Starting phenix.real_space_refine
on Sat May  2 07:35:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iu9_60894/05_2026/9iu9_60894.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iu9_60894/05_2026/9iu9_60894.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.21
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iu9_60894/05_2026/9iu9_60894.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iu9_60894/05_2026/9iu9_60894.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iu9_60894/05_2026/9iu9_60894.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iu9_60894/05_2026/9iu9_60894.cif"
  }
  resolution = 3.21
  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=   0.041
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      47      5.49       5
     S      10      5.16       5
     C    1916      2.51       5
     N     606      2.21       5
     O     697      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3277
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2312
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2312
          Classifications: {'peptide': 290}
          Link IDs: {'PTRANS': 16, 'TRANS': 273}
          Chain breaks: 3
    Chain: "E"
      Number of atoms: 473
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 473
          Classifications: {'DNA': 23}
          Link IDs: {'rna3p': 22}
    Chain: "F"
      Number of atoms: 491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 491
          Classifications: {'DNA': 24}
          Link IDs: {'rna3p': 23}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1221  SG  CYS B 304      40.717  28.517  37.508  1.00123.35           S
  ATOM   1239  SG  CYS B 307      40.635  30.005  34.038  1.00120.16           S
  ATOM   1390  SG  CYS B 326      37.782  29.702  35.393  1.00113.50           S
  ATOM   1462  SG  CYS B 335      39.396  26.331  34.884  1.00123.42           S

  Time building chain proxies: 0.93, per 1000 atoms: 0.28
  Number of scatterers: 3277
  At special positions: 0
  Unit cell: (65.8465, 96.4181, 74.0773, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      10     16.00
     P      47     15.00
     O     697      8.00
     N     606      7.00
     C    1916      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: 0.30
  Conformation dependent library (CDL) restraints added in 56.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B1000 "
        pdb="ZN    ZN B1000 " - pdb=" SG  CYS B 335 "
        pdb="ZN    ZN B1000 " - pdb=" SG  CYS B 307 "
        pdb="ZN    ZN B1000 " - pdb=" SG  CYS B 326 "
        pdb="ZN    ZN B1000 " - pdb=" SG  CYS B 304 "
      Number of angles added : 6


  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  532

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 5 sheets defined
      46.2% alpha, 14.1% beta
      23 base pairs and 37 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'B' and resid 146 through 151
    Processing helix  chain 'B' and resid 177 through 193
    Processing helix  chain 'B' and resid 197 through 208
    Processing helix  chain 'B' and resid 212 through 221
    Processing helix  chain 'B' and resid 231 through 240
    Processing helix  chain 'B' and resid 241 through 246
    Processing helix  chain 'B' and resid 271 through 283
    Processing helix  chain 'B' and resid 328 through 331
    Processing helix  chain 'B' and resid 342 through 358
    Processing helix  chain 'B' and resid 371 through 389
      removed outlier: 3.912A  pdb=" N   VAL B 375 " --> pdb=" O   SER B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 446
      removed outlier: 3.516A  pdb=" N   GLN B 446 " --> pdb=" O   TRP B 442 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 458
    Processing sheet with id=AA1, first strand: chain 'B' and resid 163 through 165
    Processing sheet with id=AA2, first strand: chain 'B' and resid 249 through 250
    Processing sheet with id=AA3, first strand: chain 'B' and resid 302 through 304
    Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 315
    Processing sheet with id=AA5, first strand: chain 'B' and resid 361 through 368
      removed outlier: 7.063A  pdb=" N   ARG B 362 " --> pdb=" O   THR B 435 " (cutoff:3.500A)

    111 hydrogen bonds defined for protein.
    306 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      58 hydrogen bonds
      116 hydrogen bond angles
      0 basepair planarities
      23 basepair parallelities
      37 stacking parallelities
  Total time for adding SS restraints: 0.60

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 692
        1.33 -     1.45: 1119
        1.45 -     1.57: 1529
        1.57 -     1.69: 92
        1.69 -     1.81: 15
  Bond restraints: 3447
  Sorted by residual:
  bond pdb=" CA  PRO B 159 "
       pdb=" CB  PRO B 159 "
    ideal  model  delta    sigma   weight residual
    1.539  1.499  0.040 9.30e-03 1.16e+04 1.84e+01
  bond pdb=" CA  SER B 157 "
       pdb=" CB  SER B 157 "
    ideal  model  delta    sigma   weight residual
    1.530  1.474  0.056 1.69e-02 3.50e+03 1.09e+01
  bond pdb=" CA  SER B 212 "
       pdb=" CB  SER B 212 "
    ideal  model  delta    sigma   weight residual
    1.526  1.484  0.042 1.53e-02 4.27e+03 7.61e+00
  bond pdb=" CA  PRO B 176 "
       pdb=" CB  PRO B 176 "
    ideal  model  delta    sigma   weight residual
    1.532  1.497  0.035 1.33e-02 5.65e+03 7.08e+00
  bond pdb=" NE  ARG B 207 "
       pdb=" CZ  ARG B 207 "
    ideal  model  delta    sigma   weight residual
    1.326  1.353 -0.027 1.10e-02 8.26e+03 5.86e+00
  ... (remaining 3442 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 4459
        2.76 -     5.53: 361
        5.53 -     8.29: 41
        8.29 -    11.05: 3
       11.05 -    13.81: 3
  Bond angle restraints: 4867
  Sorted by residual:
  angle pdb=" O3'  DT E  36 "
        pdb=" P    DG E  37 "
        pdb=" O5'  DG E  37 "
      ideal   model   delta    sigma   weight residual
     104.00   92.09   11.91 1.50e+00 4.44e-01 6.31e+01
  angle pdb=" CB  GLU B 445 "
        pdb=" CG  GLU B 445 "
        pdb=" CD  GLU B 445 "
      ideal   model   delta    sigma   weight residual
     112.60  123.76  -11.16 1.70e+00 3.46e-01 4.31e+01
  angle pdb=" C4'  DG E  32 "
        pdb=" C3'  DG E  32 "
        pdb=" O3'  DG E  32 "
      ideal   model   delta    sigma   weight residual
     110.00  100.84    9.16 1.50e+00 4.44e-01 3.73e+01
  angle pdb=" CA  ASP B 441 "
        pdb=" CB  ASP B 441 "
        pdb=" CG  ASP B 441 "
      ideal   model   delta    sigma   weight residual
     112.60  118.43   -5.83 1.00e+00 1.00e+00 3.40e+01
  angle pdb=" N   LYS B 214 "
        pdb=" CA  LYS B 214 "
        pdb=" CB  LYS B 214 "
      ideal   model   delta    sigma   weight residual
     110.07  117.92   -7.85 1.45e+00 4.76e-01 2.93e+01
  ... (remaining 4862 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 1464
       17.34 -    34.68: 244
       34.68 -    52.01: 150
       52.01 -    69.35: 58
       69.35 -    86.69: 5
  Dihedral angle restraints: 1921
    sinusoidal: 1096
      harmonic: 825
  Sorted by residual:
  dihedral pdb=" CA  TYR B 154 "
           pdb=" C   TYR B 154 "
           pdb=" N   ARG B 155 "
           pdb=" CA  ARG B 155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.30  -17.70     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  LEU B 470 "
           pdb=" C   LEU B 470 "
           pdb=" N   THR B 471 "
           pdb=" CA  THR B 471 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.71   16.29     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CG  ARG B 208 "
           pdb=" CD  ARG B 208 "
           pdb=" NE  ARG B 208 "
           pdb=" CZ  ARG B 208 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.39   44.61     2      1.50e+01 4.44e-03 1.05e+01
  ... (remaining 1918 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 469
       0.131 -    0.261: 50
       0.261 -    0.391: 3
       0.391 -    0.522: 4
       0.522 -    0.652: 2
  Chirality restraints: 528
  Sorted by residual:
  chirality pdb=" P    DC E  30 "
            pdb=" OP1  DC E  30 "
            pdb=" OP2  DC E  30 "
            pdb=" O5'  DC E  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -3.00   -0.65 2.00e-01 2.50e+01 1.06e+01
  chirality pdb=" P    DT F   1 "
            pdb=" OP1  DT F   1 "
            pdb=" OP2  DT F   1 "
            pdb=" O5'  DT F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.99   -0.64 2.00e-01 2.50e+01 1.02e+01
  chirality pdb=" P    DT F  22 "
            pdb=" OP1  DT F  22 "
            pdb=" OP2  DT F  22 "
            pdb=" O5'  DT F  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.83   -0.48 2.00e-01 2.50e+01 5.77e+00
  ... (remaining 525 not shown)

  Planarity restraints: 463
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC F  21 "   -0.085 2.00e-02 2.50e+03   4.21e-02 3.99e+01
        pdb=" N1   DC F  21 "    0.067 2.00e-02 2.50e+03
        pdb=" C2   DC F  21 "    0.036 2.00e-02 2.50e+03
        pdb=" O2   DC F  21 "    0.014 2.00e-02 2.50e+03
        pdb=" N3   DC F  21 "   -0.028 2.00e-02 2.50e+03
        pdb=" C4   DC F  21 "   -0.029 2.00e-02 2.50e+03
        pdb=" N4   DC F  21 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5   DC F  21 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DC F  21 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG E  42 "    0.060 2.00e-02 2.50e+03   2.43e-02 1.77e+01
        pdb=" N9   DG E  42 "   -0.050 2.00e-02 2.50e+03
        pdb=" C8   DG E  42 "   -0.011 2.00e-02 2.50e+03
        pdb=" N7   DG E  42 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5   DG E  42 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DG E  42 "    0.011 2.00e-02 2.50e+03
        pdb=" O6   DG E  42 "    0.016 2.00e-02 2.50e+03
        pdb=" N1   DG E  42 "    0.007 2.00e-02 2.50e+03
        pdb=" C2   DG E  42 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2   DG E  42 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DG E  42 "   -0.015 2.00e-02 2.50e+03
        pdb=" C4   DG E  42 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 472 "    0.327 9.50e-02 1.11e+02   1.47e-01 1.65e+01
        pdb=" NE  ARG B 472 "   -0.030 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 472 "    0.028 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 472 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 472 "    0.001 2.00e-02 2.50e+03
  ... (remaining 460 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 459
        2.77 -     3.30: 2867
        3.30 -     3.84: 6293
        3.84 -     4.37: 7045
        4.37 -     4.90: 10946
  Nonbonded interactions: 27610
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 312 "
            pdb=" OP2  DT E  43 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" NH1 ARG B 223 "
            pdb=" OP1  DG F  23 "
     model   vdw
     2.401 3.120
  nonbonded pdb=" OG  SER B 157 "
            pdb=" O2   DT F  22 "
     model   vdw
     2.407 3.040
  nonbonded pdb=" NH2 ARG B 190 "
            pdb=" OE2 GLU B 196 "
     model   vdw
     2.410 3.120
  nonbonded pdb=" NE1 TRP B 161 "
            pdb=" OE1 GLN B 180 "
     model   vdw
     2.446 3.120
  ... (remaining 27605 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             0.990
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.250
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6462
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   0.078   3451  Z= 0.537
  Angle     :  1.660  21.141   4873  Z= 1.005
  Chirality :  0.095   0.652    528
  Planarity :  0.017   0.147    463
  Dihedral  : 22.835  86.685   1389
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  2.13 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  :  6.67 %
    Favored  : 89.58 %
  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 are not related in a simple way.
  whole:  0.54 (0.47), residues: 282
  helix:  0.50 (0.41), residues: 124
  sheet: -0.40 (0.67), residues: 49
  loop :  0.88 (0.62), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.032   0.004   ARG B 472 
 TYR   0.034   0.007   TYR B 312 
 PHE   0.028   0.004   PHE B 439 
 TRP   0.021   0.005   TRP B 367 
 HIS   0.008   0.003   HIS B 146 

Details of bonding type rmsd
  covalent geometry    : bond        0.00924 ( 3447)
  covalent geometry    : angle       1.62028 ( 4867)
  hydrogen bonds       : bond        0.14482 (  169)
  hydrogen bonds       : angle       5.91496 (  422)
  metal coordination   : bond        0.05838 (    4)
  metal coordination   : angle      10.41935 (    6)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.147 
Fit side-chains
REVERT: B  164 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7941 (pt)
REVERT: B  204 ASP cc_start: 0.7943 (t70) cc_final: 0.7605 (t0)
REVERT: B  215 ASP cc_start: 0.7825 (m-30) cc_final: 0.7417 (m-30)
REVERT: B  219 GLN cc_start: 0.7112 (tt0) cc_final: 0.6633 (tp-100)
REVERT: B  239 MET cc_start: 0.7890 (mmm) cc_final: 0.7528 (mmm)
REVERT: B  250 LEU cc_start: 0.7396 (tp) cc_final: 0.7153 (tp)
REVERT: B  253 LYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5114 (mtmm)
REVERT: B  351 GLU cc_start: 0.6769 (tt0) cc_final: 0.6347 (tp30)
REVERT: B  366 VAL cc_start: 0.5789 (t) cc_final: 0.5427 (m)
REVERT: B  445 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7697 (mm-30)
REVERT: B  472 ARG cc_start: 0.8078 (ptp-170) cc_final: 0.7174 (mtm110)
REVERT: B  478 ASP cc_start: 0.7812 (m-30) cc_final: 0.7559 (m-30)
  outliers start: 9
  outliers final: 0
  residues processed: 65
  average time/residue: 0.1098
  time to fit residues: 8.0450
Evaluate side-chains
  47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 44
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  164 LEU
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  445 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 251 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.173225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.136913 restraints weight = 3605.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3433 rms_B_bonded: 1.45
r_work: 0.3195 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3451  Z= 0.226
  Angle     :  0.660   8.426   4873  Z= 0.365
  Chirality :  0.039   0.137    528
  Planarity :  0.005   0.051    463
  Dihedral  : 26.106  88.957    843
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 10.00 %
    Favored  : 87.08 %
  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 are not related in a simple way.
  whole:  1.85 (0.50), residues: 282
  helix:  1.93 (0.46), residues: 124
  sheet: -0.52 (0.64), residues: 49
  loop :  1.53 (0.64), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 444 
 TYR   0.012   0.002   TYR B 312 
 PHE   0.010   0.002   PHE B 464 
 TRP   0.012   0.001   TRP B 230 
 HIS   0.002   0.001   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 3447)
  covalent geometry    : angle       0.63351 ( 4867)
  hydrogen bonds       : bond        0.04263 (  169)
  hydrogen bonds       : angle       3.60720 (  422)
  metal coordination   : bond        0.00874 (    4)
  metal coordination   : angle       5.34293 (    6)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.059 
Fit side-chains
   revert: symmetry clash
REVERT: B  221 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7638 (mm110)
REVERT: B  253 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7110 (mtmt)
REVERT: B  351 GLU cc_start: 0.7886 (tt0) cc_final: 0.7408 (tp30)
REVERT: B  366 VAL cc_start: 0.8343 (t) cc_final: 0.7879 (m)
REVERT: B  431 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7470 (mt-10)
REVERT: B  445 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7900 (mm-30)
  outliers start: 7
  outliers final: 3
  residues processed: 40
  average time/residue: 0.1181
  time to fit residues: 5.3192
Evaluate side-chains
  35 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 30
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  192 VAL
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain B residue  445 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 18 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0570
   overall best weight:    0.7300

-------------------------------------------------------------------------------
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 = 0.3817 r_free = 0.3817 target = 0.171188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.132836 restraints weight = 3600.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.35
r_work: 0.3202 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3451  Z= 0.196
  Angle     :  0.610   6.783   4873  Z= 0.338
  Chirality :  0.036   0.144    528
  Planarity :  0.005   0.038    463
  Dihedral  : 26.203  86.625    841
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 11.67 %
    Favored  : 85.42 %
  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 are not related in a simple way.
  whole:  1.87 (0.50), residues: 282
  helix:  1.99 (0.47), residues: 123
  sheet: -0.84 (0.64), residues: 49
  loop :  1.67 (0.63), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 190 
 TYR   0.010   0.002   TYR B 154 
 PHE   0.008   0.001   PHE B 303 
 TRP   0.011   0.001   TRP B 230 
 HIS   0.002   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 3447)
  covalent geometry    : angle       0.58937 ( 4867)
  hydrogen bonds       : bond        0.03726 (  169)
  hydrogen bonds       : angle       3.52474 (  422)
  metal coordination   : bond        0.00755 (    4)
  metal coordination   : angle       4.57346 (    6)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
REVERT: B  189 HIS cc_start: 0.7910 (m170) cc_final: 0.7633 (t70)
REVERT: B  219 GLN cc_start: 0.8089 (tp-100) cc_final: 0.7821 (tp-100)
REVERT: B  221 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7646 (mm110)
REVERT: B  253 LYS cc_start: 0.7680 (OUTLIER) cc_final: 0.7049 (mtmt)
REVERT: B  351 GLU cc_start: 0.7937 (tt0) cc_final: 0.7530 (tp30)
REVERT: B  431 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7264 (mt-10)
REVERT: B  444 ARG cc_start: 0.8170 (mtm110) cc_final: 0.7945 (mtm110)
REVERT: B  445 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7783 (mp0)
  outliers start: 7
  outliers final: 1
  residues processed: 38
  average time/residue: 0.1005
  time to fit residues: 4.3942
Evaluate side-chains
  33 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 30
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  445 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 21 optimal weight:    0.0470
   chunk 26 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.5278

-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.173751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.139176 restraints weight = 3566.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 1.25
r_work: 0.3225 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3451  Z= 0.164
  Angle     :  0.556   5.501   4873  Z= 0.312
  Chirality :  0.034   0.130    528
  Planarity :  0.004   0.033    463
  Dihedral  : 26.079  85.630    841
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 13.75 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.02 (0.51), residues: 282
  helix:  2.28 (0.47), residues: 123
  sheet: -1.07 (0.63), residues: 49
  loop :  1.69 (0.62), residues: 110

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 444 
 TYR   0.008   0.001   TYR B 154 
 PHE   0.008   0.001   PHE B 464 
 TRP   0.009   0.001   TRP B 230 
 HIS   0.002   0.001   HIS B 334 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 3447)
  covalent geometry    : angle       0.53935 ( 4867)
  hydrogen bonds       : bond        0.03168 (  169)
  hydrogen bonds       : angle       3.31558 (  422)
  metal coordination   : bond        0.00619 (    4)
  metal coordination   : angle       3.94130 (    6)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 32
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: B  189 HIS cc_start: 0.7886 (m170) cc_final: 0.7649 (t70)
REVERT: B  219 GLN cc_start: 0.8045 (tp-100) cc_final: 0.7773 (tp-100)
REVERT: B  221 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7632 (mm110)
REVERT: B  253 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7111 (mtmt)
REVERT: B  351 GLU cc_start: 0.7992 (tt0) cc_final: 0.7525 (tp30)
REVERT: B  431 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7497 (mt-10)
REVERT: B  445 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7748 (mp0)
  outliers start: 8
  outliers final: 2
  residues processed: 37
  average time/residue: 0.1219
  time to fit residues: 5.0789
Evaluate side-chains
  35 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 31
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  445 GLU
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0980
   chunk 20 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3790 r_free = 0.3790 target = 0.168895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.130149 restraints weight = 3591.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3356 rms_B_bonded: 1.38
r_work: 0.3165 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   3451  Z= 0.236
  Angle     :  0.621   6.008   4873  Z= 0.342
  Chirality :  0.038   0.154    528
  Planarity :  0.005   0.043    463
  Dihedral  : 26.360  85.142    841
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 12.50 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.50), residues: 282
  helix:  2.04 (0.47), residues: 124
  sheet: -1.18 (0.65), residues: 49
  loop :  1.61 (0.61), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 444 
 TYR   0.006   0.002   TYR B 154 
 PHE   0.009   0.002   PHE B 464 
 TRP   0.011   0.001   TRP B 230 
 HIS   0.002   0.001   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 ( 3447)
  covalent geometry    : angle       0.60751 ( 4867)
  hydrogen bonds       : bond        0.04035 (  169)
  hydrogen bonds       : angle       3.58737 (  422)
  metal coordination   : bond        0.00840 (    4)
  metal coordination   : angle       3.77551 (    6)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.100 
Fit side-chains
REVERT: B  155 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7395 (ptt90)
REVERT: B  189 HIS cc_start: 0.7851 (m170) cc_final: 0.7588 (t70)
REVERT: B  219 GLN cc_start: 0.8070 (tp-100) cc_final: 0.7815 (tp-100)
REVERT: B  253 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7150 (mtmt)
REVERT: B  319 ARG cc_start: 0.8340 (mtt90) cc_final: 0.7910 (mtt90)
REVERT: B  431 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7355 (mt-10)
REVERT: B  445 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7727 (mp0)
  outliers start: 11
  outliers final: 4
  residues processed: 42
  average time/residue: 0.1210
  time to fit residues: 5.7684
Evaluate side-chains
  38 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 ARG
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  445 GLU
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 8 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 9 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 19 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.170534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.132365 restraints weight = 3628.999|
|-----------------------------------------------------------------------------|
r_work (start): 0.3375 rms_B_bonded: 1.37
r_work: 0.3187 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3451  Z= 0.198
  Angle     :  0.605   6.846   4873  Z= 0.335
  Chirality :  0.037   0.211    528
  Planarity :  0.005   0.046    463
  Dihedral  : 26.259  85.264    841
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 14.17 %
    Favored  : 82.08 %
  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 are not related in a simple way.
  whole:  1.81 (0.51), residues: 282
  helix:  2.06 (0.48), residues: 124
  sheet: -1.17 (0.67), residues: 49
  loop :  1.64 (0.61), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 444 
 TYR   0.006   0.001   TYR B 154 
 PHE   0.009   0.001   PHE B 464 
 TRP   0.010   0.001   TRP B 230 
 HIS   0.002   0.001   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 3447)
  covalent geometry    : angle       0.59298 ( 4867)
  hydrogen bonds       : bond        0.03503 (  169)
  hydrogen bonds       : angle       3.52637 (  422)
  metal coordination   : bond        0.00727 (    4)
  metal coordination   : angle       3.45250 (    6)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.109 
Fit side-chains
REVERT: B  155 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7273 (ptt90)
REVERT: B  189 HIS cc_start: 0.7846 (m170) cc_final: 0.7535 (t70)
REVERT: B  219 GLN cc_start: 0.8052 (tp-100) cc_final: 0.7777 (tp-100)
REVERT: B  253 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7095 (mtmt)
REVERT: B  319 ARG cc_start: 0.8341 (mtt90) cc_final: 0.7864 (mtt90)
REVERT: B  334 HIS cc_start: 0.8400 (p-80) cc_final: 0.8128 (p90)
REVERT: B  431 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7306 (mt-10)
REVERT: B  445 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7756 (mm-30)
  outliers start: 9
  outliers final: 4
  residues processed: 40
  average time/residue: 0.1381
  time to fit residues: 6.1867
Evaluate side-chains
  40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 ARG
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain B residue  445 GLU
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.171720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.133925 restraints weight = 3660.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.36
r_work: 0.3183 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3451  Z= 0.207
  Angle     :  0.613   6.977   4873  Z= 0.340
  Chirality :  0.037   0.201    528
  Planarity :  0.005   0.042    463
  Dihedral  : 26.331  84.965    841
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 15.00 %
    Favored  : 81.67 %
  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 are not related in a simple way.
  whole:  1.75 (0.51), residues: 282
  helix:  2.04 (0.48), residues: 124
  sheet: -1.26 (0.67), residues: 49
  loop :  1.59 (0.60), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 444 
 TYR   0.006   0.001   TYR B 154 
 PHE   0.010   0.001   PHE B 464 
 TRP   0.010   0.001   TRP B 230 
 HIS   0.002   0.001   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 ( 3447)
  covalent geometry    : angle       0.60341 ( 4867)
  hydrogen bonds       : bond        0.03701 (  169)
  hydrogen bonds       : angle       3.60749 (  422)
  metal coordination   : bond        0.00748 (    4)
  metal coordination   : angle       3.19779 (    6)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.109 
Fit side-chains
REVERT: B  155 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7235 (ptt90)
REVERT: B  189 HIS cc_start: 0.7847 (m170) cc_final: 0.7535 (t-170)
REVERT: B  219 GLN cc_start: 0.8067 (tp-100) cc_final: 0.7805 (tp-100)
REVERT: B  253 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7155 (mtmt)
REVERT: B  319 ARG cc_start: 0.8316 (mtt90) cc_final: 0.7885 (mtt90)
REVERT: B  334 HIS cc_start: 0.8400 (p-80) cc_final: 0.8117 (p90)
REVERT: B  361 GLU cc_start: 0.7741 (tt0) cc_final: 0.7273 (tt0)
REVERT: B  431 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7323 (mt-10)
REVERT: B  444 ARG cc_start: 0.8155 (mtm110) cc_final: 0.7886 (mtm110)
REVERT: B  445 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7640 (mp0)
  outliers start: 8
  outliers final: 5
  residues processed: 38
  average time/residue: 0.1291
  time to fit residues: 5.5459
Evaluate side-chains
  42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 ARG
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  293 SER
Chi-restraints excluded: chain B residue  340 VAL
Chi-restraints excluded: chain B residue  354 LEU
Chi-restraints excluded: chain B residue  388 THR
Chi-restraints excluded: chain B residue  445 GLU
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0470
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0570
   overall best weight:    0.4596

-------------------------------------------------------------------------------
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 = 0.3856 r_free = 0.3856 target = 0.174561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.139819 restraints weight = 3662.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 1.66
r_work: 0.3164 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3164
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3451  Z= 0.158
  Angle     :  0.575   7.051   4873  Z= 0.322
  Chirality :  0.034   0.195    528
  Planarity :  0.005   0.036    463
  Dihedral  : 26.097  85.667    841
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 16.25 %
    Favored  : 82.08 %
  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 are not related in a simple way.
  whole:  1.94 (0.51), residues: 282
  helix:  2.15 (0.48), residues: 124
  sheet: -1.59 (0.75), residues: 40
  loop :  1.68 (0.56), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 444 
 TYR   0.006   0.001   TYR B 154 
 PHE   0.008   0.001   PHE B 464 
 TRP   0.009   0.001   TRP B 345 
 HIS   0.002   0.001   HIS B 199 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 3447)
  covalent geometry    : angle       0.56546 ( 4867)
  hydrogen bonds       : bond        0.03120 (  169)
  hydrogen bonds       : angle       3.47390 (  422)
  metal coordination   : bond        0.00528 (    4)
  metal coordination   : angle       3.05804 (    6)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.114 
Fit side-chains
REVERT: B  155 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7233 (ptt90)
REVERT: B  219 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7570 (tp-100)
REVERT: B  253 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7095 (mtmt)
REVERT: B  334 HIS cc_start: 0.8363 (p-80) cc_final: 0.8088 (p90)
REVERT: B  361 GLU cc_start: 0.7644 (tt0) cc_final: 0.6807 (mm-30)
REVERT: B  431 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7317 (mt-10)
REVERT: B  445 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7553 (mp0)
  outliers start: 4
  outliers final: 1
  residues processed: 38
  average time/residue: 0.1267
  time to fit residues: 5.4276
Evaluate side-chains
  40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 36
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 ARG
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  445 GLU
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.171490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.136262 restraints weight = 3663.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.32
r_work: 0.3207 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3451  Z= 0.200
  Angle     :  0.610   7.631   4873  Z= 0.338
  Chirality :  0.037   0.192    528
  Planarity :  0.005   0.048    463
  Dihedral  : 26.297  85.111    841
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.83 %
    Favored  : 81.25 %
  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 are not related in a simple way.
  whole:  1.74 (0.51), residues: 282
  helix:  2.05 (0.48), residues: 124
  sheet: -1.30 (0.66), residues: 49
  loop :  1.57 (0.59), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 444 
 TYR   0.006   0.001   TYR B 154 
 PHE   0.009   0.001   PHE B 464 
 TRP   0.010   0.001   TRP B 230 
 HIS   0.012   0.002   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 ( 3447)
  covalent geometry    : angle       0.60112 ( 4867)
  hydrogen bonds       : bond        0.03598 (  169)
  hydrogen bonds       : angle       3.57447 (  422)
  metal coordination   : bond        0.00707 (    4)
  metal coordination   : angle       2.98378 (    6)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.096 
Fit side-chains
REVERT: B  155 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7309 (ptt90)
REVERT: B  219 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7779 (tp-100)
REVERT: B  253 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7218 (mtmt)
REVERT: B  334 HIS cc_start: 0.8438 (p-80) cc_final: 0.8178 (p90)
REVERT: B  361 GLU cc_start: 0.7750 (tt0) cc_final: 0.6988 (mm-30)
REVERT: B  431 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7419 (mt-10)
REVERT: B  441 ASP cc_start: 0.7249 (m-30) cc_final: 0.5695 (m-30)
REVERT: B  444 ARG cc_start: 0.7979 (mtm110) cc_final: 0.7709 (mtm110)
REVERT: B  445 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7585 (mp0)
  outliers start: 7
  outliers final: 3
  residues processed: 39
  average time/residue: 0.1195
  time to fit residues: 5.2954
Evaluate side-chains
  42 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 ARG
Chi-restraints excluded: chain B residue  175 VAL
Chi-restraints excluded: chain B residue  189 HIS
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  445 GLU
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 7 optimal weight:    0.1980
   chunk 27 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.172346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.137680 restraints weight = 3650.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.30
r_work: 0.3226 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3451  Z= 0.173
  Angle     :  0.596   8.136   4873  Z= 0.333
  Chirality :  0.035   0.195    528
  Planarity :  0.005   0.046    463
  Dihedral  : 26.187  85.264    841
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 16.67 %
    Favored  : 81.25 %
  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 are not related in a simple way.
  whole:  1.75 (0.50), residues: 282
  helix:  2.05 (0.48), residues: 124
  sheet: -1.29 (0.66), residues: 49
  loop :  1.60 (0.59), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 444 
 TYR   0.006   0.001   TYR B 154 
 PHE   0.009   0.001   PHE B 464 
 TRP   0.008   0.001   TRP B 230 
 HIS   0.017   0.002   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 3447)
  covalent geometry    : angle       0.58743 ( 4867)
  hydrogen bonds       : bond        0.03280 (  169)
  hydrogen bonds       : angle       3.51299 (  422)
  metal coordination   : bond        0.00619 (    4)
  metal coordination   : angle       2.84647 (    6)

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

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

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  564 Ramachandran restraints generated.
    282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.096 
Fit side-chains
REVERT: B  155 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7293 (ptt90)
REVERT: B  219 GLN cc_start: 0.8033 (tp-100) cc_final: 0.7763 (tp-100)
REVERT: B  253 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7223 (mtmt)
REVERT: B  334 HIS cc_start: 0.8431 (p-80) cc_final: 0.8133 (p90)
REVERT: B  361 GLU cc_start: 0.7760 (tt0) cc_final: 0.6902 (mm-30)
REVERT: B  431 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7429 (mt-10)
REVERT: B  441 ASP cc_start: 0.7195 (m-30) cc_final: 0.5713 (m-30)
REVERT: B  444 ARG cc_start: 0.7984 (mtm110) cc_final: 0.7729 (mtm110)
REVERT: B  445 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7739 (mp0)
  outliers start: 5
  outliers final: 2
  residues processed: 37
  average time/residue: 0.1237
  time to fit residues: 5.1900
Evaluate side-chains
  40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  155 ARG
Chi-restraints excluded: chain B residue  189 HIS
Chi-restraints excluded: chain B residue  253 LYS
Chi-restraints excluded: chain B residue  445 GLU
Chi-restraints excluded: chain B residue  463 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 5 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 189 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.172615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.138185 restraints weight = 3675.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.32
r_work: 0.3188 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3451  Z= 0.197
  Angle     :  0.607   8.221   4873  Z= 0.338
  Chirality :  0.036   0.191    528
  Planarity :  0.005   0.045    463
  Dihedral  : 26.221  85.028    841
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 15.83 %
    Favored  : 81.25 %
  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 are not related in a simple way.
  whole:  1.70 (0.50), residues: 282
  helix:  2.00 (0.48), residues: 124
  sheet: -1.31 (0.66), residues: 49
  loop :  1.59 (0.59), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 444 
 TYR   0.005   0.001   TYR B 154 
 PHE   0.009   0.001   PHE B 464 
 TRP   0.009   0.001   TRP B 230 
 HIS   0.018   0.002   HIS B 189 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 3447)
  covalent geometry    : angle       0.59928 ( 4867)
  hydrogen bonds       : bond        0.03521 (  169)
  hydrogen bonds       : angle       3.56869 (  422)
  metal coordination   : bond        0.00691 (    4)
  metal coordination   : angle       2.85671 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1128.67 seconds
wall clock time: 19 minutes 55.46 seconds (1195.46 seconds total)