Starting phenix.real_space_refine
on Wed Mar 12 17:14:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pd5_17601/03_2025/8pd5_17601.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pd5_17601/03_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_17601/03_2025/8pd5_17601.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pd5_17601/03_2025/8pd5_17601.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pd5_17601/03_2025/8pd5_17601.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pd5_17601/03_2025/8pd5_17601.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.27, per 1000 atoms: 0.65
  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: 2.19
  Conformation dependent library (CDL) restraints added in 868.8 milliseconds
  

  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: 0.72
  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: 2.24

  Time building geometry restraints manager: 2.55 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:             2.350
  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:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.590
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  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:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.740
-------------------------------------------------------------------------------
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= 0.170
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.019   0.001   TRP A1112 
 HIS   0.003   0.001   HIS A 292 
 PHE   0.023   0.001   PHE A 699 
 TYR   0.008   0.001   TYR A1066 
 ARG   0.002   0.000   ARG A 809 

*********************** 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  : 0.816 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8019 (ttmt) cc_final: 0.7485 (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: 0.7503 (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: 0.7129 (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: 0.7668 (ttmm)
REVERT: A 1052 PRO cc_start: 0.8474 (Cg_exo) cc_final: 0.8245 (Cg_endo)
REVERT: A 1069 THR cc_start: 0.8012 (m) cc_final: 0.7681 (t)
REVERT: A 1073 MET cc_start: 0.7225 (mmm) cc_final: 0.6846 (mmm)
REVERT: A 1094 VAL cc_start: 0.7543 (t) cc_final: 0.7299 (p)
REVERT: A 1097 ARG cc_start: 0.7957 (mtm110) cc_final: 0.7708 (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: 0.8231 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.2347
  time to fit residues: 77.7851
Evaluate side-chains
  220 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    0.3980
   chunk 52 optimal weight:    4.9990
   chunk 41 optimal weight:    0.0030
   chunk 79 optimal weight:    0.0670
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.1980
   chunk 92 optimal weight:    0.8980
   overall best weight:    0.3128

-------------------------------------------------------------------------------
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 = 0.3681 r_free = 0.3681 target = 0.136440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.113984 restraints weight = 11438.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.59
r_work: 0.3160 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.1488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8251  Z= 0.149
  Angle     :  0.489   7.933  11190  Z= 0.252
  Chirality :  0.038   0.135   1343
  Planarity :  0.004   0.052   1379
  Dihedral  :  3.843  15.674   1093
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 2.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.92 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.27), residues: 1012
  helix:  2.11 (0.19), residues: 713
  sheet:  0.16 (0.76), residues: 47
  loop :  0.24 (0.43), residues: 252

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

*********************** 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
  240 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 226
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7948 (ttmt)
REVERT: A  108 ILE cc_start: 0.8376 (mm) cc_final: 0.8079 (mt)
REVERT: A  124 GLU cc_start: 0.7424 (tt0) cc_final: 0.7190 (tm-30)
REVERT: A  125 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7714 (mt-10)
REVERT: A  163 PHE cc_start: 0.8294 (t80) cc_final: 0.8009 (t80)
REVERT: A  164 SER cc_start: 0.8786 (m) cc_final: 0.8427 (p)
REVERT: A  209 ASP cc_start: 0.7659 (t0) cc_final: 0.7245 (t0)
REVERT: A  233 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7242 (tt0)
REVERT: A  249 MET cc_start: 0.8415 (tmm) cc_final: 0.8118 (ttp)
REVERT: A  250 LYS cc_start: 0.8219 (mttt) cc_final: 0.7971 (mtmm)
REVERT: A  322 SER cc_start: 0.8500 (t) cc_final: 0.7989 (p)
REVERT: A  337 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7655 (mp0)
REVERT: A  383 MET cc_start: 0.8098 (mmp) cc_final: 0.7844 (mmt)
REVERT: A  401 MET cc_start: 0.7827 (mmm) cc_final: 0.7568 (mmm)
REVERT: A  580 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7330 (mm-30)
REVERT: A  588 LYS cc_start: 0.8233 (ttpp) cc_final: 0.7955 (ttmt)
REVERT: A  609 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.7633 (tmm160)
REVERT: A  616 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7194 (mt-10)
REVERT: A  849 GLU cc_start: 0.7506 (tt0) cc_final: 0.7212 (tt0)
REVERT: A  853 ILE cc_start: 0.7990 (mm) cc_final: 0.7694 (tt)
REVERT: A  968 LYS cc_start: 0.8497 (mttt) cc_final: 0.8240 (mttt)
REVERT: A  998 LEU cc_start: 0.8702 (pp) cc_final: 0.8468 (pt)
REVERT: A 1007 LYS cc_start: 0.7904 (tttt) cc_final: 0.7625 (tttm)
REVERT: A 1009 TYR cc_start: 0.8106 (t80) cc_final: 0.7749 (t80)
REVERT: A 1033 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7811 (mt-10)
REVERT: A 1034 ASP cc_start: 0.7674 (t0) cc_final: 0.7364 (t0)
REVERT: A 1035 TYR cc_start: 0.8345 (m-80) cc_final: 0.8020 (m-80)
REVERT: A 1048 LEU cc_start: 0.8263 (mt) cc_final: 0.7989 (mt)
REVERT: A 1066 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8063 (m-80)
REVERT: A 1087 GLU cc_start: 0.8006 (tp30) cc_final: 0.7766 (tp30)
  outliers start: 14
  outliers final: 6
  residues processed: 229
  average time/residue: 0.2261
  time to fit residues: 67.7371
Evaluate side-chains
  221 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 214
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
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 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 33 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 58 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 100 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3655 r_free = 0.3655 target = 0.134338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.112132 restraints weight = 11598.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.55
r_work: 0.3151 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8251  Z= 0.219
  Angle     :  0.497  12.476  11190  Z= 0.249
  Chirality :  0.039   0.133   1343
  Planarity :  0.004   0.066   1379
  Dihedral  :  3.725  14.404   1093
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.42 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.27), residues: 1012
  helix:  2.10 (0.19), residues: 705
  sheet:  0.56 (0.78), residues: 47
  loop :  0.16 (0.42), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 635 
 HIS   0.008   0.001   HIS A1120 
 PHE   0.023   0.001   PHE A 766 
 TYR   0.009   0.001   TYR A 984 
 ARG   0.010   0.001   ARG A 887 

*********************** 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
  242 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 221
  time to evaluate  : 0.931 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7981 (ttmt)
REVERT: A  108 ILE cc_start: 0.8395 (mm) cc_final: 0.8120 (mt)
REVERT: A  124 GLU cc_start: 0.7412 (tt0) cc_final: 0.7098 (tm-30)
REVERT: A  125 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7361 (mm-30)
REVERT: A  128 ARG cc_start: 0.8466 (ptm160) cc_final: 0.8084 (ptp-170)
REVERT: A  154 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7791 (mtp)
REVERT: A  163 PHE cc_start: 0.8424 (t80) cc_final: 0.8042 (t80)
REVERT: A  164 SER cc_start: 0.8788 (m) cc_final: 0.8402 (p)
REVERT: A  209 ASP cc_start: 0.7594 (t0) cc_final: 0.7148 (t0)
REVERT: A  233 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7310 (tt0)
REVERT: A  250 LYS cc_start: 0.8274 (mttt) cc_final: 0.8029 (mtmm)
REVERT: A  322 SER cc_start: 0.8463 (t) cc_final: 0.7981 (p)
REVERT: A  337 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7639 (mp0)
REVERT: A  383 MET cc_start: 0.8083 (mmp) cc_final: 0.7859 (mmt)
REVERT: A  398 ILE cc_start: 0.8395 (mm) cc_final: 0.8074 (mt)
REVERT: A  401 MET cc_start: 0.7905 (mmm) cc_final: 0.7546 (mmm)
REVERT: A  580 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7362 (mm-30)
REVERT: A  586 MET cc_start: 0.7185 (ttm) cc_final: 0.6929 (ttt)
REVERT: A  588 LYS cc_start: 0.8294 (ttpp) cc_final: 0.8034 (ttmt)
REVERT: A  602 MET cc_start: 0.8023 (ttm) cc_final: 0.7556 (mtp)
REVERT: A  616 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7170 (mt-10)
REVERT: A  647 LYS cc_start: 0.7949 (mmtm) cc_final: 0.7694 (mmtm)
REVERT: A  841 LYS cc_start: 0.7216 (mmtt) cc_final: 0.6669 (mmtm)
REVERT: A  849 GLU cc_start: 0.7382 (tt0) cc_final: 0.7140 (tt0)
REVERT: A  853 ILE cc_start: 0.7987 (mm) cc_final: 0.7724 (tt)
REVERT: A  968 LYS cc_start: 0.8564 (mttt) cc_final: 0.8278 (mttt)
REVERT: A 1009 TYR cc_start: 0.8135 (t80) cc_final: 0.7729 (t80)
REVERT: A 1035 TYR cc_start: 0.8354 (m-80) cc_final: 0.8058 (m-80)
REVERT: A 1057 VAL cc_start: 0.8763 (t) cc_final: 0.8526 (m)
REVERT: A 1066 TYR cc_start: 0.8515 (OUTLIER) cc_final: 0.8004 (m-80)
REVERT: A 1073 MET cc_start: 0.8209 (mmm) cc_final: 0.7659 (mmt)
  outliers start: 21
  outliers final: 15
  residues processed: 228
  average time/residue: 0.2375
  time to fit residues: 70.4980
Evaluate side-chains
  231 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 214
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  154 MET
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  579 MET
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 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 43 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.7782

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.133840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.111567 restraints weight = 11393.337|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.57
r_work: 0.3214 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8251  Z= 0.217
  Angle     :  0.477  11.194  11190  Z= 0.240
  Chirality :  0.039   0.135   1343
  Planarity :  0.004   0.053   1379
  Dihedral  :  3.674  14.078   1093
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 14.68 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.27), residues: 1012
  helix:  2.01 (0.19), residues: 709
  sheet:  0.76 (0.83), residues: 42
  loop : -0.09 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 635 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.018   0.001   PHE A 766 
 TYR   0.022   0.001   TYR A 358 
 ARG   0.005   0.000   ARG A 887 

*********************** 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
  243 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 219
  time to evaluate  : 0.821 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8317 (ttmt) cc_final: 0.8005 (ttmt)
REVERT: A  108 ILE cc_start: 0.8431 (mm) cc_final: 0.8146 (mt)
REVERT: A  125 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7781 (mt-10)
REVERT: A  163 PHE cc_start: 0.8441 (t80) cc_final: 0.8167 (t80)
REVERT: A  164 SER cc_start: 0.8814 (m) cc_final: 0.8412 (p)
REVERT: A  205 MET cc_start: 0.8116 (tpp) cc_final: 0.7553 (tpp)
REVERT: A  209 ASP cc_start: 0.7562 (t0) cc_final: 0.7142 (t0)
REVERT: A  233 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7219 (tt0)
REVERT: A  250 LYS cc_start: 0.8281 (mttt) cc_final: 0.8066 (mtmm)
REVERT: A  287 VAL cc_start: 0.8188 (m) cc_final: 0.7892 (t)
REVERT: A  322 SER cc_start: 0.8447 (t) cc_final: 0.7976 (p)
REVERT: A  337 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7632 (mp0)
REVERT: A  383 MET cc_start: 0.8073 (mmp) cc_final: 0.7873 (mmt)
REVERT: A  398 ILE cc_start: 0.8422 (mm) cc_final: 0.8080 (mt)
REVERT: A  401 MET cc_start: 0.7918 (mmm) cc_final: 0.7582 (mmm)
REVERT: A  580 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7387 (mm-30)
REVERT: A  588 LYS cc_start: 0.8302 (ttpp) cc_final: 0.8055 (ttmt)
REVERT: A  616 GLU cc_start: 0.7375 (mt-10) cc_final: 0.7112 (mt-10)
REVERT: A  647 LYS cc_start: 0.7999 (mmtm) cc_final: 0.7696 (mmtm)
REVERT: A  651 LEU cc_start: 0.7940 (mt) cc_final: 0.7550 (mp)
REVERT: A  841 LYS cc_start: 0.6996 (mmtt) cc_final: 0.6344 (mmtm)
REVERT: A  849 GLU cc_start: 0.7372 (tt0) cc_final: 0.7061 (tt0)
REVERT: A  853 ILE cc_start: 0.8106 (mm) cc_final: 0.7806 (tt)
REVERT: A  857 MET cc_start: 0.7678 (tpp) cc_final: 0.7456 (tpt)
REVERT: A  968 LYS cc_start: 0.8586 (mttt) cc_final: 0.8312 (mttt)
REVERT: A  976 ARG cc_start: 0.7931 (mtt-85) cc_final: 0.7723 (mtt-85)
REVERT: A 1035 TYR cc_start: 0.8315 (m-80) cc_final: 0.7966 (m-80)
REVERT: A 1048 LEU cc_start: 0.8283 (mt) cc_final: 0.8081 (mt)
REVERT: A 1066 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7979 (m-80)
REVERT: A 1098 ILE cc_start: 0.8890 (mm) cc_final: 0.8578 (mt)
  outliers start: 24
  outliers final: 14
  residues processed: 225
  average time/residue: 0.2231
  time to fit residues: 66.1668
Evaluate side-chains
  231 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 216
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  579 MET
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 1038 VAL
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 69 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 90 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3648 r_free = 0.3648 target = 0.133721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.111707 restraints weight = 11443.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.53
r_work: 0.3170 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8251  Z= 0.207
  Angle     :  0.470  10.688  11190  Z= 0.235
  Chirality :  0.038   0.135   1343
  Planarity :  0.004   0.055   1379
  Dihedral  :  3.598  14.252   1093
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 15.47 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.26), residues: 1012
  helix:  2.00 (0.19), residues: 714
  sheet:  0.96 (0.93), residues: 32
  loop : -0.01 (0.40), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 635 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.015   0.001   PHE A 766 
 TYR   0.016   0.001   TYR A 358 
 ARG   0.005   0.000   ARG A 887 

*********************** 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
  238 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 215
  time to evaluate  : 0.918 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8005 (ttmt)
REVERT: A  108 ILE cc_start: 0.8404 (mm) cc_final: 0.8121 (mt)
REVERT: A  163 PHE cc_start: 0.8428 (t80) cc_final: 0.8186 (t80)
REVERT: A  205 MET cc_start: 0.8107 (tpp) cc_final: 0.7486 (mpp)
REVERT: A  209 ASP cc_start: 0.7560 (t0) cc_final: 0.7144 (t0)
REVERT: A  233 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7202 (tt0)
REVERT: A  250 LYS cc_start: 0.8284 (mttt) cc_final: 0.8083 (mtmm)
REVERT: A  287 VAL cc_start: 0.8157 (m) cc_final: 0.7874 (t)
REVERT: A  322 SER cc_start: 0.8471 (t) cc_final: 0.8002 (p)
REVERT: A  337 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7580 (mp0)
REVERT: A  383 MET cc_start: 0.8062 (mmp) cc_final: 0.7847 (mmt)
REVERT: A  398 ILE cc_start: 0.8403 (mm) cc_final: 0.8048 (mt)
REVERT: A  401 MET cc_start: 0.7844 (mmm) cc_final: 0.7487 (mmm)
REVERT: A  502 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7394 (t70)
REVERT: A  580 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7344 (mm-30)
REVERT: A  586 MET cc_start: 0.7250 (ttm) cc_final: 0.7001 (ttt)
REVERT: A  588 LYS cc_start: 0.8300 (ttpp) cc_final: 0.8037 (ttmt)
REVERT: A  647 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7638 (mmtm)
REVERT: A  651 LEU cc_start: 0.7909 (mt) cc_final: 0.7505 (mp)
REVERT: A  841 LYS cc_start: 0.6988 (mmtt) cc_final: 0.6765 (mmtt)
REVERT: A  849 GLU cc_start: 0.7339 (tt0) cc_final: 0.6992 (tt0)
REVERT: A  853 ILE cc_start: 0.8036 (mm) cc_final: 0.7733 (tt)
REVERT: A  866 GLU cc_start: 0.7561 (tp30) cc_final: 0.7176 (tp30)
REVERT: A  872 GLU cc_start: 0.7463 (tp30) cc_final: 0.7161 (tp30)
REVERT: A  968 LYS cc_start: 0.8556 (mttt) cc_final: 0.8277 (mttt)
REVERT: A 1009 TYR cc_start: 0.8110 (t80) cc_final: 0.7764 (t80)
REVERT: A 1035 TYR cc_start: 0.8262 (m-80) cc_final: 0.8020 (m-80)
REVERT: A 1066 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7953 (m-80)
REVERT: A 1098 ILE cc_start: 0.8847 (mm) cc_final: 0.8539 (mt)
REVERT: A 1190 ARG cc_start: 0.6946 (mmt-90) cc_final: 0.6581 (mmt180)
  outliers start: 23
  outliers final: 17
  residues processed: 222
  average time/residue: 0.2334
  time to fit residues: 68.2158
Evaluate side-chains
  231 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 212
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
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  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  579 MET
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 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 93 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 80 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
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 = 0.133379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.111161 restraints weight = 11372.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.56
r_work: 0.3129 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8251  Z= 0.260
  Angle     :  0.496  10.640  11190  Z= 0.248
  Chirality :  0.039   0.134   1343
  Planarity :  0.004   0.058   1379
  Dihedral  :  3.650  14.875   1093
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 15.70 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.26), residues: 1012
  helix:  1.87 (0.19), residues: 712
  sheet:  0.98 (0.93), residues: 32
  loop : -0.08 (0.39), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 419 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.014   0.001   PHE A 766 
 TYR   0.015   0.001   TYR A 358 
 ARG   0.005   0.000   ARG A 585 

*********************** 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
  246 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 219
  time to evaluate  : 0.935 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8003 (ttmt)
REVERT: A  108 ILE cc_start: 0.8404 (mm) cc_final: 0.8115 (mt)
REVERT: A  116 VAL cc_start: 0.8334 (p) cc_final: 0.8125 (p)
REVERT: A  124 GLU cc_start: 0.7425 (tp30) cc_final: 0.7082 (tm-30)
REVERT: A  155 ASP cc_start: 0.7550 (t0) cc_final: 0.7320 (t70)
REVERT: A  163 PHE cc_start: 0.8485 (t80) cc_final: 0.8232 (t80)
REVERT: A  205 MET cc_start: 0.8157 (tpp) cc_final: 0.7569 (tpp)
REVERT: A  209 ASP cc_start: 0.7587 (t0) cc_final: 0.7167 (t0)
REVERT: A  233 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7213 (tt0)
REVERT: A  250 LYS cc_start: 0.8330 (mttt) cc_final: 0.8065 (mttm)
REVERT: A  287 VAL cc_start: 0.8172 (m) cc_final: 0.7899 (t)
REVERT: A  322 SER cc_start: 0.8488 (t) cc_final: 0.8003 (p)
REVERT: A  375 LYS cc_start: 0.8383 (ttmt) cc_final: 0.8059 (ttpt)
REVERT: A  398 ILE cc_start: 0.8414 (mm) cc_final: 0.8049 (mt)
REVERT: A  401 MET cc_start: 0.7833 (mmm) cc_final: 0.7474 (mmm)
REVERT: A  502 HIS cc_start: 0.7645 (OUTLIER) cc_final: 0.7403 (t70)
REVERT: A  511 MET cc_start: 0.8585 (tmm) cc_final: 0.7999 (ttt)
REVERT: A  580 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7394 (mm-30)
REVERT: A  588 LYS cc_start: 0.8317 (ttpp) cc_final: 0.8041 (ttmt)
REVERT: A  616 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7112 (mm-30)
REVERT: A  647 LYS cc_start: 0.7965 (mmtm) cc_final: 0.7632 (mmtm)
REVERT: A  651 LEU cc_start: 0.7905 (mt) cc_final: 0.7504 (mp)
REVERT: A  841 LYS cc_start: 0.6926 (mmtt) cc_final: 0.6592 (mmtt)
REVERT: A  849 GLU cc_start: 0.7350 (tt0) cc_final: 0.6991 (tt0)
REVERT: A  853 ILE cc_start: 0.7976 (mm) cc_final: 0.7703 (tt)
REVERT: A  866 GLU cc_start: 0.7566 (tp30) cc_final: 0.7184 (tp30)
REVERT: A  872 GLU cc_start: 0.7530 (tp30) cc_final: 0.7219 (tp30)
REVERT: A  968 LYS cc_start: 0.8529 (mttt) cc_final: 0.8259 (mttt)
REVERT: A 1035 TYR cc_start: 0.8270 (m-80) cc_final: 0.8030 (m-80)
REVERT: A 1066 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8015 (m-80)
REVERT: A 1098 ILE cc_start: 0.8830 (mm) cc_final: 0.8531 (mt)
REVERT: A 1186 LEU cc_start: 0.8790 (tt) cc_final: 0.8463 (tp)
  outliers start: 27
  outliers final: 19
  residues processed: 229
  average time/residue: 0.2393
  time to fit residues: 72.0754
Evaluate side-chains
  240 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 218
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
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  233 GLU
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  579 MET
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 1038 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0060
   chunk 84 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.5596

-------------------------------------------------------------------------------
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 = 0.3646 r_free = 0.3646 target = 0.133982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.111738 restraints weight = 11515.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.61
r_work: 0.3208 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.2706

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= 0.176
  Angle     :  0.464   9.472  11190  Z= 0.232
  Chirality :  0.038   0.144   1343
  Planarity :  0.004   0.063   1379
  Dihedral  :  3.551  14.936   1093
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 16.38 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.27), residues: 1012
  helix:  1.99 (0.19), residues: 713
  sheet:  1.38 (0.79), residues: 43
  loop : -0.04 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 419 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.013   0.001   PHE A 766 
 TYR   0.014   0.001   TYR A 358 
 ARG   0.004   0.000   ARG A 887 

*********************** 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
  241 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 218
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8289 (ttmt) cc_final: 0.7965 (ttmt)
REVERT: A  108 ILE cc_start: 0.8417 (mm) cc_final: 0.8134 (mt)
REVERT: A  116 VAL cc_start: 0.8359 (p) cc_final: 0.8146 (p)
REVERT: A  124 GLU cc_start: 0.7479 (tp30) cc_final: 0.7086 (tm-30)
REVERT: A  163 PHE cc_start: 0.8423 (t80) cc_final: 0.8210 (t80)
REVERT: A  205 MET cc_start: 0.8132 (tpp) cc_final: 0.7616 (tpp)
REVERT: A  209 ASP cc_start: 0.7538 (t0) cc_final: 0.7146 (t0)
REVERT: A  233 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7150 (tt0)
REVERT: A  287 VAL cc_start: 0.8144 (m) cc_final: 0.7903 (t)
REVERT: A  322 SER cc_start: 0.8472 (t) cc_final: 0.7996 (p)
REVERT: A  337 GLU cc_start: 0.7714 (mp0) cc_final: 0.7505 (mp0)
REVERT: A  375 LYS cc_start: 0.8426 (ttmt) cc_final: 0.8163 (ttpt)
REVERT: A  398 ILE cc_start: 0.8457 (mm) cc_final: 0.8113 (mt)
REVERT: A  401 MET cc_start: 0.7813 (mmm) cc_final: 0.7451 (mmm)
REVERT: A  511 MET cc_start: 0.8650 (tmm) cc_final: 0.7949 (ttt)
REVERT: A  580 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7478 (mm-30)
REVERT: A  588 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7999 (ttmt)
REVERT: A  616 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7105 (mm-30)
REVERT: A  841 LYS cc_start: 0.7003 (mmtt) cc_final: 0.6753 (mmtt)
REVERT: A  849 GLU cc_start: 0.7252 (tt0) cc_final: 0.6913 (tt0)
REVERT: A  853 ILE cc_start: 0.8026 (mm) cc_final: 0.7780 (tt)
REVERT: A  866 GLU cc_start: 0.7569 (tp30) cc_final: 0.7200 (tp30)
REVERT: A  872 GLU cc_start: 0.7499 (tp30) cc_final: 0.7213 (tp30)
REVERT: A  968 LYS cc_start: 0.8472 (mttt) cc_final: 0.8217 (mttt)
REVERT: A 1009 TYR cc_start: 0.8075 (t80) cc_final: 0.7718 (t80)
REVERT: A 1035 TYR cc_start: 0.8263 (m-80) cc_final: 0.8033 (m-80)
REVERT: A 1066 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7974 (m-80)
REVERT: A 1073 MET cc_start: 0.8112 (mmm) cc_final: 0.7566 (mmm)
REVERT: A 1098 ILE cc_start: 0.8871 (mm) cc_final: 0.8564 (mt)
REVERT: A 1186 LEU cc_start: 0.8766 (tt) cc_final: 0.8466 (tp)
REVERT: A 1190 ARG cc_start: 0.6905 (mmt-90) cc_final: 0.6510 (mmt180)
  outliers start: 23
  outliers final: 17
  residues processed: 226
  average time/residue: 0.2717
  time to fit residues: 79.9591
Evaluate side-chains
  228 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 210
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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  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  579 MET
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  911 GLU
Chi-restraints excluded: chain A residue 1038 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 93 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 76 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0030
   chunk 53 optimal weight:    0.3980
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.4790

-------------------------------------------------------------------------------
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 = 0.3651 r_free = 0.3651 target = 0.134125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.111856 restraints weight = 11643.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.63
r_work: 0.3214 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.2804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8251  Z= 0.161
  Angle     :  0.454  10.307  11190  Z= 0.227
  Chirality :  0.037   0.135   1343
  Planarity :  0.004   0.065   1379
  Dihedral  :  3.462  14.451   1093
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 17.06 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.27), residues: 1012
  helix:  2.06 (0.19), residues: 714
  sheet:  1.45 (0.80), residues: 43
  loop :  0.07 (0.41), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 419 
 HIS   0.005   0.000   HIS A1120 
 PHE   0.013   0.001   PHE A 766 
 TYR   0.013   0.001   TYR A 358 
 ARG   0.008   0.000   ARG A 887 

*********************** 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
  244 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 219
  time to evaluate  : 0.996 
Fit side-chains
REVERT: A   87 PHE cc_start: 0.8092 (m-10) cc_final: 0.7882 (m-10)
REVERT: A   96 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7969 (ttmt)
REVERT: A  108 ILE cc_start: 0.8418 (mm) cc_final: 0.8142 (mt)
REVERT: A  116 VAL cc_start: 0.8345 (p) cc_final: 0.8127 (p)
REVERT: A  124 GLU cc_start: 0.7486 (tp30) cc_final: 0.7105 (tm-30)
REVERT: A  163 PHE cc_start: 0.8421 (t80) cc_final: 0.8182 (t80)
REVERT: A  205 MET cc_start: 0.8127 (tpp) cc_final: 0.7672 (tpp)
REVERT: A  209 ASP cc_start: 0.7520 (t0) cc_final: 0.7095 (t0)
REVERT: A  233 GLU cc_start: 0.7440 (tm-30) cc_final: 0.7159 (tt0)
REVERT: A  287 VAL cc_start: 0.8158 (m) cc_final: 0.7897 (t)
REVERT: A  322 SER cc_start: 0.8493 (t) cc_final: 0.8008 (p)
REVERT: A  375 LYS cc_start: 0.8432 (ttmt) cc_final: 0.8135 (ttpt)
REVERT: A  398 ILE cc_start: 0.8425 (mm) cc_final: 0.8086 (mt)
REVERT: A  401 MET cc_start: 0.7774 (mmm) cc_final: 0.7413 (mmm)
REVERT: A  511 MET cc_start: 0.8666 (tmm) cc_final: 0.8043 (ttt)
REVERT: A  580 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7482 (mm-30)
REVERT: A  588 LYS cc_start: 0.8270 (ttpp) cc_final: 0.8003 (ttmt)
REVERT: A  616 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7138 (mm-30)
REVERT: A  841 LYS cc_start: 0.7018 (mmtt) cc_final: 0.6763 (mmtt)
REVERT: A  853 ILE cc_start: 0.8004 (mm) cc_final: 0.7785 (tt)
REVERT: A  857 MET cc_start: 0.7816 (tpp) cc_final: 0.7442 (tpt)
REVERT: A  866 GLU cc_start: 0.7549 (tp30) cc_final: 0.7300 (tp30)
REVERT: A  872 GLU cc_start: 0.7529 (tp30) cc_final: 0.7253 (tp30)
REVERT: A  931 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7412 (mt-10)
REVERT: A  968 LYS cc_start: 0.8514 (mttt) cc_final: 0.8244 (mttt)
REVERT: A 1009 TYR cc_start: 0.8032 (t80) cc_final: 0.7691 (t80)
REVERT: A 1066 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.7961 (m-80)
REVERT: A 1073 MET cc_start: 0.8114 (mmm) cc_final: 0.7443 (mmm)
REVERT: A 1098 ILE cc_start: 0.8824 (mm) cc_final: 0.8507 (mt)
REVERT: A 1186 LEU cc_start: 0.8767 (tt) cc_final: 0.8477 (tp)
  outliers start: 25
  outliers final: 18
  residues processed: 230
  average time/residue: 0.2817
  time to fit residues: 87.5810
Evaluate side-chains
  235 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 215
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
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  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  579 MET
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  911 GLU
Chi-restraints excluded: chain A residue  931 GLU
Chi-restraints excluded: chain A residue  995 SER
Chi-restraints excluded: chain A residue 1038 VAL
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1115 GLU
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 12 optimal weight:    1.9990
   chunk 92 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0570
   chunk 95 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   chunk 28 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0670
   chunk 98 optimal weight:    0.0770
   overall best weight:    0.2794

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.135327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.113018 restraints weight = 11639.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 1.63
r_work: 0.3230 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3087 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8251  Z= 0.133
  Angle     :  0.461   8.212  11190  Z= 0.230
  Chirality :  0.037   0.136   1343
  Planarity :  0.004   0.067   1379
  Dihedral  :  3.392  13.844   1093
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.63 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.51 (0.27), residues: 1012
  helix:  2.21 (0.19), residues: 712
  sheet:  1.51 (0.81), residues: 43
  loop :  0.19 (0.42), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 419 
 HIS   0.005   0.000   HIS A1120 
 PHE   0.013   0.001   PHE A 766 
 TYR   0.014   0.001   TYR A 358 
 ARG   0.004   0.000   ARG A 887 

*********************** 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
  242 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 219
  time to evaluate  : 2.374 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8279 (ttmt) cc_final: 0.7957 (ttmt)
REVERT: A  108 ILE cc_start: 0.8414 (mm) cc_final: 0.8124 (mt)
REVERT: A  116 VAL cc_start: 0.8285 (p) cc_final: 0.8064 (p)
REVERT: A  124 GLU cc_start: 0.7480 (tp30) cc_final: 0.7070 (tm-30)
REVERT: A  163 PHE cc_start: 0.8359 (t80) cc_final: 0.8049 (t80)
REVERT: A  205 MET cc_start: 0.8089 (tpp) cc_final: 0.7646 (tpp)
REVERT: A  209 ASP cc_start: 0.7502 (t0) cc_final: 0.7010 (t0)
REVERT: A  233 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7143 (tt0)
REVERT: A  287 VAL cc_start: 0.8169 (m) cc_final: 0.7890 (t)
REVERT: A  322 SER cc_start: 0.8486 (t) cc_final: 0.8017 (p)
REVERT: A  333 ILE cc_start: 0.8479 (mm) cc_final: 0.8074 (mt)
REVERT: A  375 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8165 (ttpt)
REVERT: A  398 ILE cc_start: 0.8360 (mm) cc_final: 0.8037 (mt)
REVERT: A  401 MET cc_start: 0.7721 (mmm) cc_final: 0.7381 (mmm)
REVERT: A  502 HIS cc_start: 0.7630 (t70) cc_final: 0.7395 (t70)
REVERT: A  580 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7403 (mm-30)
REVERT: A  588 LYS cc_start: 0.8262 (ttpp) cc_final: 0.8003 (ttmt)
REVERT: A  616 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7150 (mm-30)
REVERT: A  841 LYS cc_start: 0.6986 (mmtt) cc_final: 0.6624 (mmtt)
REVERT: A  853 ILE cc_start: 0.7978 (mm) cc_final: 0.7754 (tt)
REVERT: A  857 MET cc_start: 0.7802 (tpp) cc_final: 0.7443 (tpt)
REVERT: A  868 LYS cc_start: 0.7703 (mtpp) cc_final: 0.7467 (mttm)
REVERT: A  872 GLU cc_start: 0.7504 (tp30) cc_final: 0.7251 (tp30)
REVERT: A  968 LYS cc_start: 0.8489 (mttt) cc_final: 0.8237 (mttt)
REVERT: A 1009 TYR cc_start: 0.8012 (t80) cc_final: 0.7691 (t80)
REVERT: A 1066 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.7769 (m-80)
REVERT: A 1073 MET cc_start: 0.8088 (mmm) cc_final: 0.7584 (mmm)
REVERT: A 1186 LEU cc_start: 0.8729 (tt) cc_final: 0.8455 (tp)
  outliers start: 23
  outliers final: 16
  residues processed: 229
  average time/residue: 0.2801
  time to fit residues: 84.3601
Evaluate side-chains
  235 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 218
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
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  626 ILE
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 1038 VAL
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1115 GLU
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 48 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0980
   chunk 75 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 1 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.134049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.111858 restraints weight = 11585.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.63
r_work: 0.3177 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8251  Z= 0.186
  Angle     :  0.491   9.669  11190  Z= 0.244
  Chirality :  0.038   0.136   1343
  Planarity :  0.004   0.064   1379
  Dihedral  :  3.442  13.605   1093
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 18.09 %
    Favored  : 79.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.27), residues: 1012
  helix:  2.11 (0.19), residues: 713
  sheet:  1.28 (0.80), residues: 43
  loop :  0.15 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 419 
 HIS   0.004   0.000   HIS A1120 
 PHE   0.031   0.001   PHE A 766 
 TYR   0.013   0.001   TYR A 358 
 ARG   0.005   0.000   ARG A 887 

********************** 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
  238 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 217
  time to evaluate  : 1.139 
Fit side-chains
REVERT: A   87 PHE cc_start: 0.8071 (m-10) cc_final: 0.7845 (m-10)
REVERT: A   96 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7986 (ttmt)
REVERT: A  108 ILE cc_start: 0.8378 (mm) cc_final: 0.8096 (mt)
REVERT: A  116 VAL cc_start: 0.8259 (p) cc_final: 0.8035 (p)
REVERT: A  124 GLU cc_start: 0.7526 (tp30) cc_final: 0.7096 (tm-30)
REVERT: A  163 PHE cc_start: 0.8385 (t80) cc_final: 0.8139 (t80)
REVERT: A  205 MET cc_start: 0.8119 (tpp) cc_final: 0.7664 (tpp)
REVERT: A  209 ASP cc_start: 0.7596 (t0) cc_final: 0.7068 (t0)
REVERT: A  233 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7174 (tt0)
REVERT: A  287 VAL cc_start: 0.8150 (m) cc_final: 0.7896 (t)
REVERT: A  322 SER cc_start: 0.8480 (t) cc_final: 0.7998 (p)
REVERT: A  337 GLU cc_start: 0.7540 (mp0) cc_final: 0.7271 (mp0)
REVERT: A  347 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8157 (t)
REVERT: A  398 ILE cc_start: 0.8375 (mm) cc_final: 0.8040 (mt)
REVERT: A  401 MET cc_start: 0.7662 (mmm) cc_final: 0.7314 (mmm)
REVERT: A  511 MET cc_start: 0.8629 (tmm) cc_final: 0.7930 (ttt)
REVERT: A  580 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7424 (mm-30)
REVERT: A  586 MET cc_start: 0.7154 (ttt) cc_final: 0.6890 (ttt)
REVERT: A  588 LYS cc_start: 0.8255 (ttpp) cc_final: 0.7975 (ttmt)
REVERT: A  616 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7161 (mm-30)
REVERT: A  841 LYS cc_start: 0.6926 (mmtt) cc_final: 0.6614 (mmtt)
REVERT: A  849 GLU cc_start: 0.7275 (tt0) cc_final: 0.6859 (tt0)
REVERT: A  853 ILE cc_start: 0.7954 (mm) cc_final: 0.7497 (tt)
REVERT: A  857 MET cc_start: 0.7793 (tpp) cc_final: 0.7556 (tpt)
REVERT: A  866 GLU cc_start: 0.7556 (tp30) cc_final: 0.7302 (tp30)
REVERT: A  872 GLU cc_start: 0.7555 (tp30) cc_final: 0.7275 (tp30)
REVERT: A  968 LYS cc_start: 0.8508 (mttt) cc_final: 0.8245 (mttt)
REVERT: A 1009 TYR cc_start: 0.8037 (t80) cc_final: 0.7706 (t80)
REVERT: A 1033 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7630 (mt-10)
REVERT: A 1066 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.7790 (m-80)
REVERT: A 1073 MET cc_start: 0.8084 (mmm) cc_final: 0.7404 (mmm)
REVERT: A 1186 LEU cc_start: 0.8763 (tt) cc_final: 0.8468 (tp)
  outliers start: 21
  outliers final: 17
  residues processed: 226
  average time/residue: 0.2620
  time to fit residues: 78.6173
Evaluate side-chains
  235 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 216
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
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  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  647 LYS
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue 1038 VAL
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1115 GLU
Chi-restraints excluded: chain A residue 1129 LEU
Chi-restraints excluded: chain A residue 1136 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 42 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 63 optimal weight:    5.9990
   chunk 72 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 41 optimal weight:    0.4980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.133451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.111471 restraints weight = 11675.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3331 rms_B_bonded: 1.64
r_work: 0.3219 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8251  Z= 0.206
  Angle     :  0.489  10.410  11190  Z= 0.246
  Chirality :  0.039   0.135   1343
  Planarity :  0.004   0.067   1379
  Dihedral  :  3.498  15.179   1093
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 18.43 %
    Favored  : 79.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.27), residues: 1012
  helix:  2.06 (0.19), residues: 713
  sheet:  1.19 (0.82), residues: 43
  loop :  0.15 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 419 
 HIS   0.004   0.001   HIS A1120 
 PHE   0.032   0.001   PHE A 766 
 TYR   0.012   0.001   TYR A 358 
 ARG   0.003   0.000   ARG A1123 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4829.56 seconds
wall clock time: 85 minutes 0.92 seconds (5100.92 seconds total)