final: 0.5600 (tpp)
REVERT: A   16 ARG cc_start: 0.8714 (ttt90) cc_final: 0.8167 (ttm170)
REVERT: A   29 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8734 (mm-30)
REVERT: A  149 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8069 (p0)
  outliers start: 6
  outliers final: 2
  residues processed: 57
  average time/residue: 0.7997
  time to fit residues: 46.5541
Evaluate side-chains
  55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 52
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 GLN
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  388 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 31 optimal weight:    0.2980
   chunk 19 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 26 optimal weight:    7.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.105509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.087751 restraints weight = 4450.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.2694 rms_B_bonded: 1.51
r_work: 0.2592 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2479 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8956
moved from start:          0.1398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3432  Z= 0.112
  Angle     :  0.448   4.190   4659  Z= 0.236
  Chirality :  0.041   0.133    505
  Planarity :  0.004   0.042    596
  Dihedral  : 10.057 155.588    478
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 10.53 %
    Favored  : 87.43 %
  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:  1.63 (0.44), residues: 417
  helix:  2.07 (0.36), residues: 212
  sheet:  0.58 (0.73), residues: 61
  loop : -0.13 (0.56), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  16 
 TYR   0.009   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 341 
 TRP   0.006   0.001   TRP A  63 
 HIS   0.005   0.002   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 3432)
  covalent geometry    : angle       0.44774 ( 4659)
  hydrogen bonds       : bond        0.03812 (  184)
  hydrogen bonds       : angle       4.12252 (  570)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6178 (tpp) cc_final: 0.5572 (tpp)
REVERT: A   16 ARG cc_start: 0.8640 (ttt90) cc_final: 0.8151 (ttm170)
REVERT: A  118 ARG cc_start: 0.8542 (mmp80) cc_final: 0.8318 (mmp80)
REVERT: A  149 ASN cc_start: 0.8626 (OUTLIER) cc_final: 0.8079 (p0)
REVERT: A  388 HIS cc_start: 0.8813 (OUTLIER) cc_final: 0.7920 (t70)
  outliers start: 7
  outliers final: 0
  residues processed: 56
  average time/residue: 0.8348
  time to fit residues: 47.7143
Evaluate side-chains
  55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  388 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0770
   chunk 16 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0570
   chunk 13 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.4256

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 337 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.104558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.085112 restraints weight = 4412.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 1.61
r_work: 0.2669 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2555 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.2555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8915
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3432  Z= 0.087
  Angle     :  0.415   3.799   4659  Z= 0.219
  Chirality :  0.040   0.130    505
  Planarity :  0.004   0.043    596
  Dihedral  :  8.968 150.217    475
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 12.28 %
    Favored  : 86.84 %
  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:  1.82 (0.44), residues: 417
  helix:  2.22 (0.36), residues: 212
  sheet:  0.46 (0.73), residues: 62
  loop :  0.08 (0.57), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  16 
 TYR   0.006   0.001   TYR A 408 
 PHE   0.006   0.001   PHE A 341 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.001   0.001   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00187 ( 3432)
  covalent geometry    : angle       0.41452 ( 4659)
  hydrogen bonds       : bond        0.03291 (  184)
  hydrogen bonds       : angle       3.91321 (  570)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.082 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5987 (tpp) cc_final: 0.5502 (tpp)
REVERT: A   16 ARG cc_start: 0.8631 (ttt90) cc_final: 0.8166 (ttm170)
REVERT: A  113 LYS cc_start: 0.9302 (mmtm) cc_final: 0.8931 (mttp)
REVERT: A  118 ARG cc_start: 0.8505 (mmp80) cc_final: 0.8255 (mmp80)
REVERT: A  388 HIS cc_start: 0.8593 (OUTLIER) cc_final: 0.7860 (t70)
  outliers start: 3
  outliers final: 0
  residues processed: 58
  average time/residue: 0.7625
  time to fit residues: 45.1200
Evaluate side-chains
  54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  388 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 33 optimal weight:    0.4980
   chunk 13 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    2.6988

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

Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
A 337 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.095507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.075624 restraints weight = 4541.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.2702 rms_B_bonded: 1.59
r_work: 0.2601 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2487 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9009
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3432  Z= 0.199
  Angle     :  0.495   4.749   4659  Z= 0.261
  Chirality :  0.044   0.131    505
  Planarity :  0.004   0.042    596
  Dihedral  :  8.948 143.133    475
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.16 %
    Favored  : 85.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.43), residues: 417
  helix:  1.98 (0.35), residues: 212
  sheet:  0.47 (0.73), residues: 61
  loop : -0.13 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  16 
 TYR   0.015   0.001   TYR A 363 
 PHE   0.017   0.002   PHE A 341 
 TRP   0.007   0.001   TRP A 382 
 HIS   0.007   0.002   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00485 ( 3432)
  covalent geometry    : angle       0.49469 ( 4659)
  hydrogen bonds       : bond        0.04711 (  184)
  hydrogen bonds       : angle       4.36069 (  570)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A    1 MET cc_start: 0.6071 (tpp) cc_final: 0.5607 (tpp)
REVERT: A    3 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7102 (tm-30)
REVERT: A   16 ARG cc_start: 0.8711 (ttt90) cc_final: 0.8192 (ttm170)
REVERT: A  113 LYS cc_start: 0.9312 (mmtm) cc_final: 0.8898 (mttp)
  outliers start: 5
  outliers final: 1
  residues processed: 55
  average time/residue: 0.8500
  time to fit residues: 47.7123
Evaluate side-chains
  55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue  388 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 23 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 5 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 31 optimal weight:   10.0000
   chunk 4 optimal weight:    0.5980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.098211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2669 r_free = 0.2669 target = 0.078508 restraints weight = 4494.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.2728 rms_B_bonded: 1.59
r_work: 0.2625 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2512 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8985
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3432  Z= 0.131
  Angle     :  0.453   4.447   4659  Z= 0.241
  Chirality :  0.042   0.132    505
  Planarity :  0.004   0.044    596
  Dihedral  :  8.532 137.265    475
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.74 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.43), residues: 417
  helix:  2.06 (0.35), residues: 212
  sheet:  0.43 (0.72), residues: 61
  loop : -0.09 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  16 
 TYR   0.011   0.001   TYR A 363 
 PHE   0.011   0.001   PHE A 341 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3432)
  covalent geometry    : angle       0.45279 ( 4659)
  hydrogen bonds       : bond        0.04069 (  184)
  hydrogen bonds       : angle       4.18654 (  570)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.143 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5980 (tpp) cc_final: 0.5596 (tpp)
REVERT: A    3 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7067 (tm-30)
REVERT: A   16 ARG cc_start: 0.8674 (ttt90) cc_final: 0.8165 (ttm170)
REVERT: A  388 HIS cc_start: 0.8921 (OUTLIER) cc_final: 0.7998 (t70)
  outliers start: 5
  outliers final: 2
  residues processed: 53
  average time/residue: 0.8302
  time to fit residues: 44.9644
Evaluate side-chains
  54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue    4 ILE
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  388 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 30 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    0.2980
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.099774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.080190 restraints weight = 4529.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.2741 rms_B_bonded: 1.61
r_work: 0.2639 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2525 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8974
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3432  Z= 0.116
  Angle     :  0.443   5.045   4659  Z= 0.235
  Chirality :  0.042   0.137    505
  Planarity :  0.004   0.044    596
  Dihedral  :  8.140 128.166    475
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.16 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.43), residues: 417
  helix:  2.13 (0.36), residues: 212
  sheet:  0.40 (0.72), residues: 61
  loop : -0.07 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 331 
 TYR   0.009   0.001   TYR A 363 
 PHE   0.010   0.001   PHE A 341 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 3432)
  covalent geometry    : angle       0.44262 ( 4659)
  hydrogen bonds       : bond        0.03883 (  184)
  hydrogen bonds       : angle       4.10416 (  570)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.136 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5898 (tpp) cc_final: 0.5532 (tpp)
REVERT: A    3 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7071 (tt0)
REVERT: A   16 ARG cc_start: 0.8652 (ttt90) cc_final: 0.8195 (ttm170)
REVERT: A  149 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8106 (p0)
REVERT: A  312 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8590 (mttp)
REVERT: A  371 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: A  388 HIS cc_start: 0.8871 (OUTLIER) cc_final: 0.8152 (t70)
  outliers start: 7
  outliers final: 1
  residues processed: 55
  average time/residue: 0.8673
  time to fit residues: 48.7700
Evaluate side-chains
  57 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue   19 GLN
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain A residue  388 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   chunk 28 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 3 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 39 optimal weight:    7.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.100741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.080970 restraints weight = 4525.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.2694 rms_B_bonded: 1.62
r_work: 0.2593 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.2480 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8977
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3432  Z= 0.120
  Angle     :  0.439   5.347   4659  Z= 0.234
  Chirality :  0.042   0.132    505
  Planarity :  0.004   0.044    596
  Dihedral  :  7.796 117.575    475
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.16 %
    Favored  : 85.09 %
  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:  1.66 (0.43), residues: 417
  helix:  2.13 (0.35), residues: 212
  sheet:  0.39 (0.71), residues: 61
  loop : -0.08 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  16 
 TYR   0.010   0.001   TYR A 363 
 PHE   0.011   0.001   PHE A 341 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3432)
  covalent geometry    : angle       0.43865 ( 4659)
  hydrogen bonds       : bond        0.03921 (  184)
  hydrogen bonds       : angle       4.10112 (  570)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5912 (tpp) cc_final: 0.5599 (tpp)
REVERT: A    3 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7089 (tt0)
REVERT: A   16 ARG cc_start: 0.8669 (ttt90) cc_final: 0.8209 (ttm170)
REVERT: A  149 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8147 (p0)
REVERT: A  312 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8577 (mttp)
REVERT: A  371 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7786 (tm-30)
REVERT: A  388 HIS cc_start: 0.8895 (OUTLIER) cc_final: 0.8165 (t70)
  outliers start: 6
  outliers final: 0
  residues processed: 54
  average time/residue: 0.8904
  time to fit residues: 49.0989
Evaluate side-chains
  55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain A residue  388 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.102026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.082825 restraints weight = 4453.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.2727 rms_B_bonded: 1.57
r_work: 0.2628 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2515 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.2515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8981
moved from start:          0.1743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3432  Z= 0.129
  Angle     :  0.459   6.283   4659  Z= 0.244
  Chirality :  0.042   0.133    505
  Planarity :  0.004   0.044    596
  Dihedral  :  7.487 106.476    475
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 13.45 %
    Favored  : 85.09 %
  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:  1.65 (0.43), residues: 417
  helix:  2.13 (0.35), residues: 212
  sheet:  0.37 (0.71), residues: 61
  loop : -0.08 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  16 
 TYR   0.010   0.001   TYR A 363 
 PHE   0.011   0.001   PHE A 341 
 TRP   0.006   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3432)
  covalent geometry    : angle       0.45920 ( 4659)
  hydrogen bonds       : bond        0.03975 (  184)
  hydrogen bonds       : angle       4.11096 (  570)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5880 (tpp) cc_final: 0.5588 (tpp)
REVERT: A    3 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7079 (tt0)
REVERT: A   16 ARG cc_start: 0.8668 (ttt90) cc_final: 0.8214 (ttm170)
REVERT: A  312 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8608 (mttp)
REVERT: A  371 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7774 (tm-30)
REVERT: A  388 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8180 (t70)
  outliers start: 5
  outliers final: 1
  residues processed: 54
  average time/residue: 0.8833
  time to fit residues: 48.7706
Evaluate side-chains
  57 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain A residue  388 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   chunk 39 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.100895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.081160 restraints weight = 4432.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.2680 rms_B_bonded: 1.61
r_work: 0.2579 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2463 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8978
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3432  Z= 0.114
  Angle     :  0.440   6.203   4659  Z= 0.235
  Chirality :  0.042   0.132    505
  Planarity :  0.004   0.044    596
  Dihedral  :  7.341 103.389    475
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 13.74 %
    Favored  : 85.09 %
  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:  1.68 (0.43), residues: 417
  helix:  2.17 (0.36), residues: 212
  sheet:  0.36 (0.71), residues: 61
  loop : -0.07 (0.57), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  16 
 TYR   0.009   0.001   TYR A 363 
 PHE   0.010   0.001   PHE A 341 
 TRP   0.007   0.001   TRP A  63 
 HIS   0.004   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 3432)
  covalent geometry    : angle       0.44023 ( 4659)
  hydrogen bonds       : bond        0.03827 (  184)
  hydrogen bonds       : angle       4.07072 (  570)

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.139 
Fit side-chains
REVERT: A    1 MET cc_start: 0.5848 (tpp) cc_final: 0.5602 (tpp)
REVERT: A    3 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7071 (tt0)
REVERT: A   16 ARG cc_start: 0.8657 (ttt90) cc_final: 0.8220 (ttm170)
REVERT: A  149 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8102 (p0)
REVERT: A  312 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8586 (mttp)
REVERT: A  371 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7783 (tm-30)
REVERT: A  388 HIS cc_start: 0.8883 (OUTLIER) cc_final: 0.8239 (t70)
  outliers start: 4
  outliers final: 0
  residues processed: 55
  average time/residue: 0.8556
  time to fit residues: 48.0680
Evaluate side-chains
  55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 GLU
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  312 LYS
Chi-restraints excluded: chain A residue  388 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 29 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 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 337 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.101446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.081777 restraints weight = 4501.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 1.62
r_work: 0.2655 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2542 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8962
moved from start:          0.1768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3432  Z= 0.111
  Angle     :  0.454   6.999   4659  Z= 0.241
  Chirality :  0.041   0.132    505
  Planarity :  0.004   0.044    596
  Dihedral  :  7.217 100.961    475
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 13.74 %
    Favored  : 85.09 %
  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:  1.69 (0.43), residues: 417
  helix:  2.21 (0.35), residues: 211
  sheet:  0.34 (0.71), residues: 61
  loop : -0.09 (0.57), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  16 
 TYR   0.008   0.001   TYR A 363 
 PHE   0.009   0.001   PHE A 341 
 TRP   0.008   0.001   TRP A  63 
 HIS   0.003   0.001   HIS A 388 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 3432)
  covalent geometry    : angle       0.45366 ( 4659)
  hydrogen bonds       : bond        0.03721 (  184)
  hydrogen bonds       : angle       4.03066 (  570)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1506.23 seconds
wall clock time: 26 minutes 26.48 seconds (1586.48 seconds total)