Starting phenix.real_space_refine
on Fri Aug 22 15:32:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wqi_37746/08_2025/8wqi_37746.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wqi_37746/08_2025/8wqi_37746.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wqi_37746/08_2025/8wqi_37746.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wqi_37746/08_2025/8wqi_37746.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wqi_37746/08_2025/8wqi_37746.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wqi_37746/08_2025/8wqi_37746.map"
  }
  resolution = 3.5
  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=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    3186      2.51       5
     N     909      2.21       5
     O     950      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5074
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "D"
      Number of atoms: 4929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 4929
          Classifications: {'peptide': 627}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "G"
      Number of atoms: 145
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 145
          Classifications: {'peptide': 17}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 16}
          Chain breaks: 1
  Time building chain proxies: 1.32, per 1000 atoms: 0.26
  Number of scatterers: 5074
  At special positions: 0
  Unit cell: (109.88, 101.68, 78.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O     950      8.00
     N     909      7.00
     C    3186      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: 0.36
  Conformation dependent library (CDL) restraints added in 198.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1222

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 0 sheets defined
      62.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'D' and resid 4 through 14
      removed outlier: 4.278A  pdb=" N   VAL D   8 " --> pdb=" O   LEU D   4 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLU D  14 " --> pdb=" O   LYS D  10 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 17 through 24
    Processing helix  chain 'D' and resid 28 through 37
    Processing helix  chain 'D' and resid 48 through 56
      removed outlier: 3.791A  pdb=" N   ILE D  52 " --> pdb=" O   THR D  48 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   ALA D  54 " --> pdb=" O   LEU D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 58 through 66
      removed outlier: 3.902A  pdb=" N   VAL D  62 " --> pdb=" O   HIS D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 99
    Processing helix  chain 'D' and resid 100 through 106
      removed outlier: 3.604A  pdb=" N   VAL D 104 " --> pdb=" O   HIS D 100 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 132
    Processing helix  chain 'D' and resid 133 through 143
      removed outlier: 3.636A  pdb=" N   VAL D 137 " --> pdb=" O   ARG D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 156 through 164
      removed outlier: 3.501A  pdb=" N   ILE D 160 " --> pdb=" O   THR D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 176
    Processing helix  chain 'D' and resid 189 through 198
      removed outlier: 3.694A  pdb=" N   PHE D 193 " --> pdb=" O   THR D 189 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA D 194 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 199 through 209
      removed outlier: 3.547A  pdb=" N   VAL D 203 " --> pdb=" O   HIS D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 221 through 229
      removed outlier: 3.545A  pdb=" N   SER D 229 " --> pdb=" O   VAL D 225 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 231 through 239
      removed outlier: 3.676A  pdb=" N   VAL D 235 " --> pdb=" O   LYS D 231 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LEU D 237 " --> pdb=" O   ASP D 233 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 240 through 242
      No H-bonds generated for 'chain 'D' and resid 240 through 242'
    Processing helix  chain 'D' and resid 244 through 260
      removed outlier: 3.722A  pdb=" N   SER D 248 " --> pdb=" O   CYS D 244 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   GLU D 251 " --> pdb=" O   ARG D 247 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 269 through 284
      removed outlier: 3.780A  pdb=" N   HIS D 274 " --> pdb=" O   ILE D 270 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   TYR D 275 " --> pdb=" O   LYS D 271 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLU D 282 " --> pdb=" O   LEU D 278 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ARG D 283 " --> pdb=" O   ALA D 279 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 310 through 316
    Processing helix  chain 'D' and resid 320 through 337
      removed outlier: 3.668A  pdb=" N   HIS D 325 " --> pdb=" O   ARG D 321 " (cutoff:3.500A)
      removed outlier: 4.103A  pdb=" N   MET D 326 " --> pdb=" O   ASP D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 343 through 357
      removed outlier: 4.317A  pdb=" N   ILE D 347 " --> pdb=" O   VAL D 343 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 359 through 376
      removed outlier: 3.515A  pdb=" N   CYS D 363 " --> pdb=" O   GLU D 359 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LYS D 365 " --> pdb=" O   GLU D 361 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 383 through 399
      removed outlier: 3.921A  pdb=" N   ASN D 399 " --> pdb=" O   MET D 395 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 403 through 427
    Processing helix  chain 'D' and resid 432 through 456
    Processing helix  chain 'D' and resid 460 through 478
      removed outlier: 3.661A  pdb=" N   LEU D 474 " --> pdb=" O   GLN D 470 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 488 through 493
    Processing helix  chain 'D' and resid 511 through 520
    Processing helix  chain 'D' and resid 534 through 541
      removed outlier: 3.569A  pdb=" N   ILE D 538 " --> pdb=" O   SER D 534 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ILE D 539 " --> pdb=" O   ALA D 535 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   GLN D 541 " --> pdb=" O   HIS D 537 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 549 through 554
    Processing helix  chain 'D' and resid 575 through 580
      removed outlier: 3.993A  pdb=" N   SER D 580 " --> pdb=" O   LEU D 577 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 583 through 592
      removed outlier: 3.607A  pdb=" N   LEU D 588 " --> pdb=" O   VAL D 584 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU D 589 " --> pdb=" O   SER D 585 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 596 through 608
    Processing helix  chain 'D' and resid 617 through 627
      removed outlier: 3.952A  pdb=" N   GLU D 622 " --> pdb=" O   ARG D 618 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLY D 625 " --> pdb=" O   GLU D 621 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   HIS D 627 " --> pdb=" O   PHE D 623 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid -21 through -14
      removed outlier: 3.742A  pdb=" N   LYS G -16 " --> pdb=" O   HIS G -19 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   HIS G -14 " --> pdb=" O   HIS G -17 " (cutoff:3.500A)

    227 hydrogen bonds defined for protein.
    666 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: 0.72

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1734
        1.34 -     1.46: 933
        1.46 -     1.58: 2457
        1.58 -     1.69: 0
        1.69 -     1.81: 41
  Bond restraints: 5165
  Sorted by residual:
  bond pdb=" CB  ILE D 555 "
       pdb=" CG2 ILE D 555 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.55e+00
  bond pdb=" CB  VAL D 391 "
       pdb=" CG2 VAL D 391 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.32e-01
  bond pdb=" CB  VAL D 540 "
       pdb=" CG1 VAL D 540 "
    ideal  model  delta    sigma   weight residual
    1.521  1.495  0.026 3.30e-02 9.18e+02 6.03e-01
  bond pdb=" CB  THR D 569 "
       pdb=" CG2 THR D 569 "
    ideal  model  delta    sigma   weight residual
    1.521  1.496  0.025 3.30e-02 9.18e+02 5.90e-01
  bond pdb=" CE  LYS D 293 "
       pdb=" NZ  LYS D 293 "
    ideal  model  delta    sigma   weight residual
    1.489  1.466  0.023 3.00e-02 1.11e+03 5.86e-01
  ... (remaining 5160 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 6941
        2.72 -     5.44: 52
        5.44 -     8.15: 5
        8.15 -    10.87: 0
       10.87 -    13.59: 1
  Bond angle restraints: 6999
  Sorted by residual:
  angle pdb=" CA  LEU D  50 "
        pdb=" CB  LEU D  50 "
        pdb=" CG  LEU D  50 "
      ideal   model   delta    sigma   weight residual
     116.30  129.89  -13.59 3.50e+00 8.16e-02 1.51e+01
  angle pdb=" CA  GLN D 285 "
        pdb=" CB  GLN D 285 "
        pdb=" CG  GLN D 285 "
      ideal   model   delta    sigma   weight residual
     114.10  120.63   -6.53 2.00e+00 2.50e-01 1.07e+01
  angle pdb=" C   ASN D 155 "
        pdb=" N   THR D 156 "
        pdb=" CA  THR D 156 "
      ideal   model   delta    sigma   weight residual
     120.82  125.22   -4.40 1.47e+00 4.63e-01 8.95e+00
  angle pdb=" N   ASN D 399 "
        pdb=" CA  ASN D 399 "
        pdb=" C   ASN D 399 "
      ideal   model   delta    sigma   weight residual
     114.16  110.57    3.59 1.48e+00 4.57e-01 5.90e+00
  angle pdb=" C   GLN D 285 "
        pdb=" CA  GLN D 285 "
        pdb=" CB  GLN D 285 "
      ideal   model   delta    sigma   weight residual
     111.42  114.31   -2.89 1.31e+00 5.83e-01 4.86e+00
  ... (remaining 6994 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.80: 2678
       15.80 -    31.60: 346
       31.60 -    47.39: 76
       47.39 -    63.19: 11
       63.19 -    78.99: 3
  Dihedral angle restraints: 3114
    sinusoidal: 1228
      harmonic: 1886
  Sorted by residual:
  dihedral pdb=" CA  ASN D 399 "
           pdb=" C   ASN D 399 "
           pdb=" N   GLU D 400 "
           pdb=" CA  GLU D 400 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.74  -21.26     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  LEU D  50 "
           pdb=" C   LEU D  50 "
           pdb=" N   ILE D  51 "
           pdb=" CA  ILE D  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.87   21.13     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  THR D 551 "
           pdb=" C   THR D 551 "
           pdb=" N   LEU D 552 "
           pdb=" CA  LEU D 552 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.60   17.40     0      5.00e+00 4.00e-02 1.21e+01
  ... (remaining 3111 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 587
       0.042 -    0.084: 177
       0.084 -    0.126: 34
       0.126 -    0.168: 4
       0.168 -    0.210: 1
  Chirality restraints: 803
  Sorted by residual:
  chirality pdb=" CG  LEU D  50 "
            pdb=" CB  LEU D  50 "
            pdb=" CD1 LEU D  50 "
            pdb=" CD2 LEU D  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.80    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CB  ILE D 610 "
            pdb=" CA  ILE D 610 "
            pdb=" CG1 ILE D 610 "
            pdb=" CG2 ILE D 610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.79   -0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CB  VAL D  71 "
            pdb=" CA  VAL D  71 "
            pdb=" CG1 VAL D  71 "
            pdb=" CG2 VAL D  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.31e-01
  ... (remaining 800 not shown)

  Planarity restraints: 909
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 616 "    0.042 5.00e-02 4.00e+02   6.44e-02 6.65e+00
        pdb=" N   PRO D 617 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO D 617 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO D 617 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D 123 "    0.034 5.00e-02 4.00e+02   5.10e-02 4.17e+00
        pdb=" N   PRO D 124 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO D 124 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO D 124 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 404 "    0.032 5.00e-02 4.00e+02   4.85e-02 3.76e+00
        pdb=" N   PRO D 405 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO D 405 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 405 "    0.027 5.00e-02 4.00e+02
  ... (remaining 906 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 300
        2.73 -     3.27: 5332
        3.27 -     3.82: 8581
        3.82 -     4.36: 10027
        4.36 -     4.90: 16903
  Nonbonded interactions: 41143
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP D 548 "
            pdb=" OG1 THR D 551 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" OD1 ASP D 322 "
            pdb=" OH  TYR D 354 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OH  TYR D 449 "
            pdb=" O   PRO D 497 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" O   ASP G -20 "
            pdb=" ND1 HIS G -17 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" O   ASP D  87 "
            pdb=" OG1 THR D 118 "
     model   vdw
     2.315 3.040
  ... (remaining 41138 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             13.970
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.300
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
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      :  0.003   0.041   5165  Z= 0.143
  Angle     :  0.620  13.589   6999  Z= 0.325
  Chirality :  0.040   0.210    803
  Planarity :  0.005   0.064    909
  Dihedral  : 14.513  78.990   1892
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.75 (0.32), residues: 638
  helix: -0.58 (0.25), residues: 389
  sheet:  None (None), residues: 0
  loop : -1.99 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 387 
 TYR   0.015   0.001   TYR D 472 
 PHE   0.011   0.001   PHE D 388 
 TRP   0.004   0.001   TRP D 367 
 HIS   0.005   0.001   HIS D 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5165)
  covalent geometry    : angle       0.62047 ( 6999)
  hydrogen bonds       : bond        0.16255 (  227)
  hydrogen bonds       : angle       5.98237 (  666)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.205 
Fit side-chains
REVERT: D  153 TYR cc_start: 0.6567 (m-80) cc_final: 0.5894 (m-10)
REVERT: D  163 TYR cc_start: 0.8603 (t80) cc_final: 0.8109 (t80)
REVERT: D  318 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.7047 (ttt-90)
REVERT: D  616 ILE cc_start: 0.9110 (tt) cc_final: 0.8845 (mm)
REVERT: D  619 THR cc_start: 0.8598 (t) cc_final: 0.8255 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.0942
  time to fit residues: 13.4165
Evaluate side-chains
  72 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0570
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   overall best weight:    0.6498

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

Flipped N/Q/H residues before XYZ refinement:
D 146 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.198539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.168498 restraints weight = 6310.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.168419 restraints weight = 6318.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.169754 restraints weight = 5424.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.169544 restraints weight = 3667.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.170205 restraints weight = 3407.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5165  Z= 0.187
  Angle     :  0.615   7.193   6999  Z= 0.326
  Chirality :  0.040   0.122    803
  Planarity :  0.005   0.068    909
  Dihedral  :  4.572  22.357    700
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.95 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.22 (0.33), residues: 638
  helix: -0.10 (0.26), residues: 390
  sheet:  None (None), residues: 0
  loop : -1.90 (0.39), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 387 
 TYR   0.024   0.002   TYR D 472 
 PHE   0.009   0.001   PHE D 549 
 TRP   0.008   0.002   TRP D 209 
 HIS   0.008   0.001   HIS D 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 5165)
  covalent geometry    : angle       0.61476 ( 6999)
  hydrogen bonds       : bond        0.04097 (  227)
  hydrogen bonds       : angle       4.53196 (  666)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.200 
Fit side-chains
REVERT: D  153 TYR cc_start: 0.6258 (m-80) cc_final: 0.5306 (m-10)
REVERT: D  163 TYR cc_start: 0.8530 (t80) cc_final: 0.8146 (t80)
REVERT: D  318 ARG cc_start: 0.7799 (ttp-110) cc_final: 0.7490 (ttt-90)
REVERT: D  399 ASN cc_start: 0.7833 (t0) cc_final: 0.7613 (t0)
REVERT: D  423 ASN cc_start: 0.7680 (m-40) cc_final: 0.7296 (t0)
REVERT: D  448 LEU cc_start: 0.8377 (mt) cc_final: 0.8123 (mt)
REVERT: D  544 ARG cc_start: 0.8269 (mtm-85) cc_final: 0.7830 (ptp90)
REVERT: D  567 ASP cc_start: 0.8691 (t0) cc_final: 0.8457 (t0)
  outliers start: 11
  outliers final: 6
  residues processed: 82
  average time/residue: 0.0887
  time to fit residues: 9.2256
Evaluate side-chains
  71 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  146 ASN
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  438 ASP
Chi-restraints excluded: chain D residue  498 VAL
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 15 optimal weight:    0.0770
   chunk 34 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 45 optimal weight:    0.4980
   chunk 38 optimal weight:    0.0980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.3538

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

Flipped N/Q/H residues before XYZ refinement:
D 116 HIS
D 511 ASN
G -19 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.196905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.169371 restraints weight = 6168.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.168906 restraints weight = 7482.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.170313 restraints weight = 6084.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.169751 restraints weight = 4333.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.170495 restraints weight = 3562.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5165  Z= 0.134
  Angle     :  0.588   7.760   6999  Z= 0.311
  Chirality :  0.038   0.135    803
  Planarity :  0.005   0.067    909
  Dihedral  :  4.453  21.916    700
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 15.69 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.95 (0.34), residues: 638
  helix:  0.16 (0.27), residues: 391
  sheet:  None (None), residues: 0
  loop : -1.88 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 309 
 TYR   0.020   0.002   TYR D 472 
 PHE   0.010   0.001   PHE D 284 
 TRP   0.008   0.001   TRP G  -2 
 HIS   0.006   0.001   HIS D 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 5165)
  covalent geometry    : angle       0.58791 ( 6999)
  hydrogen bonds       : bond        0.03580 (  227)
  hydrogen bonds       : angle       4.32184 (  666)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.202 
Fit side-chains
REVERT: D  163 TYR cc_start: 0.8614 (t80) cc_final: 0.8211 (t80)
REVERT: D  290 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.6010 (mm)
REVERT: D  399 ASN cc_start: 0.7842 (t0) cc_final: 0.7598 (t0)
REVERT: D  423 ASN cc_start: 0.7829 (m-40) cc_final: 0.7339 (t0)
REVERT: D  544 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.7853 (ptp90)
REVERT: D  616 ILE cc_start: 0.8951 (tt) cc_final: 0.8452 (mm)
  outliers start: 10
  outliers final: 5
  residues processed: 80
  average time/residue: 0.0730
  time to fit residues: 7.6126
Evaluate side-chains
  70 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 64
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  201 ASP
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  438 ASP
Chi-restraints excluded: chain D residue  498 VAL
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 29 optimal weight:    0.0370
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0470
   chunk 26 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.4756

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

Flipped N/Q/H residues before XYZ refinement:
G -19 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.198260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.168693 restraints weight = 6288.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.168549 restraints weight = 6356.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.170151 restraints weight = 5149.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.169856 restraints weight = 3352.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.170447 restraints weight = 3194.180|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5165  Z= 0.153
  Angle     :  0.592   7.684   6999  Z= 0.313
  Chirality :  0.039   0.127    803
  Planarity :  0.005   0.067    909
  Dihedral  :  4.453  22.007    700
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.13 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.88 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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 (0.34), residues: 638
  helix:  0.22 (0.27), residues: 392
  sheet:  None (None), residues: 0
  loop : -1.90 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 264 
 TYR   0.017   0.002   TYR D 472 
 PHE   0.007   0.001   PHE D 284 
 TRP   0.009   0.001   TRP G  -2 
 HIS   0.006   0.001   HIS D 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5165)
  covalent geometry    : angle       0.59237 ( 6999)
  hydrogen bonds       : bond        0.03563 (  227)
  hydrogen bonds       : angle       4.25946 (  666)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 74
  time to evaluate  : 0.140 
Fit side-chains
REVERT: D   69 TYR cc_start: 0.6159 (OUTLIER) cc_final: 0.4901 (p90)
REVERT: D  163 TYR cc_start: 0.8594 (t80) cc_final: 0.8228 (t80)
REVERT: D  290 ILE cc_start: 0.6215 (OUTLIER) cc_final: 0.5872 (mm)
REVERT: D  342 ASP cc_start: 0.7381 (t70) cc_final: 0.7142 (t0)
REVERT: D  399 ASN cc_start: 0.7755 (t0) cc_final: 0.7518 (t0)
REVERT: D  423 ASN cc_start: 0.7734 (m-40) cc_final: 0.7378 (t0)
REVERT: D  544 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7871 (ptp90)
  outliers start: 11
  outliers final: 4
  residues processed: 81
  average time/residue: 0.0879
  time to fit residues: 9.0269
Evaluate side-chains
  71 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 65
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   69 TYR
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  438 ASP
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 29 optimal weight:    0.0870
   chunk 51 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9990
   chunk 8 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0070
   chunk 39 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.4576

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

Flipped N/Q/H residues before XYZ refinement:
D 116 HIS
D 146 ASN
D 543 ASN
G -19 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.198148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.168246 restraints weight = 6388.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.167195 restraints weight = 6693.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.168689 restraints weight = 4911.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.169022 restraints weight = 3539.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.169375 restraints weight = 3573.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5165  Z= 0.148
  Angle     :  0.600   9.317   6999  Z= 0.315
  Chirality :  0.038   0.130    803
  Planarity :  0.005   0.066    909
  Dihedral  :  4.459  21.946    700
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.03 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 18.98 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.82 (0.34), residues: 638
  helix:  0.25 (0.27), residues: 393
  sheet:  None (None), residues: 0
  loop : -1.83 (0.41), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 171 
 TYR   0.024   0.002   TYR D 472 
 PHE   0.007   0.001   PHE D 623 
 TRP   0.009   0.001   TRP G  -2 
 HIS   0.007   0.001   HIS D 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 5165)
  covalent geometry    : angle       0.60029 ( 6999)
  hydrogen bonds       : bond        0.03460 (  227)
  hydrogen bonds       : angle       4.10729 (  666)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.204 
Fit side-chains
REVERT: D    1 MET cc_start: 0.6526 (ptp) cc_final: 0.6175 (ptm)
REVERT: D   38 TYR cc_start: 0.5538 (OUTLIER) cc_final: 0.5083 (m-80)
REVERT: D   69 TYR cc_start: 0.6010 (OUTLIER) cc_final: 0.4604 (p90)
REVERT: D  163 TYR cc_start: 0.8704 (t80) cc_final: 0.8319 (t80)
REVERT: D  290 ILE cc_start: 0.6167 (OUTLIER) cc_final: 0.5682 (mm)
REVERT: D  342 ASP cc_start: 0.7490 (t70) cc_final: 0.7172 (t0)
REVERT: D  399 ASN cc_start: 0.7899 (t0) cc_final: 0.7648 (t0)
REVERT: D  423 ASN cc_start: 0.7898 (m-40) cc_final: 0.7341 (t0)
  outliers start: 14
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0737
  time to fit residues: 8.3859
Evaluate side-chains
  74 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   38 TYR
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   69 TYR
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  438 ASP
Chi-restraints excluded: chain D residue  498 VAL
Chi-restraints excluded: chain D residue  511 ASN
Chi-restraints excluded: chain D residue  609 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 15 optimal weight:    0.1980
   chunk 30 optimal weight:    0.0370
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0570
   chunk 14 optimal weight:    0.0470
   chunk 61 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.1874

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

Flipped N/Q/H residues before XYZ refinement:
D 146 ASN
G -19 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.201367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.172271 restraints weight = 6384.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.171071 restraints weight = 5545.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.173140 restraints weight = 4373.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.173162 restraints weight = 2946.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.173643 restraints weight = 2603.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5165  Z= 0.111
  Angle     :  0.570  10.798   6999  Z= 0.299
  Chirality :  0.037   0.126    803
  Planarity :  0.004   0.065    909
  Dihedral  :  4.326  20.940    700
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 20.26 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.63 (0.34), residues: 638
  helix:  0.40 (0.27), residues: 394
  sheet:  None (None), residues: 0
  loop : -1.75 (0.41), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D 264 
 TYR   0.022   0.001   TYR D 472 
 PHE   0.005   0.001   PHE D 388 
 TRP   0.006   0.001   TRP G  -2 
 HIS   0.007   0.001   HIS D 166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 5165)
  covalent geometry    : angle       0.57003 ( 6999)
  hydrogen bonds       : bond        0.03080 (  227)
  hydrogen bonds       : angle       3.90715 (  666)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.142 
Fit side-chains
REVERT: D    1 MET cc_start: 0.6527 (ptp) cc_final: 0.6203 (ptm)
REVERT: D   69 TYR cc_start: 0.5960 (OUTLIER) cc_final: 0.4632 (p90)
REVERT: D  163 TYR cc_start: 0.8738 (t80) cc_final: 0.8385 (t80)
REVERT: D  290 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5426 (mm)
REVERT: D  342 ASP cc_start: 0.7285 (t70) cc_final: 0.7071 (t0)
REVERT: D  423 ASN cc_start: 0.7868 (m-40) cc_final: 0.7305 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 76
  average time/residue: 0.0624
  time to fit residues: 6.3556
Evaluate side-chains
  69 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   69 TYR
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  438 ASP
Chi-restraints excluded: chain D residue  582 THR
Chi-restraints excluded: chain G residue  -20 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 4 optimal weight:    0.2980
   chunk 39 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
D 146 ASN
G -19 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.196953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.168770 restraints weight = 6378.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.171884 restraints weight = 8495.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.172141 restraints weight = 3954.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.170821 restraints weight = 4648.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.171732 restraints weight = 3443.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5165  Z= 0.178
  Angle     :  0.634  11.119   6999  Z= 0.327
  Chirality :  0.039   0.129    803
  Planarity :  0.005   0.065    909
  Dihedral  :  4.449  22.674    700
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 21.53 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.84 (0.34), residues: 638
  helix:  0.26 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -1.93 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 171 
 TYR   0.023   0.002   TYR D 472 
 PHE   0.009   0.001   PHE D 623 
 TRP   0.011   0.002   TRP G  -2 
 HIS   0.006   0.001   HIS D 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 5165)
  covalent geometry    : angle       0.63401 ( 6999)
  hydrogen bonds       : bond        0.03496 (  227)
  hydrogen bonds       : angle       4.06326 (  666)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.126 
Fit side-chains
REVERT: D    1 MET cc_start: 0.6621 (ptp) cc_final: 0.6416 (ptm)
REVERT: D   36 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6177 (mp)
REVERT: D   38 TYR cc_start: 0.5463 (OUTLIER) cc_final: 0.5069 (m-80)
REVERT: D   69 TYR cc_start: 0.6332 (OUTLIER) cc_final: 0.4958 (p90)
REVERT: D  163 TYR cc_start: 0.8718 (t80) cc_final: 0.8419 (t80)
REVERT: D  290 ILE cc_start: 0.6161 (OUTLIER) cc_final: 0.5545 (mm)
REVERT: D  399 ASN cc_start: 0.7709 (t0) cc_final: 0.7481 (t0)
REVERT: D  423 ASN cc_start: 0.7734 (m-40) cc_final: 0.7408 (t0)
REVERT: D  482 ARG cc_start: 0.8385 (ptm160) cc_final: 0.7979 (ptm160)
REVERT: D  557 ILE cc_start: 0.8480 (tt) cc_final: 0.8247 (tt)
  outliers start: 13
  outliers final: 7
  residues processed: 83
  average time/residue: 0.0652
  time to fit residues: 7.0835
Evaluate side-chains
  72 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   24 LEU
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   38 TYR
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   69 TYR
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  438 ASP
Chi-restraints excluded: chain D residue  511 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 57 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 58 optimal weight:    0.3980
   chunk 55 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
G -19 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.193663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.167818 restraints weight = 6297.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.166873 restraints weight = 8365.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.167250 restraints weight = 6767.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.165829 restraints weight = 5654.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.166590 restraints weight = 3942.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5165  Z= 0.166
  Angle     :  0.631  11.552   6999  Z= 0.327
  Chirality :  0.039   0.129    803
  Planarity :  0.005   0.064    909
  Dihedral  :  4.477  22.595    700
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.13 %
    Favored  : 88.87 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.26 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.83 (0.34), residues: 638
  helix:  0.28 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -1.94 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D 264 
 TYR   0.022   0.002   TYR D 472 
 PHE   0.008   0.001   PHE D 623 
 TRP   0.012   0.002   TRP G  -2 
 HIS   0.005   0.001   HIS D 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 5165)
  covalent geometry    : angle       0.63149 ( 6999)
  hydrogen bonds       : bond        0.03417 (  227)
  hydrogen bonds       : angle       4.05840 (  666)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.193 
Fit side-chains
REVERT: D   36 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6267 (mp)
REVERT: D   38 TYR cc_start: 0.5492 (OUTLIER) cc_final: 0.5107 (m-80)
REVERT: D   69 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.4929 (p90)
REVERT: D  163 TYR cc_start: 0.8685 (t80) cc_final: 0.8353 (t80)
REVERT: D  200 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7361 (mt)
REVERT: D  290 ILE cc_start: 0.6096 (OUTLIER) cc_final: 0.5499 (mm)
REVERT: D  399 ASN cc_start: 0.7651 (t0) cc_final: 0.7407 (t0)
REVERT: D  482 ARG cc_start: 0.8320 (ptm160) cc_final: 0.7939 (ptm160)
REVERT: D  557 ILE cc_start: 0.8453 (tt) cc_final: 0.8226 (tt)
  outliers start: 15
  outliers final: 7
  residues processed: 77
  average time/residue: 0.0576
  time to fit residues: 6.1257
Evaluate side-chains
  74 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   38 TYR
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain D residue   69 TYR
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  438 ASP
Chi-restraints excluded: chain D residue  582 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 59 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0770
   chunk 23 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 27 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 30 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
G -19 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.197325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.169991 restraints weight = 6421.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.167129 restraints weight = 5364.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.168303 restraints weight = 4926.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.168800 restraints weight = 3394.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.169067 restraints weight = 3261.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5165  Z= 0.161
  Angle     :  0.638  12.062   6999  Z= 0.329
  Chirality :  0.039   0.128    803
  Planarity :  0.005   0.063    909
  Dihedral  :  4.473  22.525    700
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.50 %
    Favored  : 89.50 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 22.08 %
    Favored  : 75.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.83 (0.34), residues: 638
  helix:  0.28 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -1.94 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 171 
 TYR   0.022   0.001   TYR D 472 
 PHE   0.008   0.001   PHE D 623 
 TRP   0.013   0.002   TRP G  -2 
 HIS   0.005   0.001   HIS D 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 5165)
  covalent geometry    : angle       0.63764 ( 6999)
  hydrogen bonds       : bond        0.03407 (  227)
  hydrogen bonds       : angle       3.99070 (  666)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.175 
Fit side-chains
REVERT: D   38 TYR cc_start: 0.5962 (OUTLIER) cc_final: 0.5290 (m-80)
REVERT: D   69 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.4630 (p90)
REVERT: D  163 TYR cc_start: 0.8776 (t80) cc_final: 0.8441 (t80)
REVERT: D  200 ILE cc_start: 0.7528 (OUTLIER) cc_final: 0.7197 (mt)
REVERT: D  290 ILE cc_start: 0.6077 (OUTLIER) cc_final: 0.5391 (mm)
REVERT: D  482 ARG cc_start: 0.8603 (ptm160) cc_final: 0.8212 (ptm160)
REVERT: D  557 ILE cc_start: 0.8491 (tt) cc_final: 0.8242 (tt)
  outliers start: 15
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0502
  time to fit residues: 5.2271
Evaluate side-chains
  71 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   24 LEU
Chi-restraints excluded: chain D residue   38 TYR
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain D residue   69 TYR
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  438 ASP
Chi-restraints excluded: chain D residue  582 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 17 optimal weight:    0.4980
   chunk 9 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
G -19 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.196343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.167609 restraints weight = 6462.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.167442 restraints weight = 7255.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.169126 restraints weight = 5507.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.168841 restraints weight = 4302.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.169040 restraints weight = 3971.172|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5165  Z= 0.174
  Angle     :  0.673  13.434   6999  Z= 0.342
  Chirality :  0.040   0.134    803
  Planarity :  0.005   0.063    909
  Dihedral  :  4.526  22.712    700
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.97 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 22.45 %
    Favored  : 74.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.86 (0.34), residues: 638
  helix:  0.27 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -1.97 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 264 
 TYR   0.022   0.002   TYR D 472 
 PHE   0.008   0.001   PHE D 623 
 TRP   0.013   0.002   TRP G  -2 
 HIS   0.005   0.001   HIS D 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 5165)
  covalent geometry    : angle       0.67345 ( 6999)
  hydrogen bonds       : bond        0.03540 (  227)
  hydrogen bonds       : angle       4.08398 (  666)

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

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

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1276 Ramachandran restraints generated.
    638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.117 
Fit side-chains
REVERT: D   36 LEU cc_start: 0.6336 (mp) cc_final: 0.5667 (mp)
REVERT: D   38 TYR cc_start: 0.5567 (OUTLIER) cc_final: 0.5107 (m-80)
REVERT: D   69 TYR cc_start: 0.6188 (OUTLIER) cc_final: 0.4914 (p90)
REVERT: D  163 TYR cc_start: 0.8712 (t80) cc_final: 0.8391 (t80)
REVERT: D  200 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7382 (mt)
REVERT: D  399 ASN cc_start: 0.7761 (t0) cc_final: 0.7523 (t0)
REVERT: D  482 ARG cc_start: 0.8466 (ptm160) cc_final: 0.8096 (ptm160)
REVERT: D  557 ILE cc_start: 0.8462 (tt) cc_final: 0.8222 (tt)
  outliers start: 16
  outliers final: 11
  residues processed: 78
  average time/residue: 0.0491
  time to fit residues: 5.2295
Evaluate side-chains
  75 residues out of total 549 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   24 LEU
Chi-restraints excluded: chain D residue   38 TYR
Chi-restraints excluded: chain D residue   48 THR
Chi-restraints excluded: chain D residue   64 LEU
Chi-restraints excluded: chain D residue   68 HIS
Chi-restraints excluded: chain D residue   69 TYR
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain D residue  200 ILE
Chi-restraints excluded: chain D residue  290 ILE
Chi-restraints excluded: chain D residue  364 ILE
Chi-restraints excluded: chain D residue  402 VAL
Chi-restraints excluded: chain D residue  438 ASP
Chi-restraints excluded: chain D residue  511 ASN
Chi-restraints excluded: chain D residue  582 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    0.4980
   chunk 29 optimal weight:    0.0570
   chunk 27 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
G -19 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.187721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.158660 restraints weight = 6560.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.160892 restraints weight = 8249.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.162919 restraints weight = 4135.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.161961 restraints weight = 3591.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.162349 restraints weight = 3090.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5165  Z= 0.183
  Angle     :  0.675  12.929   6999  Z= 0.345
  Chirality :  0.040   0.141    803
  Planarity :  0.005   0.063    909
  Dihedral  :  4.565  22.967    700
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 22.81 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.90 (0.34), residues: 638
  helix:  0.24 (0.26), residues: 397
  sheet:  None (None), residues: 0
  loop : -1.99 (0.41), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 171 
 TYR   0.022   0.002   TYR D 472 
 PHE   0.008   0.001   PHE D 623 
 TRP   0.014   0.002   TRP G  -2 
 HIS   0.005   0.001   HIS D 627 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 5165)
  covalent geometry    : angle       0.67489 ( 6999)
  hydrogen bonds       : bond        0.03611 (  227)
  hydrogen bonds       : angle       4.14263 (  666)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1177.91 seconds
wall clock time: 21 minutes 4.95 seconds (1264.95 seconds total)