Starting phenix.real_space_refine
on Fri Aug 22 21:45:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pd5_17601/08_2025/8pd5_17601.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pd5_17601/08_2025/8pd5_17601.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pd5_17601/08_2025/8pd5_17601.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pd5_17601/08_2025/8pd5_17601.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pd5_17601/08_2025/8pd5_17601.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pd5_17601/08_2025/8pd5_17601.cif"
  }
  resolution = 3.4
  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=   0.001 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      41      5.16       5
     C    5286      2.51       5
     N    1344      2.21       5
     O    1422      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  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: 8093
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8093
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1024, 8093
          Classifications: {'peptide': 1024}
          Link IDs: {'PTRANS': 30, 'TRANS': 993}
          Chain breaks: 5
  Time building chain proxies: 2.16, per 1000 atoms: 0.27
  Number of scatterers: 8093
  At special positions: 0
  Unit cell: (82.764, 114.532, 124.564, 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      41     16.00
     O    1422      8.00
     N    1344      7.00
     C    5286      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: 0.71
  Conformation dependent library (CDL) restraints added in 447.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      65.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 77 through 96
      removed outlier: 3.984A  pdb=" N   LYS A  96 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 119
    Processing helix  chain 'A' and resid 121 through 131
      removed outlier: 3.749A  pdb=" N   HIS A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   ASP A 129 " --> pdb=" O   GLU A 125 " (cutoff:3.500A)
      removed outlier: 5.526A  pdb=" N   VAL A 130 " --> pdb=" O   HIS A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 152
      Proline residue:  A 144  - end of helix
    Processing helix  chain 'A' and resid 156 through 187
      removed outlier: 5.152A  pdb=" N   SER A 164 " --> pdb=" O   MET A 160 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   GLN A 165 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU A 169 " --> pdb=" O   GLN A 165 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   LEU A 174 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 205
    Processing helix  chain 'A' and resid 210 through 217
      removed outlier: 4.048A  pdb=" N   LEU A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 253
      removed outlier: 3.990A  pdb=" N   THR A 228 " --> pdb=" O   LYS A 224 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ILE A 229 " --> pdb=" O   GLN A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 272
    Processing helix  chain 'A' and resid 274 through 292
    Processing helix  chain 'A' and resid 297 through 317
    Processing helix  chain 'A' and resid 323 through 336
    Processing helix  chain 'A' and resid 338 through 340
      No H-bonds generated for 'chain 'A' and resid 338 through 340'
    Processing helix  chain 'A' and resid 343 through 374
      removed outlier: 3.817A  pdb=" N   ARG A 351 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 379
      No H-bonds generated for 'chain 'A' and resid 377 through 379'
    Processing helix  chain 'A' and resid 382 through 412
      removed outlier: 4.010A  pdb=" N   PHE A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
      Proline residue:  A 408  - end of helix
      removed outlier: 4.656A  pdb=" N   ARG A 412 " --> pdb=" O   PRO A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 427
    Processing helix  chain 'A' and resid 433 through 445
    Processing helix  chain 'A' and resid 450 through 468
    Processing helix  chain 'A' and resid 470 through 480
      removed outlier: 4.854A  pdb=" N   GLN A 475 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   THR A 476 " --> pdb=" O   THR A 472 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ARG A 479 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 513
    Processing helix  chain 'A' and resid 523 through 529
    Processing helix  chain 'A' and resid 572 through 599
    Processing helix  chain 'A' and resid 605 through 620
    Processing helix  chain 'A' and resid 628 through 635
      removed outlier: 4.543A  pdb=" N   LYS A 633 " --> pdb=" O   ASP A 629 " (cutoff:3.500A)
      removed outlier: 5.144A  pdb=" N   SER A 634 " --> pdb=" O   ASP A 630 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   TRP A 635 " --> pdb=" O   LEU A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 651
    Processing helix  chain 'A' and resid 655 through 658
      No H-bonds generated for 'chain 'A' and resid 655 through 658'
    Processing helix  chain 'A' and resid 678 through 706
      removed outlier: 4.979A  pdb=" N   VAL A 693 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      Proline residue:  A 694  - end of helix
      removed outlier: 4.151A  pdb=" N   ASP A 703 " --> pdb=" O   PHE A 699 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ALA A 706 " --> pdb=" O   GLN A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 762 through 782
      removed outlier: 3.523A  pdb=" N   VAL A 776 " --> pdb=" O   VAL A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 857
      removed outlier: 4.859A  pdb=" N   LYS A 815 " --> pdb=" O   LEU A 811 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   ALA A 816 " --> pdb=" O   ARG A 812 " (cutoff:3.500A)
      Proline residue:  A 819  - end of helix
      removed outlier: 3.588A  pdb=" N   LEU A 835 " --> pdb=" O   ASN A 831 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LYS A 852 " --> pdb=" O   GLU A 848 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   ARG A 856 " --> pdb=" O   LYS A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 888
      removed outlier: 3.589A  pdb=" N   GLN A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 918
    Processing helix  chain 'A' and resid 924 through 940
    Processing helix  chain 'A' and resid 953 through 959
    Processing helix  chain 'A' and resid 967 through 976
      removed outlier: 3.570A  pdb=" N   ARG A 976 " --> pdb=" O   PHE A 972 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1049
    Processing helix  chain 'A' and resid 1070 through 1079
    Processing helix  chain 'A' and resid 1086 through 1107
      removed outlier: 3.673A  pdb=" N   ARG A1097 " --> pdb=" O   VAL A1093 " (cutoff:3.500A)
      Proline residue:  A1101  - end of helix
    Processing helix  chain 'A' and resid 1114 through 1123
      removed outlier: 3.794A  pdb=" N   ARG A1123 " --> pdb=" O   LEU A1119 " (cutoff:3.500A)

    472 hydrogen bonds defined for protein.
    1416 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: 1.24

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2565
        1.35 -     1.46: 1847
        1.46 -     1.58: 3763
        1.58 -     1.70: 0
        1.70 -     1.82: 76
  Bond restraints: 8251
  Sorted by residual:
  bond pdb=" N   HIS A  71 "
       pdb=" CA  HIS A  71 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.84e+00
  bond pdb=" CA  PHE A1032 "
       pdb=" CB  PHE A1032 "
    ideal  model  delta    sigma   weight residual
    1.526  1.552 -0.026 1.53e-02 4.27e+03 2.81e+00
  bond pdb=" CA  ILE A 488 "
       pdb=" CB  ILE A 488 "
    ideal  model  delta    sigma   weight residual
    1.539  1.532  0.007 5.40e-03 3.43e+04 1.87e+00
  bond pdb=" CB  LYS A 224 "
       pdb=" CG  LYS A 224 "
    ideal  model  delta    sigma   weight residual
    1.520  1.558 -0.038 3.00e-02 1.11e+03 1.56e+00
  bond pdb=" C   THR A1181 "
       pdb=" N   GLU A1182 "
    ideal  model  delta    sigma   weight residual
    1.330  1.342 -0.012 1.36e-02 5.41e+03 7.81e-01
  ... (remaining 8246 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 11109
        2.21 -     4.41: 72
        4.41 -     6.62: 6
        6.62 -     8.82: 2
        8.82 -    11.03: 1
  Bond angle restraints: 11190
  Sorted by residual:
  angle pdb=" CB  MET A 857 "
        pdb=" CG  MET A 857 "
        pdb=" SD  MET A 857 "
      ideal   model   delta    sigma   weight residual
     112.70  123.73  -11.03 3.00e+00 1.11e-01 1.35e+01
  angle pdb=" N   ILE A 657 "
        pdb=" CA  ILE A 657 "
        pdb=" C   ILE A 657 "
      ideal   model   delta    sigma   weight residual
     111.62  109.15    2.47 7.90e-01 1.60e+00 9.76e+00
  angle pdb=" CA  LYS A 224 "
        pdb=" CB  LYS A 224 "
        pdb=" CG  LYS A 224 "
      ideal   model   delta    sigma   weight residual
     114.10  120.23   -6.13 2.00e+00 2.50e-01 9.40e+00
  angle pdb=" N   VAL A 273 "
        pdb=" CA  VAL A 273 "
        pdb=" C   VAL A 273 "
      ideal   model   delta    sigma   weight residual
     111.62  109.21    2.41 7.90e-01 1.60e+00 9.32e+00
  angle pdb=" CA  MET A 857 "
        pdb=" CB  MET A 857 "
        pdb=" CG  MET A 857 "
      ideal   model   delta    sigma   weight residual
     114.10  119.25   -5.15 2.00e+00 2.50e-01 6.64e+00
  ... (remaining 11185 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.18: 4483
       16.18 -    32.37: 322
       32.37 -    48.55: 92
       48.55 -    64.73: 25
       64.73 -    80.92: 4
  Dihedral angle restraints: 4926
    sinusoidal: 1947
      harmonic: 2979
  Sorted by residual:
  dihedral pdb=" CA  LEU A 417 "
           pdb=" C   LEU A 417 "
           pdb=" N   THR A 418 "
           pdb=" CA  THR A 418 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.31   17.69     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CA  ARG A1162 "
           pdb=" C   ARG A1162 "
           pdb=" N   SER A1163 "
           pdb=" CA  SER A1163 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.74  -17.26     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CG  ARG A 899 "
           pdb=" CD  ARG A 899 "
           pdb=" NE  ARG A 899 "
           pdb=" CZ  ARG A 899 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -135.59  -44.41     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 4923 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 873
       0.029 -    0.058: 297
       0.058 -    0.087: 120
       0.087 -    0.116: 42
       0.116 -    0.145: 11
  Chirality restraints: 1343
  Sorted by residual:
  chirality pdb=" CA  ILE A 948 "
            pdb=" N   ILE A 948 "
            pdb=" C   ILE A 948 "
            pdb=" CB  ILE A 948 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.27e-01
  chirality pdb=" CA  ILE A1068 "
            pdb=" N   ILE A1068 "
            pdb=" C   ILE A1068 "
            pdb=" CB  ILE A1068 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  ILE A1042 "
            pdb=" N   ILE A1042 "
            pdb=" C   ILE A1042 "
            pdb=" CB  ILE A1042 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1340 not shown)

  Planarity restraints: 1379
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 693 "   -0.040 5.00e-02 4.00e+02   6.11e-02 5.97e+00
        pdb=" N   PRO A 694 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A 694 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 694 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 224 "   -0.008 2.00e-02 2.50e+03   1.66e-02 2.74e+00
        pdb=" C   LYS A 224 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LYS A 224 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLN A 225 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 275 "   -0.025 5.00e-02 4.00e+02   3.85e-02 2.37e+00
        pdb=" N   PRO A 276 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 276 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 276 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1376 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 99
        2.70 -     3.25: 8582
        3.25 -     3.80: 12532
        3.80 -     4.35: 15777
        4.35 -     4.90: 26717
  Nonbonded interactions: 63707
  Sorted by model distance:
  nonbonded pdb=" N   GLU A1071 "
            pdb=" OE1 GLU A1071 "
     model   vdw
     2.148 3.120
  nonbonded pdb=" OD1 ASP A1034 "
            pdb=" N   TYR A1035 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" OD1 ASP A 855 "
            pdb=" N   ARG A 856 "
     model   vdw
     2.395 3.120
  nonbonded pdb=" O   ILE A 293 "
            pdb=" NZ  LYS A 939 "
     model   vdw
     2.432 3.120
  nonbonded pdb=" NH2 ARG A1092 "
            pdb=" O   GLU A1122 "
     model   vdw
     2.488 3.120
  ... (remaining 63702 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.450
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.970
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
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   0.038   8251  Z= 0.133
  Angle     :  0.534  11.027  11190  Z= 0.301
  Chirality :  0.038   0.145   1343
  Planarity :  0.004   0.061   1379
  Dihedral  : 13.122  80.917   2994
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 2.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.46 %
    Favored  : 94.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.83 (0.26), residues: 1012
  helix:  1.80 (0.19), residues: 702
  sheet:  0.65 (0.70), residues: 47
  loop : -0.20 (0.41), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 809 
 TYR   0.008   0.001   TYR A1066 
 PHE   0.023   0.001   PHE A 699 
 TRP   0.019   0.001   TRP A1112 
 HIS   0.003   0.001   HIS A 292 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8251)
  covalent geometry    : angle       0.53376 (11190)
  hydrogen bonds       : bond        0.08770 (  472)
  hydrogen bonds       : angle       4.58019 ( 1416)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8019 (ttmt) cc_final: 0.7484 (ttpp)
REVERT: A   97 LYS cc_start: 0.8121 (mttt) cc_final: 0.7915 (mttt)
REVERT: A  108 ILE cc_start: 0.7425 (mm) cc_final: 0.7166 (mt)
REVERT: A  125 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7504 (mm-30)
REVERT: A  128 ARG cc_start: 0.7442 (ttp-170) cc_final: 0.7229 (ttm170)
REVERT: A  154 MET cc_start: 0.7790 (mtm) cc_final: 0.7350 (mtp)
REVERT: A  155 ASP cc_start: 0.6929 (t70) cc_final: 0.6471 (t70)
REVERT: A  163 PHE cc_start: 0.7732 (t80) cc_final: 0.7323 (t80)
REVERT: A  164 SER cc_start: 0.8123 (m) cc_final: 0.7753 (p)
REVERT: A  233 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7248 (tt0)
REVERT: A  249 MET cc_start: 0.7810 (tmm) cc_final: 0.7542 (ttp)
REVERT: A  250 LYS cc_start: 0.7393 (mttt) cc_final: 0.7138 (mtmm)
REVERT: A  284 LYS cc_start: 0.7862 (mmtp) cc_final: 0.7654 (mmtm)
REVERT: A  316 ASP cc_start: 0.7646 (t0) cc_final: 0.7122 (m-30)
REVERT: A  337 GLU cc_start: 0.7550 (mm-30) cc_final: 0.6908 (mp0)
REVERT: A  375 LYS cc_start: 0.7823 (mtpp) cc_final: 0.7570 (mtmt)
REVERT: A  383 MET cc_start: 0.7573 (mmp) cc_final: 0.7339 (mmm)
REVERT: A  483 MET cc_start: 0.8549 (mtp) cc_final: 0.8081 (mtm)
REVERT: A  579 MET cc_start: 0.6339 (tpt) cc_final: 0.6052 (tpp)
REVERT: A  580 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6663 (mm-30)
REVERT: A  586 MET cc_start: 0.6535 (ttm) cc_final: 0.6296 (ttt)
REVERT: A  588 LYS cc_start: 0.7523 (ttpp) cc_final: 0.7247 (ttmm)
REVERT: A  602 MET cc_start: 0.7693 (mtm) cc_final: 0.7489 (ttm)
REVERT: A  609 ARG cc_start: 0.7558 (ttm-80) cc_final: 0.6950 (tmm160)
REVERT: A  638 LYS cc_start: 0.7758 (mttt) cc_final: 0.7476 (mttt)
REVERT: A  647 LYS cc_start: 0.7566 (mmtm) cc_final: 0.7272 (mmtm)
REVERT: A  650 ASP cc_start: 0.7406 (m-30) cc_final: 0.6687 (m-30)
REVERT: A  678 MET cc_start: 0.7459 (mmm) cc_final: 0.7239 (mmm)
REVERT: A  766 PHE cc_start: 0.6423 (t80) cc_final: 0.6135 (t80)
REVERT: A  841 LYS cc_start: 0.7951 (ttpp) cc_final: 0.7641 (mmtt)
REVERT: A  849 GLU cc_start: 0.7131 (tt0) cc_final: 0.6698 (tt0)
REVERT: A  866 GLU cc_start: 0.7124 (tp30) cc_final: 0.6773 (tp30)
REVERT: A  938 MET cc_start: 0.7863 (ttm) cc_final: 0.7605 (ttt)
REVERT: A  968 LYS cc_start: 0.7804 (mttt) cc_final: 0.7459 (mttt)
REVERT: A  994 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7130 (mt-10)
REVERT: A 1007 LYS cc_start: 0.7600 (tttt) cc_final: 0.7327 (tttm)
REVERT: A 1009 TYR cc_start: 0.7631 (t80) cc_final: 0.7284 (t80)
REVERT: A 1034 ASP cc_start: 0.7319 (t0) cc_final: 0.7099 (t70)
REVERT: A 1035 TYR cc_start: 0.7948 (m-80) cc_final: 0.7556 (m-80)
REVERT: A 1051 LYS cc_start: 0.7904 (ttmm) cc_final: 0.7667 (ttmm)
REVERT: A 1052 PRO cc_start: 0.8474 (Cg_exo) cc_final: 0.8244 (Cg_endo)
REVERT: A 1073 MET cc_start: 0.7225 (mmm) cc_final: 0.6856 (mmm)
REVERT: A 1094 VAL cc_start: 0.7543 (t) cc_final: 0.7300 (p)
REVERT: A 1097 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7709 (mtm-85)
REVERT: A 1127 VAL cc_start: 0.8130 (t) cc_final: 0.7811 (p)
REVERT: A 1128 ASP cc_start: 0.7271 (m-30) cc_final: 0.6705 (t0)
REVERT: A 1186 LEU cc_start: 0.8475 (tp) cc_final: 0.8230 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.1104
  time to fit residues: 36.8016
Evaluate side-chains
  221 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.3980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.0980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN
A 448 ASN
A 597 GLN
A 955 ASN
A1106 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.135101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.112662 restraints weight = 11568.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 1.59
r_work: 0.3132 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8251  Z= 0.140
  Angle     :  0.506   7.413  11190  Z= 0.261
  Chirality :  0.039   0.133   1343
  Planarity :  0.004   0.051   1379
  Dihedral  :  3.896  16.031   1093
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 11.04 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.27), residues: 1012
  helix:  2.00 (0.19), residues: 713
  sheet:  0.70 (0.68), residues: 58
  loop :  0.12 (0.44), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 161 
 TYR   0.015   0.001   TYR A 984 
 PHE   0.016   0.001   PHE A 999 
 TRP   0.017   0.001   TRP A 635 
 HIS   0.005   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8251)
  covalent geometry    : angle       0.50624 (11190)
  hydrogen bonds       : bond        0.04723 (  472)
  hydrogen bonds       : angle       3.69762 ( 1416)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 223
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7982 (ttmt)
REVERT: A  108 ILE cc_start: 0.8369 (mm) cc_final: 0.8082 (mt)
REVERT: A  124 GLU cc_start: 0.7468 (tt0) cc_final: 0.7221 (tm-30)
REVERT: A  125 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7755 (mt-10)
REVERT: A  154 MET cc_start: 0.8035 (mtm) cc_final: 0.7770 (mtp)
REVERT: A  163 PHE cc_start: 0.8340 (t80) cc_final: 0.8056 (t80)
REVERT: A  164 SER cc_start: 0.8786 (m) cc_final: 0.8434 (p)
REVERT: A  209 ASP cc_start: 0.7699 (t0) cc_final: 0.7302 (t0)
REVERT: A  233 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7301 (tt0)
REVERT: A  249 MET cc_start: 0.8418 (tmm) cc_final: 0.8140 (ttp)
REVERT: A  250 LYS cc_start: 0.8253 (mttt) cc_final: 0.7991 (mtmm)
REVERT: A  322 SER cc_start: 0.8513 (t) cc_final: 0.8025 (p)
REVERT: A  337 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7655 (mp0)
REVERT: A  383 MET cc_start: 0.8118 (mmp) cc_final: 0.7879 (mmt)
REVERT: A  401 MET cc_start: 0.7813 (mmm) cc_final: 0.7456 (mmm)
REVERT: A  580 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7362 (mm-30)
REVERT: A  588 LYS cc_start: 0.8280 (ttpp) cc_final: 0.8003 (ttmt)
REVERT: A  609 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7655 (tmm160)
REVERT: A  616 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7231 (mt-10)
REVERT: A  849 GLU cc_start: 0.7519 (tt0) cc_final: 0.7236 (tt0)
REVERT: A  853 ILE cc_start: 0.8005 (mm) cc_final: 0.7703 (tt)
REVERT: A  866 GLU cc_start: 0.7629 (tp30) cc_final: 0.7419 (tp30)
REVERT: A  968 LYS cc_start: 0.8521 (mttt) cc_final: 0.8260 (mttt)
REVERT: A 1007 LYS cc_start: 0.7945 (tttt) cc_final: 0.7698 (tttm)
REVERT: A 1009 TYR cc_start: 0.8165 (t80) cc_final: 0.7791 (t80)
REVERT: A 1033 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7863 (mt-10)
REVERT: A 1034 ASP cc_start: 0.7702 (t0) cc_final: 0.7401 (t0)
REVERT: A 1035 TYR cc_start: 0.8357 (m-80) cc_final: 0.8059 (m-80)
REVERT: A 1066 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8059 (m-80)
REVERT: A 1087 GLU cc_start: 0.8003 (tp30) cc_final: 0.7740 (tp30)
  outliers start: 15
  outliers final: 7
  residues processed: 227
  average time/residue: 0.1158
  time to fit residues: 34.2331
Evaluate side-chains
  222 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 214
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0870
   chunk 7 optimal weight:    0.0970
   chunk 39 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 83 optimal weight:    0.8980
   chunk 70 optimal weight:    0.3980
   chunk 60 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
A 225 GLN
A 955 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.135531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.113104 restraints weight = 11428.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.57
r_work: 0.3259 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8251  Z= 0.117
  Angle     :  0.476  11.750  11190  Z= 0.239
  Chirality :  0.038   0.136   1343
  Planarity :  0.004   0.051   1379
  Dihedral  :  3.694  14.407   1093
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.42 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.27), residues: 1012
  helix:  2.12 (0.19), residues: 715
  sheet:  0.54 (0.76), residues: 47
  loop :  0.15 (0.43), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 161 
 TYR   0.019   0.001   TYR A 358 
 PHE   0.023   0.001   PHE A 766 
 TRP   0.015   0.001   TRP A 635 
 HIS   0.007   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8251)
  covalent geometry    : angle       0.47624 (11190)
  hydrogen bonds       : bond        0.04315 (  472)
  hydrogen bonds       : angle       3.55236 ( 1416)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 220
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7980 (ttmt)
REVERT: A  108 ILE cc_start: 0.8430 (mm) cc_final: 0.8159 (mt)
REVERT: A  125 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7808 (mt-10)
REVERT: A  163 PHE cc_start: 0.8340 (t80) cc_final: 0.8054 (t80)
REVERT: A  164 SER cc_start: 0.8830 (m) cc_final: 0.8464 (p)
REVERT: A  209 ASP cc_start: 0.7567 (t0) cc_final: 0.7146 (t0)
REVERT: A  233 GLU cc_start: 0.7570 (tm-30) cc_final: 0.7241 (tt0)
REVERT: A  250 LYS cc_start: 0.8225 (mttt) cc_final: 0.8012 (mtmm)
REVERT: A  322 SER cc_start: 0.8485 (t) cc_final: 0.7975 (p)
REVERT: A  337 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7691 (mp0)
REVERT: A  383 MET cc_start: 0.8088 (mmp) cc_final: 0.7869 (mmt)
REVERT: A  398 ILE cc_start: 0.8407 (mm) cc_final: 0.8083 (mt)
REVERT: A  401 MET cc_start: 0.7857 (mmm) cc_final: 0.7493 (mmm)
REVERT: A  580 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7354 (mm-30)
REVERT: A  586 MET cc_start: 0.7190 (ttm) cc_final: 0.6916 (ttt)
REVERT: A  588 LYS cc_start: 0.8281 (ttpp) cc_final: 0.8034 (ttmt)
REVERT: A  602 MET cc_start: 0.8028 (ttm) cc_final: 0.7541 (mtp)
REVERT: A  616 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7098 (mt-10)
REVERT: A  647 LYS cc_start: 0.7926 (mmtm) cc_final: 0.7690 (mmtm)
REVERT: A  849 GLU cc_start: 0.7349 (tt0) cc_final: 0.7138 (tt0)
REVERT: A  853 ILE cc_start: 0.8047 (mm) cc_final: 0.7765 (tt)
REVERT: A  938 MET cc_start: 0.8367 (tpp) cc_final: 0.8037 (ttt)
REVERT: A  968 LYS cc_start: 0.8582 (mttt) cc_final: 0.8299 (mttt)
REVERT: A 1009 TYR cc_start: 0.8101 (t80) cc_final: 0.7741 (t80)
REVERT: A 1035 TYR cc_start: 0.8340 (m-80) cc_final: 0.8065 (m-80)
REVERT: A 1048 LEU cc_start: 0.8266 (mt) cc_final: 0.8002 (mt)
REVERT: A 1066 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.7968 (m-80)
REVERT: A 1073 MET cc_start: 0.8252 (mmm) cc_final: 0.7794 (mmm)
  outliers start: 19
  outliers final: 14
  residues processed: 227
  average time/residue: 0.1081
  time to fit residues: 32.1796
Evaluate side-chains
  230 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 215
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  229 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1060 GLU
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 70 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 80 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 955 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.133302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.111146 restraints weight = 11612.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.55
r_work: 0.3194 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8251  Z= 0.187
  Angle     :  0.519  11.383  11190  Z= 0.261
  Chirality :  0.040   0.133   1343
  Planarity :  0.004   0.053   1379
  Dihedral  :  3.747  14.250   1093
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.22 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.27), residues: 1012
  helix:  1.90 (0.19), residues: 710
  sheet:  0.33 (0.79), residues: 47
  loop : -0.06 (0.41), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 887 
 TYR   0.015   0.001   TYR A 358 
 PHE   0.017   0.002   PHE A 766 
 TRP   0.016   0.001   TRP A 635 
 HIS   0.004   0.001   HIS A 614 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 8251)
  covalent geometry    : angle       0.51866 (11190)
  hydrogen bonds       : bond        0.04718 (  472)
  hydrogen bonds       : angle       3.61925 ( 1416)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 215
  time to evaluate  : 0.312 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8330 (ttmt) cc_final: 0.8019 (ttmt)
REVERT: A  108 ILE cc_start: 0.8434 (mm) cc_final: 0.8156 (mt)
REVERT: A  124 GLU cc_start: 0.7515 (tm-30) cc_final: 0.5999 (tm-30)
REVERT: A  125 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7601 (mm-30)
REVERT: A  163 PHE cc_start: 0.8473 (t80) cc_final: 0.8086 (t80)
REVERT: A  164 SER cc_start: 0.8821 (m) cc_final: 0.8445 (p)
REVERT: A  209 ASP cc_start: 0.7598 (t0) cc_final: 0.7161 (t0)
REVERT: A  233 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7248 (tt0)
REVERT: A  250 LYS cc_start: 0.8281 (mttt) cc_final: 0.8054 (mtmm)
REVERT: A  322 SER cc_start: 0.8433 (t) cc_final: 0.7965 (p)
REVERT: A  337 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7620 (mp0)
REVERT: A  398 ILE cc_start: 0.8441 (mm) cc_final: 0.8096 (mt)
REVERT: A  401 MET cc_start: 0.7864 (mmm) cc_final: 0.7497 (mmm)
REVERT: A  502 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7411 (t70)
REVERT: A  580 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7445 (mm-30)
REVERT: A  586 MET cc_start: 0.7240 (ttm) cc_final: 0.6975 (ttt)
REVERT: A  588 LYS cc_start: 0.8298 (ttpp) cc_final: 0.8064 (ttmt)
REVERT: A  616 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7157 (mm-30)
REVERT: A  849 GLU cc_start: 0.7365 (tt0) cc_final: 0.7064 (tt0)
REVERT: A  853 ILE cc_start: 0.8131 (mm) cc_final: 0.7837 (tt)
REVERT: A  857 MET cc_start: 0.7656 (tpp) cc_final: 0.7300 (tpt)
REVERT: A  968 LYS cc_start: 0.8569 (mttt) cc_final: 0.8298 (mttt)
REVERT: A 1035 TYR cc_start: 0.8335 (m-80) cc_final: 0.8040 (m-80)
REVERT: A 1057 VAL cc_start: 0.8804 (t) cc_final: 0.8576 (m)
REVERT: A 1066 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.8005 (m-80)
REVERT: A 1073 MET cc_start: 0.8168 (mmm) cc_final: 0.7941 (mmm)
REVERT: A 1098 ILE cc_start: 0.8915 (mm) cc_final: 0.8626 (mt)
  outliers start: 22
  outliers final: 13
  residues processed: 221
  average time/residue: 0.1092
  time to fit residues: 31.5584
Evaluate side-chains
  227 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 212
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1136 PHE
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 97 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0980
   chunk 95 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0970
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A 165 GLN
A 225 GLN
A 955 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.134679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.112439 restraints weight = 11504.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.57
r_work: 0.3223 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3081 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8251  Z= 0.114
  Angle     :  0.448  10.172  11190  Z= 0.228
  Chirality :  0.038   0.145   1343
  Planarity :  0.004   0.056   1379
  Dihedral  :  3.602  14.187   1093
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.02 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.22 (0.26), residues: 1012
  helix:  2.04 (0.19), residues: 714
  sheet:  0.93 (0.95), residues: 32
  loop :  0.03 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 887 
 TYR   0.014   0.001   TYR A 358 
 PHE   0.016   0.001   PHE A 766 
 TRP   0.016   0.001   TRP A 635 
 HIS   0.004   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8251)
  covalent geometry    : angle       0.44846 (11190)
  hydrogen bonds       : bond        0.04220 (  472)
  hydrogen bonds       : angle       3.49391 ( 1416)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 217
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7907 (ttpp)
REVERT: A  108 ILE cc_start: 0.8429 (mm) cc_final: 0.8145 (mt)
REVERT: A  163 PHE cc_start: 0.8425 (t80) cc_final: 0.8177 (t80)
REVERT: A  164 SER cc_start: 0.8828 (m) cc_final: 0.8428 (p)
REVERT: A  205 MET cc_start: 0.8182 (tpp) cc_final: 0.7800 (tpp)
REVERT: A  209 ASP cc_start: 0.7590 (t0) cc_final: 0.7171 (t0)
REVERT: A  233 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7175 (tt0)
REVERT: A  250 LYS cc_start: 0.8243 (mttt) cc_final: 0.8028 (mtmm)
REVERT: A  287 VAL cc_start: 0.8177 (m) cc_final: 0.7883 (t)
REVERT: A  322 SER cc_start: 0.8462 (t) cc_final: 0.7992 (p)
REVERT: A  398 ILE cc_start: 0.8404 (mm) cc_final: 0.8069 (mt)
REVERT: A  401 MET cc_start: 0.7855 (mmm) cc_final: 0.7487 (mmm)
REVERT: A  502 HIS cc_start: 0.7610 (OUTLIER) cc_final: 0.7394 (t70)
REVERT: A  580 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7414 (mm-30)
REVERT: A  588 LYS cc_start: 0.8307 (ttpp) cc_final: 0.8060 (ttmt)
REVERT: A  849 GLU cc_start: 0.7339 (tt0) cc_final: 0.7029 (tt0)
REVERT: A  853 ILE cc_start: 0.8095 (mm) cc_final: 0.7810 (tt)
REVERT: A  872 GLU cc_start: 0.7435 (tp30) cc_final: 0.7167 (tp30)
REVERT: A  938 MET cc_start: 0.8408 (tpp) cc_final: 0.8088 (ttt)
REVERT: A  968 LYS cc_start: 0.8588 (mttt) cc_final: 0.8308 (mttt)
REVERT: A 1009 TYR cc_start: 0.8109 (t80) cc_final: 0.7767 (t80)
REVERT: A 1035 TYR cc_start: 0.8343 (m-80) cc_final: 0.8012 (m-80)
REVERT: A 1066 TYR cc_start: 0.8582 (OUTLIER) cc_final: 0.8034 (m-80)
REVERT: A 1073 MET cc_start: 0.8173 (mmm) cc_final: 0.7736 (mmm)
REVERT: A 1098 ILE cc_start: 0.8867 (mm) cc_final: 0.8563 (mt)
  outliers start: 22
  outliers final: 15
  residues processed: 224
  average time/residue: 0.1079
  time to fit residues: 32.0889
Evaluate side-chains
  228 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 211
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  228 THR
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1136 PHE
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 7 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    0.4980
   chunk 83 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 955 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.134702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.112455 restraints weight = 11452.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.56
r_work: 0.3217 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8251  Z= 0.120
  Angle     :  0.461   9.871  11190  Z= 0.232
  Chirality :  0.038   0.166   1343
  Planarity :  0.004   0.061   1379
  Dihedral  :  3.563  14.241   1093
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 16.50 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.26), residues: 1012
  helix:  2.08 (0.19), residues: 712
  sheet:  1.10 (0.93), residues: 32
  loop :  0.02 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 887 
 TYR   0.014   0.001   TYR A 984 
 PHE   0.014   0.001   PHE A 766 
 TRP   0.014   0.001   TRP A 635 
 HIS   0.004   0.000   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8251)
  covalent geometry    : angle       0.46065 (11190)
  hydrogen bonds       : bond        0.04167 (  472)
  hydrogen bonds       : angle       3.49609 ( 1416)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 213
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7998 (ttmt)
REVERT: A  108 ILE cc_start: 0.8436 (mm) cc_final: 0.8158 (mt)
REVERT: A  163 PHE cc_start: 0.8391 (t80) cc_final: 0.8143 (t80)
REVERT: A  205 MET cc_start: 0.8155 (tpp) cc_final: 0.7723 (tpp)
REVERT: A  209 ASP cc_start: 0.7573 (t0) cc_final: 0.7128 (t0)
REVERT: A  233 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7168 (tt0)
REVERT: A  287 VAL cc_start: 0.8150 (m) cc_final: 0.7876 (t)
REVERT: A  322 SER cc_start: 0.8456 (t) cc_final: 0.8013 (p)
REVERT: A  375 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8038 (ttpt)
REVERT: A  398 ILE cc_start: 0.8445 (mm) cc_final: 0.8099 (mt)
REVERT: A  401 MET cc_start: 0.7829 (mmm) cc_final: 0.7457 (mmm)
REVERT: A  502 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.7392 (t70)
REVERT: A  580 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7426 (mm-30)
REVERT: A  586 MET cc_start: 0.7125 (ttm) cc_final: 0.6831 (ttt)
REVERT: A  588 LYS cc_start: 0.8301 (ttpp) cc_final: 0.8047 (ttmt)
REVERT: A  608 LEU cc_start: 0.8383 (tp) cc_final: 0.8144 (tt)
REVERT: A  616 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7012 (mm-30)
REVERT: A  849 GLU cc_start: 0.7299 (tt0) cc_final: 0.6956 (tt0)
REVERT: A  853 ILE cc_start: 0.8030 (mm) cc_final: 0.7754 (tt)
REVERT: A  868 LYS cc_start: 0.7710 (mtpp) cc_final: 0.7505 (mttp)
REVERT: A  872 GLU cc_start: 0.7450 (tp30) cc_final: 0.7192 (tp30)
REVERT: A  968 LYS cc_start: 0.8567 (mttt) cc_final: 0.8298 (mttt)
REVERT: A 1009 TYR cc_start: 0.8100 (t80) cc_final: 0.7764 (t80)
REVERT: A 1035 TYR cc_start: 0.8257 (m-80) cc_final: 0.7928 (m-80)
REVERT: A 1066 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7990 (m-80)
REVERT: A 1073 MET cc_start: 0.8162 (mmm) cc_final: 0.7730 (mmm)
REVERT: A 1098 ILE cc_start: 0.8856 (mm) cc_final: 0.8549 (mt)
REVERT: A 1122 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7753 (mm-30)
REVERT: A 1190 ARG cc_start: 0.6851 (mmt-90) cc_final: 0.6547 (mmt180)
  outliers start: 24
  outliers final: 15
  residues processed: 220
  average time/residue: 0.1054
  time to fit residues: 30.7130
Evaluate side-chains
  226 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 209
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1105 GLU
Chi-restraints excluded: chain A residue 1136 PHE
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 83 optimal weight:    0.4980
   chunk 62 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 64 optimal weight:    8.9990
   chunk 20 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0370
   chunk 67 optimal weight:    0.9980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
A 955 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.133983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.111617 restraints weight = 11710.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.64
r_work: 0.3207 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8251  Z= 0.121
  Angle     :  0.453   9.227  11190  Z= 0.230
  Chirality :  0.038   0.152   1343
  Planarity :  0.004   0.064   1379
  Dihedral  :  3.511  14.181   1093
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.06 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.26), residues: 1012
  helix:  2.07 (0.19), residues: 715
  sheet:  1.58 (0.78), residues: 43
  loop :  0.07 (0.40), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 887 
 TYR   0.012   0.001   TYR A 358 
 PHE   0.013   0.001   PHE A 766 
 TRP   0.016   0.001   TRP A 419 
 HIS   0.005   0.001   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8251)
  covalent geometry    : angle       0.45345 (11190)
  hydrogen bonds       : bond        0.04166 (  472)
  hydrogen bonds       : angle       3.48734 ( 1416)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 225
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8310 (ttmt) cc_final: 0.7997 (ttmt)
REVERT: A  108 ILE cc_start: 0.8409 (mm) cc_final: 0.8124 (mt)
REVERT: A  116 VAL cc_start: 0.8348 (p) cc_final: 0.8125 (p)
REVERT: A  163 PHE cc_start: 0.8429 (t80) cc_final: 0.8163 (t80)
REVERT: A  205 MET cc_start: 0.8147 (tpp) cc_final: 0.7729 (tpp)
REVERT: A  209 ASP cc_start: 0.7525 (t0) cc_final: 0.7264 (t0)
REVERT: A  233 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7218 (tt0)
REVERT: A  287 VAL cc_start: 0.8154 (m) cc_final: 0.7876 (t)
REVERT: A  322 SER cc_start: 0.8494 (t) cc_final: 0.8026 (p)
REVERT: A  375 LYS cc_start: 0.8433 (ttmt) cc_final: 0.8126 (ttpt)
REVERT: A  398 ILE cc_start: 0.8426 (mm) cc_final: 0.8080 (mt)
REVERT: A  401 MET cc_start: 0.7725 (mmm) cc_final: 0.7362 (mmm)
REVERT: A  502 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7397 (t70)
REVERT: A  580 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7457 (mm-30)
REVERT: A  588 LYS cc_start: 0.8253 (ttpp) cc_final: 0.8000 (ttmt)
REVERT: A  616 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7130 (mm-30)
REVERT: A  651 LEU cc_start: 0.7918 (mt) cc_final: 0.7551 (mp)
REVERT: A  853 ILE cc_start: 0.8003 (mm) cc_final: 0.7761 (tt)
REVERT: A  866 GLU cc_start: 0.7579 (tp30) cc_final: 0.7353 (tp30)
REVERT: A  868 LYS cc_start: 0.7732 (mtpp) cc_final: 0.7493 (mttm)
REVERT: A  872 GLU cc_start: 0.7516 (tp30) cc_final: 0.7258 (tp30)
REVERT: A  968 LYS cc_start: 0.8510 (mttt) cc_final: 0.8250 (mttt)
REVERT: A 1009 TYR cc_start: 0.8074 (t80) cc_final: 0.7725 (t80)
REVERT: A 1035 TYR cc_start: 0.8243 (m-80) cc_final: 0.8019 (m-80)
REVERT: A 1066 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8010 (m-80)
REVERT: A 1073 MET cc_start: 0.8128 (mmm) cc_final: 0.7707 (mmm)
REVERT: A 1098 ILE cc_start: 0.8838 (mm) cc_final: 0.8526 (mt)
REVERT: A 1186 LEU cc_start: 0.8761 (tt) cc_final: 0.8444 (tp)
REVERT: A 1190 ARG cc_start: 0.6888 (mmt-90) cc_final: 0.6582 (mmt180)
  outliers start: 22
  outliers final: 15
  residues processed: 234
  average time/residue: 0.1004
  time to fit residues: 31.1761
Evaluate side-chains
  240 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 223
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1136 PHE
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 97 optimal weight:    4.9990
   chunk 22 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 92 optimal weight:    0.5980
   chunk 64 optimal weight:   10.0000
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 955 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.133210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.110992 restraints weight = 11530.070|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.60
r_work: 0.3185 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8251  Z= 0.129
  Angle     :  0.456   9.683  11190  Z= 0.232
  Chirality :  0.039   0.198   1343
  Planarity :  0.004   0.066   1379
  Dihedral  :  3.501  14.284   1093
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.72 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.26), residues: 1012
  helix:  2.06 (0.19), residues: 714
  sheet:  1.58 (0.78), residues: 43
  loop :  0.08 (0.40), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 887 
 TYR   0.011   0.001   TYR A 358 
 PHE   0.012   0.001   PHE A 766 
 TRP   0.015   0.001   TRP A 419 
 HIS   0.004   0.000   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8251)
  covalent geometry    : angle       0.45570 (11190)
  hydrogen bonds       : bond        0.04235 (  472)
  hydrogen bonds       : angle       3.49656 ( 1416)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 226
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8005 (ttmt)
REVERT: A  108 ILE cc_start: 0.8390 (mm) cc_final: 0.8108 (mt)
REVERT: A  116 VAL cc_start: 0.8298 (p) cc_final: 0.8092 (p)
REVERT: A  155 ASP cc_start: 0.7552 (t70) cc_final: 0.7260 (t70)
REVERT: A  163 PHE cc_start: 0.8434 (t80) cc_final: 0.8206 (t80)
REVERT: A  205 MET cc_start: 0.8137 (tpp) cc_final: 0.7751 (tpp)
REVERT: A  209 ASP cc_start: 0.7550 (t0) cc_final: 0.7263 (t0)
REVERT: A  233 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7183 (tt0)
REVERT: A  287 VAL cc_start: 0.8141 (m) cc_final: 0.7886 (t)
REVERT: A  322 SER cc_start: 0.8493 (t) cc_final: 0.8003 (p)
REVERT: A  337 GLU cc_start: 0.7758 (mp0) cc_final: 0.7548 (mp0)
REVERT: A  375 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8114 (ttpt)
REVERT: A  398 ILE cc_start: 0.8402 (mm) cc_final: 0.8054 (mt)
REVERT: A  401 MET cc_start: 0.7686 (mmm) cc_final: 0.7319 (mmm)
REVERT: A  502 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.7336 (t70)
REVERT: A  511 MET cc_start: 0.8609 (tmm) cc_final: 0.8024 (ttt)
REVERT: A  580 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7415 (mm-30)
REVERT: A  588 LYS cc_start: 0.8270 (ttpp) cc_final: 0.8002 (ttmt)
REVERT: A  616 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7107 (mm-30)
REVERT: A  849 GLU cc_start: 0.7255 (tt0) cc_final: 0.6888 (tt0)
REVERT: A  853 ILE cc_start: 0.7968 (mm) cc_final: 0.7735 (tt)
REVERT: A  866 GLU cc_start: 0.7565 (tp30) cc_final: 0.7337 (tp30)
REVERT: A  868 LYS cc_start: 0.7711 (mtpp) cc_final: 0.7482 (mttm)
REVERT: A  872 GLU cc_start: 0.7522 (tp30) cc_final: 0.7261 (tp30)
REVERT: A  968 LYS cc_start: 0.8506 (mttt) cc_final: 0.8249 (mttt)
REVERT: A 1009 TYR cc_start: 0.8081 (t80) cc_final: 0.7717 (t80)
REVERT: A 1033 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7682 (mt-10)
REVERT: A 1035 TYR cc_start: 0.8276 (m-80) cc_final: 0.8014 (m-80)
REVERT: A 1066 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.7947 (m-80)
REVERT: A 1098 ILE cc_start: 0.8830 (mm) cc_final: 0.8526 (mt)
REVERT: A 1186 LEU cc_start: 0.8769 (tt) cc_final: 0.8456 (tp)
REVERT: A 1190 ARG cc_start: 0.6921 (mmt-90) cc_final: 0.6593 (mmt180)
  outliers start: 20
  outliers final: 14
  residues processed: 235
  average time/residue: 0.1032
  time to fit residues: 32.1145
Evaluate side-chains
  237 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 221
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1136 PHE
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0020
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 80 optimal weight:    0.4980
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
A 955 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.134560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.112192 restraints weight = 11528.120|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.62
r_work: 0.3206 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8251  Z= 0.113
  Angle     :  0.452   8.787  11190  Z= 0.230
  Chirality :  0.038   0.150   1343
  Planarity :  0.004   0.067   1379
  Dihedral  :  3.462  14.266   1093
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.06 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.41 (0.26), residues: 1012
  helix:  2.14 (0.19), residues: 713
  sheet:  1.49 (0.78), residues: 43
  loop :  0.12 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 887 
 TYR   0.011   0.001   TYR A 358 
 PHE   0.013   0.001   PHE A 766 
 TRP   0.016   0.001   TRP A 419 
 HIS   0.004   0.000   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 8251)
  covalent geometry    : angle       0.45203 (11190)
  hydrogen bonds       : bond        0.04082 (  472)
  hydrogen bonds       : angle       3.47891 ( 1416)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 231
  time to evaluate  : 0.325 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8327 (ttmt) cc_final: 0.8014 (ttmt)
REVERT: A  108 ILE cc_start: 0.8411 (mm) cc_final: 0.8125 (mt)
REVERT: A  116 VAL cc_start: 0.8316 (p) cc_final: 0.8102 (p)
REVERT: A  155 ASP cc_start: 0.7528 (t70) cc_final: 0.7218 (t70)
REVERT: A  163 PHE cc_start: 0.8405 (t80) cc_final: 0.8155 (t80)
REVERT: A  205 MET cc_start: 0.8118 (tpp) cc_final: 0.7798 (tpp)
REVERT: A  209 ASP cc_start: 0.7590 (t0) cc_final: 0.7295 (t0)
REVERT: A  233 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7180 (tt0)
REVERT: A  287 VAL cc_start: 0.8152 (m) cc_final: 0.7898 (t)
REVERT: A  322 SER cc_start: 0.8477 (t) cc_final: 0.8016 (p)
REVERT: A  333 ILE cc_start: 0.8535 (mm) cc_final: 0.8183 (mt)
REVERT: A  375 LYS cc_start: 0.8415 (ttmt) cc_final: 0.8124 (ttpt)
REVERT: A  398 ILE cc_start: 0.8409 (mm) cc_final: 0.8058 (mt)
REVERT: A  401 MET cc_start: 0.7733 (mmm) cc_final: 0.7363 (mmm)
REVERT: A  494 MET cc_start: 0.8065 (tpp) cc_final: 0.7855 (tpt)
REVERT: A  502 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.7346 (t70)
REVERT: A  511 MET cc_start: 0.8643 (tmm) cc_final: 0.7957 (ttt)
REVERT: A  580 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7453 (mm-30)
REVERT: A  588 LYS cc_start: 0.8270 (ttpp) cc_final: 0.8011 (ttmt)
REVERT: A  616 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7121 (mm-30)
REVERT: A  647 LYS cc_start: 0.7927 (mmtm) cc_final: 0.7722 (mmtp)
REVERT: A  849 GLU cc_start: 0.7224 (tt0) cc_final: 0.6829 (tt0)
REVERT: A  853 ILE cc_start: 0.7972 (mm) cc_final: 0.7515 (tt)
REVERT: A  866 GLU cc_start: 0.7595 (tp30) cc_final: 0.7373 (tp30)
REVERT: A  872 GLU cc_start: 0.7506 (tp30) cc_final: 0.7251 (tp30)
REVERT: A  968 LYS cc_start: 0.8525 (mttt) cc_final: 0.8254 (mttt)
REVERT: A 1009 TYR cc_start: 0.8078 (t80) cc_final: 0.7735 (t80)
REVERT: A 1033 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7685 (mt-10)
REVERT: A 1035 TYR cc_start: 0.8204 (m-80) cc_final: 0.7973 (m-80)
REVERT: A 1066 TYR cc_start: 0.8652 (OUTLIER) cc_final: 0.7814 (m-80)
REVERT: A 1073 MET cc_start: 0.8135 (mmm) cc_final: 0.7472 (mmm)
REVERT: A 1098 ILE cc_start: 0.8828 (mm) cc_final: 0.8512 (mt)
REVERT: A 1186 LEU cc_start: 0.8744 (tt) cc_final: 0.8443 (tp)
REVERT: A 1190 ARG cc_start: 0.6932 (mmt-90) cc_final: 0.6611 (mmt180)
  outliers start: 20
  outliers final: 17
  residues processed: 239
  average time/residue: 0.1040
  time to fit residues: 32.9030
Evaluate side-chains
  248 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 229
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1136 PHE
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 53 optimal weight:    0.1980
   chunk 95 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 59 optimal weight:    0.5980
   chunk 101 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 14 optimal weight:    0.6980
   chunk 84 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 955 ASN
A1106 GLN
A1149 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.133885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.111640 restraints weight = 11502.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.61
r_work: 0.3212 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8251  Z= 0.129
  Angle     :  0.475   9.279  11190  Z= 0.241
  Chirality :  0.039   0.144   1343
  Planarity :  0.004   0.069   1379
  Dihedral  :  3.488  14.234   1093
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.84 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.26), residues: 1012
  helix:  2.10 (0.19), residues: 713
  sheet:  1.50 (0.78), residues: 43
  loop :  0.19 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 887 
 TYR   0.011   0.001   TYR A 984 
 PHE   0.015   0.001   PHE A 999 
 TRP   0.016   0.001   TRP A 419 
 HIS   0.004   0.000   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8251)
  covalent geometry    : angle       0.47491 (11190)
  hydrogen bonds       : bond        0.04168 (  472)
  hydrogen bonds       : angle       3.51639 ( 1416)

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 229
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8001 (ttmt)
REVERT: A  108 ILE cc_start: 0.8422 (mm) cc_final: 0.8140 (mt)
REVERT: A  116 VAL cc_start: 0.8330 (p) cc_final: 0.8117 (p)
REVERT: A  155 ASP cc_start: 0.7539 (t70) cc_final: 0.7238 (t70)
REVERT: A  163 PHE cc_start: 0.8470 (t80) cc_final: 0.8248 (t80)
REVERT: A  205 MET cc_start: 0.8121 (tpp) cc_final: 0.7785 (tpp)
REVERT: A  209 ASP cc_start: 0.7593 (t0) cc_final: 0.7293 (t0)
REVERT: A  233 GLU cc_start: 0.7479 (tm-30) cc_final: 0.7200 (tt0)
REVERT: A  287 VAL cc_start: 0.8173 (m) cc_final: 0.7913 (t)
REVERT: A  322 SER cc_start: 0.8463 (t) cc_final: 0.8002 (p)
REVERT: A  333 ILE cc_start: 0.8471 (mm) cc_final: 0.8225 (mt)
REVERT: A  398 ILE cc_start: 0.8415 (mm) cc_final: 0.8063 (mt)
REVERT: A  401 MET cc_start: 0.7683 (mmm) cc_final: 0.7321 (mmm)
REVERT: A  502 HIS cc_start: 0.7565 (OUTLIER) cc_final: 0.7333 (t70)
REVERT: A  511 MET cc_start: 0.8628 (tmm) cc_final: 0.8028 (ttt)
REVERT: A  580 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7460 (mm-30)
REVERT: A  586 MET cc_start: 0.7118 (ttt) cc_final: 0.6864 (ttt)
REVERT: A  588 LYS cc_start: 0.8258 (ttpp) cc_final: 0.8000 (ttmt)
REVERT: A  616 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7139 (mm-30)
REVERT: A  849 GLU cc_start: 0.7241 (tt0) cc_final: 0.6828 (tt0)
REVERT: A  853 ILE cc_start: 0.8001 (mm) cc_final: 0.7552 (tt)
REVERT: A  866 GLU cc_start: 0.7583 (tp30) cc_final: 0.7371 (tp30)
REVERT: A  872 GLU cc_start: 0.7494 (tp30) cc_final: 0.7243 (tp30)
REVERT: A 1009 TYR cc_start: 0.8079 (t80) cc_final: 0.7743 (t80)
REVERT: A 1033 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7646 (mt-10)
REVERT: A 1035 TYR cc_start: 0.8165 (m-80) cc_final: 0.7947 (m-80)
REVERT: A 1066 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7849 (m-80)
REVERT: A 1073 MET cc_start: 0.8153 (mmm) cc_final: 0.7434 (mmm)
REVERT: A 1107 MET cc_start: 0.7477 (ptm) cc_final: 0.7103 (ptp)
REVERT: A 1186 LEU cc_start: 0.8734 (tt) cc_final: 0.8453 (tp)
REVERT: A 1190 ARG cc_start: 0.6930 (mmt-90) cc_final: 0.6631 (mmt180)
  outliers start: 23
  outliers final: 19
  residues processed: 238
  average time/residue: 0.1051
  time to fit residues: 33.0045
Evaluate side-chains
  253 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 232
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  154 MET
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  638 LYS
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1136 PHE
Chi-restraints excluded: chain A residue 1188 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 95 optimal weight:    0.0970
   chunk 23 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 38 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 15 optimal weight:    0.1980
   chunk 19 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 955 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.133574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.111280 restraints weight = 11570.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 1.63
r_work: 0.3227 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3084 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8251  Z= 0.124
  Angle     :  0.475  10.629  11190  Z= 0.241
  Chirality :  0.039   0.139   1343
  Planarity :  0.004   0.067   1379
  Dihedral  :  3.483  14.456   1093
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.72 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.27), residues: 1012
  helix:  2.10 (0.19), residues: 713
  sheet:  1.52 (0.79), residues: 43
  loop :  0.17 (0.40), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 887 
 TYR   0.010   0.001   TYR A 358 
 PHE   0.012   0.001   PHE A 766 
 TRP   0.015   0.001   TRP A 419 
 HIS   0.004   0.000   HIS A1120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 8251)
  covalent geometry    : angle       0.47493 (11190)
  hydrogen bonds       : bond        0.04119 (  472)
  hydrogen bonds       : angle       3.51003 ( 1416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2347.68 seconds
wall clock time: 40 minutes 56.96 seconds (2456.96 seconds total)