Starting phenix.real_space_refine
on Sun May 11 14:28:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pd5_17601/05_2025/8pd5_17601.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pd5_17601/05_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_17601/05_2025/8pd5_17601.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pd5_17601/05_2025/8pd5_17601.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pd5_17601/05_2025/8pd5_17601.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pd5_17601/05_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.20, per 1000 atoms: 0.64
  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: 2.30
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.68
  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: 2.33

  Time building geometry restraints manager: 2.68 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:             3.510
  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:             0.020
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.740
  Find NCS groups from input model:        0.080
  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:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7339
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8251  Z= 0.133
  Angle     :  0.534  11.027  11190  Z= 0.301
  Chirality :  0.038   0.145   1343
  Planarity :  0.004   0.061   1379
  Dihedral  : 13.122  80.917   2994
  Min Nonbonded Distance : 2.148

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

Rama-Z (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 

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

*********************** 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  : 0.914 
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: 0.2336
  time to fit residues: 77.7759
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  : 0.896 
-------------------------------------------------------------------------------
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 = 44)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.113984 restraints weight = 11438.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.59
r_work: 0.3235 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
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= 0.112
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04453 (  472)
  hydrogen bonds       : angle       3.62224 ( 1416)
  covalent geometry    : bond        0.00232 ( 8251)
  covalent geometry    : angle       0.48892 (11190)

*********************** 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  : 0.842 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 LYS cc_start: 0.8297 (ttmt) cc_final: 0.7955 (ttmt)
REVERT: A  108 ILE cc_start: 0.8417 (mm) cc_final: 0.8124 (mt)
REVERT: A  125 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7709 (mt-10)
REVERT: A  163 PHE cc_start: 0.8323 (t80) cc_final: 0.8045 (t80)
REVERT: A  164 SER cc_start: 0.8814 (m) cc_final: 0.8476 (p)
REVERT: A  209 ASP cc_start: 0.7616 (t0) cc_final: 0.7237 (t0)
REVERT: A  233 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7191 (tt0)
REVERT: A  249 MET cc_start: 0.8408 (tmm) cc_final: 0.8100 (ttp)
REVERT: A  250 LYS cc_start: 0.8212 (mttt) cc_final: 0.7984 (mtmm)
REVERT: A  322 SER cc_start: 0.8489 (t) cc_final: 0.7993 (p)
REVERT: A  337 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7691 (mp0)
REVERT: A  383 MET cc_start: 0.8117 (mmp) cc_final: 0.7882 (mmt)
REVERT: A  401 MET cc_start: 0.7872 (mmm) cc_final: 0.7622 (mmm)
REVERT: A  580 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7345 (mm-30)
REVERT: A  588 LYS cc_start: 0.8246 (ttpp) cc_final: 0.7988 (ttmt)
REVERT: A  616 GLU cc_start: 0.7394 (mt-10) cc_final: 0.7182 (mt-10)
REVERT: A  849 GLU cc_start: 0.7455 (tt0) cc_final: 0.7196 (tt0)
REVERT: A  853 ILE cc_start: 0.8073 (mm) cc_final: 0.7771 (tt)
REVERT: A  968 LYS cc_start: 0.8514 (mttt) cc_final: 0.8277 (mttt)
REVERT: A  998 LEU cc_start: 0.8739 (pp) cc_final: 0.8520 (pt)
REVERT: A 1007 LYS cc_start: 0.7892 (tttt) cc_final: 0.7620 (tttm)
REVERT: A 1009 TYR cc_start: 0.8100 (t80) cc_final: 0.7757 (t80)
REVERT: A 1033 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7805 (mt-10)
REVERT: A 1034 ASP cc_start: 0.7657 (t0) cc_final: 0.7352 (t0)
REVERT: A 1035 TYR cc_start: 0.8339 (m-80) cc_final: 0.8010 (m-80)
REVERT: A 1048 LEU cc_start: 0.8247 (mt) cc_final: 0.7972 (mt)
REVERT: A 1066 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.8050 (m-80)
REVERT: A 1087 GLU cc_start: 0.7974 (tp30) cc_final: 0.7754 (tp30)
  outliers start: 14
  outliers final: 6
  residues processed: 229
  average time/residue: 0.2309
  time to fit residues: 69.6081
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  : 0.886 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0770
   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:    0.0470
   chunk 86 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.4236

-------------------------------------------------------------------------------
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 = 0.3674 r_free = 0.3674 target = 0.135690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.113281 restraints weight = 11569.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.55
r_work: 0.3173 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8251  Z= 0.116
  Angle     :  0.471  11.805  11190  Z= 0.237
  Chirality :  0.038   0.135   1343
  Planarity :  0.004   0.066   1379
  Dihedral  :  3.643  13.975   1093
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 13.99 %
    Favored  : 83.96 %
  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:  2.46 (0.27), residues: 1012
  helix:  2.20 (0.19), residues: 713
  sheet:  0.61 (0.78), residues: 47
  loop :  0.26 (0.43), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 635 
 HIS   0.008   0.001   HIS A1120 
 PHE   0.022   0.001   PHE A 766 
 TYR   0.012   0.001   TYR A 984 
 ARG   0.011   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04233 (  472)
  hydrogen bonds       : angle       3.51041 ( 1416)
  covalent geometry    : bond        0.00244 ( 8251)
  covalent geometry    : angle       0.47137 (11190)

*********************** 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
  241 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 223
  time to evaluate  : 0.917 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7965 (ttmt)
REVERT: A  108 ILE cc_start: 0.8387 (mm) cc_final: 0.8112 (mt)
REVERT: A  128 ARG cc_start: 0.8449 (ptm160) cc_final: 0.8175 (ptp90)
REVERT: A  154 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7696 (mtp)
REVERT: A  163 PHE cc_start: 0.8368 (t80) cc_final: 0.8088 (t80)
REVERT: A  164 SER cc_start: 0.8762 (m) cc_final: 0.8364 (p)
REVERT: A  194 ASN cc_start: 0.8376 (p0) cc_final: 0.8175 (p0)
REVERT: A  209 ASP cc_start: 0.7586 (t0) cc_final: 0.7134 (t0)
REVERT: A  233 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7261 (tt0)
REVERT: A  250 LYS cc_start: 0.8232 (mttt) cc_final: 0.7996 (mtmm)
REVERT: A  322 SER cc_start: 0.8463 (t) cc_final: 0.7979 (p)
REVERT: A  337 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7636 (mp0)
REVERT: A  383 MET cc_start: 0.8093 (mmp) cc_final: 0.7862 (mmt)
REVERT: A  398 ILE cc_start: 0.8384 (mm) cc_final: 0.8066 (mt)
REVERT: A  401 MET cc_start: 0.7927 (mmm) cc_final: 0.7586 (mmm)
REVERT: A  580 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7341 (mm-30)
REVERT: A  586 MET cc_start: 0.7147 (ttm) cc_final: 0.6886 (ttt)
REVERT: A  588 LYS cc_start: 0.8281 (ttpp) cc_final: 0.8007 (ttmt)
REVERT: A  602 MET cc_start: 0.7971 (ttm) cc_final: 0.7475 (mtp)
REVERT: A  616 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7149 (mt-10)
REVERT: A  647 LYS cc_start: 0.7919 (mmtm) cc_final: 0.7702 (mmtm)
REVERT: A  849 GLU cc_start: 0.7365 (tt0) cc_final: 0.7125 (tt0)
REVERT: A  853 ILE cc_start: 0.7969 (mm) cc_final: 0.7700 (tt)
REVERT: A  857 MET cc_start: 0.7287 (tmm) cc_final: 0.7048 (tpt)
REVERT: A  938 MET cc_start: 0.8392 (tpp) cc_final: 0.8028 (ttt)
REVERT: A  968 LYS cc_start: 0.8551 (mttt) cc_final: 0.8273 (mttt)
REVERT: A 1009 TYR cc_start: 0.8099 (t80) cc_final: 0.7710 (t80)
REVERT: A 1035 TYR cc_start: 0.8347 (m-80) cc_final: 0.8001 (m-80)
REVERT: A 1048 LEU cc_start: 0.8279 (mt) cc_final: 0.8009 (mt)
REVERT: A 1057 VAL cc_start: 0.8756 (t) cc_final: 0.8503 (m)
REVERT: A 1066 TYR cc_start: 0.8520 (OUTLIER) cc_final: 0.8010 (m-80)
REVERT: A 1073 MET cc_start: 0.8248 (mmm) cc_final: 0.7613 (mmm)
  outliers start: 18
  outliers final: 11
  residues processed: 227
  average time/residue: 0.2283
  time to fit residues: 67.9218
Evaluate side-chains
  229 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 216
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
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  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 1041 VAL
Chi-restraints excluded: chain A residue 1060 GLU
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:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    0.1980
   chunk 16 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0370
   chunk 33 optimal weight:    0.8980
   chunk 96 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.5258

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.135124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.112835 restraints weight = 11400.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.56
r_work: 0.3236 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
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   0.036   8251  Z= 0.120
  Angle     :  0.476  10.603  11190  Z= 0.236
  Chirality :  0.038   0.139   1343
  Planarity :  0.004   0.054   1379
  Dihedral  :  3.561  13.489   1093
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 13.99 %
    Favored  : 83.16 %
  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:  2.15 (0.19), residues: 715
  sheet:  1.31 (0.71), residues: 53
  loop : -0.04 (0.42), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 635 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.018   0.001   PHE A 766 
 TYR   0.009   0.001   TYR A 984 
 ARG   0.005   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04155 (  472)
  hydrogen bonds       : angle       3.47277 ( 1416)
  covalent geometry    : bond        0.00267 ( 8251)
  covalent geometry    : angle       0.47610 (11190)

*********************** 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
  245 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 220
  time to evaluate  : 0.825 
Fit side-chains
REVERT: A   87 PHE cc_start: 0.8070 (m-10) cc_final: 0.7845 (m-10)
REVERT: A   96 LYS cc_start: 0.8306 (ttmt) cc_final: 0.7911 (ttpp)
REVERT: A  108 ILE cc_start: 0.8419 (mm) cc_final: 0.8148 (mt)
REVERT: A  124 GLU cc_start: 0.7471 (tp30) cc_final: 0.7001 (tm-30)
REVERT: A  125 GLU cc_start: 0.7736 (mm-30) cc_final: 0.6771 (mm-30)
REVERT: A  163 PHE cc_start: 0.8421 (t80) cc_final: 0.8124 (t80)
REVERT: A  164 SER cc_start: 0.8812 (m) cc_final: 0.8410 (p)
REVERT: A  194 ASN cc_start: 0.8367 (p0) cc_final: 0.8156 (p0)
REVERT: A  205 MET cc_start: 0.8120 (tpp) cc_final: 0.7410 (mpp)
REVERT: A  209 ASP cc_start: 0.7533 (t0) cc_final: 0.7109 (t0)
REVERT: A  233 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7257 (tt0)
REVERT: A  250 LYS cc_start: 0.8261 (mttt) cc_final: 0.8036 (mtmm)
REVERT: A  287 VAL cc_start: 0.8182 (m) cc_final: 0.7870 (t)
REVERT: A  322 SER cc_start: 0.8456 (t) cc_final: 0.7984 (p)
REVERT: A  337 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7660 (mp0)
REVERT: A  383 MET cc_start: 0.8100 (mmp) cc_final: 0.7880 (mmt)
REVERT: A  398 ILE cc_start: 0.8443 (mm) cc_final: 0.8096 (mt)
REVERT: A  401 MET cc_start: 0.7906 (mmm) cc_final: 0.7571 (mmm)
REVERT: A  406 PHE cc_start: 0.7994 (m-80) cc_final: 0.7769 (m-80)
REVERT: A  580 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7376 (mm-30)
REVERT: A  586 MET cc_start: 0.7195 (ttm) cc_final: 0.6970 (ttt)
REVERT: A  588 LYS cc_start: 0.8296 (ttpp) cc_final: 0.8056 (ttmt)
REVERT: A  616 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7109 (mt-10)
REVERT: A  849 GLU cc_start: 0.7341 (tt0) cc_final: 0.7033 (tt0)
REVERT: A  853 ILE cc_start: 0.8087 (mm) cc_final: 0.7783 (tt)
REVERT: A  872 GLU cc_start: 0.7405 (tp30) cc_final: 0.7132 (tp30)
REVERT: A  887 ARG cc_start: 0.8215 (ttm-80) cc_final: 0.7982 (ttt90)
REVERT: A  968 LYS cc_start: 0.8540 (mttt) cc_final: 0.8284 (mttt)
REVERT: A 1009 TYR cc_start: 0.8130 (t80) cc_final: 0.7681 (t80)
REVERT: A 1035 TYR cc_start: 0.8305 (m-80) cc_final: 0.8029 (m-80)
REVERT: A 1057 VAL cc_start: 0.8806 (t) cc_final: 0.8567 (m)
REVERT: A 1066 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7944 (m-80)
REVERT: A 1073 MET cc_start: 0.8221 (mmm) cc_final: 0.7707 (mmt)
  outliers start: 25
  outliers final: 16
  residues processed: 227
  average time/residue: 0.2285
  time to fit residues: 67.6272
Evaluate side-chains
  233 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 216
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  225 GLN
Chi-restraints excluded: chain A residue  303 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  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:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   chunk 90 optimal weight:    0.6980
   chunk 82 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3653 r_free = 0.3653 target = 0.133879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.111704 restraints weight = 11467.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 1.55
r_work: 0.3152 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.2401

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= 0.149
  Angle     :  0.473  10.745  11190  Z= 0.237
  Chirality :  0.038   0.134   1343
  Planarity :  0.004   0.056   1379
  Dihedral  :  3.567  13.888   1093
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 15.70 %
    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:  2.24 (0.27), residues: 1012
  helix:  2.06 (0.19), residues: 715
  sheet:  0.96 (0.92), residues: 32
  loop :  0.03 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 419 
 HIS   0.004   0.001   HIS A1120 
 PHE   0.015   0.001   PHE A 766 
 TYR   0.007   0.001   TYR A 313 
 ARG   0.003   0.000   ARG A 161 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04313 (  472)
  hydrogen bonds       : angle       3.49595 ( 1416)
  covalent geometry    : bond        0.00347 ( 8251)
  covalent geometry    : angle       0.47312 (11190)

*********************** 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
  242 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 221
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A   87 PHE cc_start: 0.8073 (m-10) cc_final: 0.7863 (m-10)
REVERT: A   96 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8006 (ttmt)
REVERT: A  108 ILE cc_start: 0.8402 (mm) cc_final: 0.8142 (mt)
REVERT: A  116 VAL cc_start: 0.8313 (p) cc_final: 0.8102 (p)
REVERT: A  124 GLU cc_start: 0.7499 (tp30) cc_final: 0.7050 (tm-30)
REVERT: A  125 GLU cc_start: 0.7682 (mm-30) cc_final: 0.6877 (mm-30)
REVERT: A  154 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7756 (mtp)
REVERT: A  155 ASP cc_start: 0.7592 (t70) cc_final: 0.7158 (t70)
REVERT: A  163 PHE cc_start: 0.8407 (t80) cc_final: 0.8133 (t80)
REVERT: A  194 ASN cc_start: 0.8351 (p0) cc_final: 0.8140 (p0)
REVERT: A  209 ASP cc_start: 0.7592 (t0) cc_final: 0.7111 (t0)
REVERT: A  233 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7278 (tt0)
REVERT: A  250 LYS cc_start: 0.8296 (mttt) cc_final: 0.8059 (mtmm)
REVERT: A  287 VAL cc_start: 0.8177 (m) cc_final: 0.7880 (t)
REVERT: A  322 SER cc_start: 0.8475 (t) cc_final: 0.7999 (p)
REVERT: A  337 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7606 (mp0)
REVERT: A  383 MET cc_start: 0.8078 (mmp) cc_final: 0.7857 (mmt)
REVERT: A  398 ILE cc_start: 0.8410 (mm) cc_final: 0.8052 (mt)
REVERT: A  401 MET cc_start: 0.7854 (mmm) cc_final: 0.7497 (mmm)
REVERT: A  406 PHE cc_start: 0.7996 (m-80) cc_final: 0.7759 (m-80)
REVERT: A  580 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7373 (mm-30)
REVERT: A  586 MET cc_start: 0.7170 (ttm) cc_final: 0.6892 (ttt)
REVERT: A  588 LYS cc_start: 0.8257 (ttpp) cc_final: 0.8005 (ttmt)
REVERT: A  616 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7118 (mt-10)
REVERT: A  849 GLU cc_start: 0.7354 (tt0) cc_final: 0.7020 (tt0)
REVERT: A  853 ILE cc_start: 0.7984 (mm) cc_final: 0.7694 (tt)
REVERT: A  857 MET cc_start: 0.7713 (tpt) cc_final: 0.7494 (tpt)
REVERT: A  866 GLU cc_start: 0.7510 (tp30) cc_final: 0.7165 (tp30)
REVERT: A  872 GLU cc_start: 0.7486 (tp30) cc_final: 0.7176 (tp30)
REVERT: A  968 LYS cc_start: 0.8550 (mttt) cc_final: 0.8279 (mttt)
REVERT: A 1035 TYR cc_start: 0.8302 (m-80) cc_final: 0.7999 (m-80)
REVERT: A 1048 LEU cc_start: 0.8297 (mt) cc_final: 0.8091 (mt)
REVERT: A 1057 VAL cc_start: 0.8779 (t) cc_final: 0.8523 (m)
REVERT: A 1066 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7949 (m-80)
REVERT: A 1098 ILE cc_start: 0.8838 (mm) cc_final: 0.8528 (mt)
REVERT: A 1122 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7837 (mm-30)
REVERT: A 1125 TYR cc_start: 0.8154 (p90) cc_final: 0.7904 (p90)
  outliers start: 21
  outliers final: 16
  residues processed: 228
  average time/residue: 0.2261
  time to fit residues: 67.8210
Evaluate side-chains
  234 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 216
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
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  303 ILE
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  407 SER
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  484 SER
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  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 1105 GLU
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:    0.6980
   chunk 75 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0170
   chunk 86 optimal weight:    0.2980
   chunk 98 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.4218

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.134941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.112940 restraints weight = 11410.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.52
r_work: 0.3169 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3032 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8251  Z= 0.108
  Angle     :  0.445   9.813  11190  Z= 0.224
  Chirality :  0.037   0.146   1343
  Planarity :  0.004   0.061   1379
  Dihedral  :  3.467  13.598   1093
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 16.61 %
    Favored  : 81.34 %
  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:  2.46 (0.27), residues: 1012
  helix:  2.17 (0.19), residues: 715
  sheet:  1.50 (0.77), residues: 43
  loop :  0.16 (0.41), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 419 
 HIS   0.005   0.000   HIS A1120 
 PHE   0.014   0.001   PHE A 766 
 TYR   0.006   0.001   TYR A1066 
 ARG   0.005   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03971 (  472)
  hydrogen bonds       : angle       3.42375 ( 1416)
  covalent geometry    : bond        0.00237 ( 8251)
  covalent geometry    : angle       0.44488 (11190)

*********************** 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
  234 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 216
  time to evaluate  : 0.909 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7979 (ttmt)
REVERT: A  108 ILE cc_start: 0.8403 (mm) cc_final: 0.8121 (mt)
REVERT: A  124 GLU cc_start: 0.7505 (tp30) cc_final: 0.7057 (tm-30)
REVERT: A  125 GLU cc_start: 0.7711 (mm-30) cc_final: 0.6987 (mm-30)
REVERT: A  155 ASP cc_start: 0.7572 (t70) cc_final: 0.7131 (t70)
REVERT: A  163 PHE cc_start: 0.8333 (t80) cc_final: 0.8027 (t80)
REVERT: A  194 ASN cc_start: 0.8330 (p0) cc_final: 0.8126 (p0)
REVERT: A  205 MET cc_start: 0.8025 (tpp) cc_final: 0.7754 (tpp)
REVERT: A  209 ASP cc_start: 0.7552 (t0) cc_final: 0.7080 (t0)
REVERT: A  233 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7230 (tt0)
REVERT: A  250 LYS cc_start: 0.8253 (mttt) cc_final: 0.8052 (mttm)
REVERT: A  287 VAL cc_start: 0.8161 (m) cc_final: 0.7866 (t)
REVERT: A  322 SER cc_start: 0.8481 (t) cc_final: 0.8017 (p)
REVERT: A  375 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8143 (ttpt)
REVERT: A  383 MET cc_start: 0.8043 (mmp) cc_final: 0.7823 (mmt)
REVERT: A  398 ILE cc_start: 0.8393 (mm) cc_final: 0.8053 (mt)
REVERT: A  401 MET cc_start: 0.7844 (mmm) cc_final: 0.7495 (mmm)
REVERT: A  494 MET cc_start: 0.8112 (tpp) cc_final: 0.7904 (tpt)
REVERT: A  502 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.7389 (t70)
REVERT: A  580 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7423 (mm-30)
REVERT: A  588 LYS cc_start: 0.8263 (ttpp) cc_final: 0.8014 (ttmt)
REVERT: A  651 LEU cc_start: 0.7900 (mt) cc_final: 0.7506 (mp)
REVERT: A  849 GLU cc_start: 0.7294 (tt0) cc_final: 0.7094 (tt0)
REVERT: A  853 ILE cc_start: 0.7970 (mm) cc_final: 0.7713 (tt)
REVERT: A  872 GLU cc_start: 0.7483 (tp30) cc_final: 0.7194 (tp30)
REVERT: A  938 MET cc_start: 0.8376 (tpp) cc_final: 0.8054 (ttt)
REVERT: A  968 LYS cc_start: 0.8498 (mttt) cc_final: 0.8255 (mttt)
REVERT: A 1009 TYR cc_start: 0.8035 (t80) cc_final: 0.7684 (t80)
REVERT: A 1035 TYR cc_start: 0.8317 (m-80) cc_final: 0.8030 (m-80)
REVERT: A 1048 LEU cc_start: 0.8261 (mt) cc_final: 0.8057 (mt)
REVERT: A 1057 VAL cc_start: 0.8755 (t) cc_final: 0.8504 (m)
REVERT: A 1066 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7884 (m-80)
REVERT: A 1073 MET cc_start: 0.8116 (mmm) cc_final: 0.7583 (mmm)
REVERT: A 1122 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7743 (mm-30)
REVERT: A 1125 TYR cc_start: 0.8110 (p90) cc_final: 0.7804 (p90)
REVERT: A 1190 ARG cc_start: 0.6975 (mmt-90) cc_final: 0.6681 (mmt180)
  outliers start: 18
  outliers final: 11
  residues processed: 222
  average time/residue: 0.2288
  time to fit residues: 67.0453
Evaluate side-chains
  230 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 217
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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  347 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 63 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0050
   chunk 84 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.5994

-------------------------------------------------------------------------------
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 = 0.134106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.111911 restraints weight = 11543.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 1.60
r_work: 0.3215 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2662

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= 0.125
  Angle     :  0.449   9.853  11190  Z= 0.226
  Chirality :  0.038   0.162   1343
  Planarity :  0.004   0.064   1379
  Dihedral  :  3.455  13.756   1093
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.52 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.43 (0.27), residues: 1012
  helix:  2.13 (0.19), residues: 717
  sheet:  1.39 (0.77), residues: 43
  loop :  0.21 (0.41), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 419 
 HIS   0.004   0.000   HIS A1120 
 PHE   0.013   0.001   PHE A 766 
 TYR   0.014   0.001   TYR A 984 
 ARG   0.006   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04143 (  472)
  hydrogen bonds       : angle       3.45295 ( 1416)
  covalent geometry    : bond        0.00284 ( 8251)
  covalent geometry    : angle       0.44919 (11190)

*********************** 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
  238 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 219
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7955 (ttmt)
REVERT: A  108 ILE cc_start: 0.8441 (mm) cc_final: 0.8151 (mt)
REVERT: A  116 VAL cc_start: 0.8320 (p) cc_final: 0.8103 (p)
REVERT: A  124 GLU cc_start: 0.7546 (tp30) cc_final: 0.7106 (tm-30)
REVERT: A  125 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7066 (mm-30)
REVERT: A  163 PHE cc_start: 0.8469 (t80) cc_final: 0.8182 (t80)
REVERT: A  209 ASP cc_start: 0.7488 (t0) cc_final: 0.7059 (t0)
REVERT: A  233 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7176 (tt0)
REVERT: A  287 VAL cc_start: 0.8156 (m) cc_final: 0.7895 (t)
REVERT: A  322 SER cc_start: 0.8487 (t) cc_final: 0.8007 (p)
REVERT: A  375 LYS cc_start: 0.8445 (ttmt) cc_final: 0.8145 (ttpt)
REVERT: A  383 MET cc_start: 0.8050 (mmp) cc_final: 0.7843 (mmt)
REVERT: A  398 ILE cc_start: 0.8433 (mm) cc_final: 0.8089 (mt)
REVERT: A  401 MET cc_start: 0.7839 (mmm) cc_final: 0.7484 (mmm)
REVERT: A  406 PHE cc_start: 0.8017 (m-80) cc_final: 0.7791 (m-80)
REVERT: A  502 HIS cc_start: 0.7587 (OUTLIER) cc_final: 0.7362 (t70)
REVERT: A  580 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7463 (mm-30)
REVERT: A  588 LYS cc_start: 0.8259 (ttpp) cc_final: 0.8006 (ttmt)
REVERT: A  651 LEU cc_start: 0.7914 (mt) cc_final: 0.7541 (mp)
REVERT: A  849 GLU cc_start: 0.7260 (tt0) cc_final: 0.6918 (tt0)
REVERT: A  853 ILE cc_start: 0.7969 (mm) cc_final: 0.7732 (tt)
REVERT: A  872 GLU cc_start: 0.7504 (tp30) cc_final: 0.7228 (tp30)
REVERT: A  968 LYS cc_start: 0.8494 (mttt) cc_final: 0.8251 (mttt)
REVERT: A 1009 TYR cc_start: 0.8050 (t80) cc_final: 0.7688 (t80)
REVERT: A 1035 TYR cc_start: 0.8322 (m-80) cc_final: 0.8050 (m-80)
REVERT: A 1048 LEU cc_start: 0.8257 (mt) cc_final: 0.7989 (mt)
REVERT: A 1057 VAL cc_start: 0.8794 (t) cc_final: 0.8561 (m)
REVERT: A 1066 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7909 (m-80)
REVERT: A 1098 ILE cc_start: 0.8857 (mm) cc_final: 0.8551 (mt)
REVERT: A 1122 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7795 (mm-30)
  outliers start: 19
  outliers final: 14
  residues processed: 228
  average time/residue: 0.2274
  time to fit residues: 68.2602
Evaluate side-chains
  234 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 218
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
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  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  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue 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
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:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 79 optimal weight:    0.4980
   chunk 53 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.133672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.111406 restraints weight = 11644.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.62
r_work: 0.3216 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3073 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8251  Z= 0.128
  Angle     :  0.458   9.588  11190  Z= 0.230
  Chirality :  0.038   0.136   1343
  Planarity :  0.004   0.065   1379
  Dihedral  :  3.456  14.000   1093
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.06 %
    Favored  : 80.20 %
  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:  2.39 (0.26), residues: 1012
  helix:  2.12 (0.19), residues: 716
  sheet:  1.31 (0.77), residues: 43
  loop :  0.15 (0.41), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 419 
 HIS   0.004   0.000   HIS A1120 
 PHE   0.012   0.001   PHE A 766 
 TYR   0.011   0.001   TYR A 984 
 ARG   0.006   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04174 (  472)
  hydrogen bonds       : angle       3.45770 ( 1416)
  covalent geometry    : bond        0.00293 ( 8251)
  covalent geometry    : angle       0.45810 (11190)

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

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

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

  2024 Ramachandran restraints generated.
    1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 222
  time to evaluate  : 0.860 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7961 (ttmt)
REVERT: A  108 ILE cc_start: 0.8434 (mm) cc_final: 0.8146 (mt)
REVERT: A  116 VAL cc_start: 0.8309 (p) cc_final: 0.8096 (p)
REVERT: A  124 GLU cc_start: 0.7553 (tp30) cc_final: 0.7071 (tm-30)
REVERT: A  125 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7086 (mm-30)
REVERT: A  155 ASP cc_start: 0.7549 (t70) cc_final: 0.7286 (t70)
REVERT: A  163 PHE cc_start: 0.8459 (t80) cc_final: 0.8184 (t80)
REVERT: A  209 ASP cc_start: 0.7517 (t0) cc_final: 0.7083 (t0)
REVERT: A  233 GLU cc_start: 0.7476 (tm-30) cc_final: 0.7181 (tt0)
REVERT: A  287 VAL cc_start: 0.8168 (m) cc_final: 0.7908 (t)
REVERT: A  322 SER cc_start: 0.8486 (t) cc_final: 0.8014 (p)
REVERT: A  333 ILE cc_start: 0.8445 (mm) cc_final: 0.8229 (mt)
REVERT: A  383 MET cc_start: 0.8054 (mmp) cc_final: 0.7854 (mmt)
REVERT: A  398 ILE cc_start: 0.8419 (mm) cc_final: 0.8079 (mt)
REVERT: A  401 MET cc_start: 0.7839 (mmm) cc_final: 0.7481 (mmm)
REVERT: A  406 PHE cc_start: 0.8032 (m-80) cc_final: 0.7788 (m-80)
REVERT: A  502 HIS cc_start: 0.7581 (OUTLIER) cc_final: 0.7348 (t70)
REVERT: A  511 MET cc_start: 0.8665 (tmm) cc_final: 0.7948 (ttt)
REVERT: A  580 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7489 (mm-30)
REVERT: A  588 LYS cc_start: 0.8266 (ttpp) cc_final: 0.8009 (ttmt)
REVERT: A  616 GLU cc_start: 0.7445 (mt-10) cc_final: 0.7068 (mm-30)
REVERT: A  647 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7746 (mmtp)
REVERT: A  849 GLU cc_start: 0.7264 (tt0) cc_final: 0.6942 (tt0)
REVERT: A  853 ILE cc_start: 0.7974 (mm) cc_final: 0.7758 (tt)
REVERT: A  866 GLU cc_start: 0.7559 (tp30) cc_final: 0.7225 (tp30)
REVERT: A  872 GLU cc_start: 0.7538 (tp30) cc_final: 0.7250 (tp30)
REVERT: A  880 LYS cc_start: 0.8529 (tttt) cc_final: 0.8284 (tptp)
REVERT: A  968 LYS cc_start: 0.8497 (mttt) cc_final: 0.8253 (mttt)
REVERT: A 1009 TYR cc_start: 0.8056 (t80) cc_final: 0.7699 (t80)
REVERT: A 1035 TYR cc_start: 0.8303 (m-80) cc_final: 0.8043 (m-80)
REVERT: A 1048 LEU cc_start: 0.8242 (mt) cc_final: 0.8000 (mt)
REVERT: A 1057 VAL cc_start: 0.8781 (t) cc_final: 0.8555 (m)
REVERT: A 1066 TYR cc_start: 0.8601 (OUTLIER) cc_final: 0.7868 (m-80)
REVERT: A 1098 ILE cc_start: 0.8846 (mm) cc_final: 0.8537 (mt)
REVERT: A 1122 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7820 (mm-30)
  outliers start: 24
  outliers final: 17
  residues processed: 233
  average time/residue: 0.2195
  time to fit residues: 67.8888
Evaluate side-chains
  238 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 218
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
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  407 SER
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  638 LYS
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  647 LYS
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1136 PHE
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:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 98 optimal weight:    0.2980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 955 ASN
** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

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 = 0.133436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.111177 restraints weight = 11635.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.60
r_work: 0.3212 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2829

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8251  Z= 0.131
  Angle     :  0.457   9.391  11190  Z= 0.232
  Chirality :  0.038   0.136   1343
  Planarity :  0.004   0.068   1379
  Dihedral  :  3.484  14.136   1093
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.18 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.40 (0.26), residues: 1012
  helix:  2.12 (0.19), residues: 713
  sheet:  1.36 (0.79), residues: 43
  loop :  0.18 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 419 
 HIS   0.004   0.000   HIS A1120 
 PHE   0.017   0.001   PHE A 999 
 TYR   0.011   0.001   TYR A 984 
 ARG   0.007   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04205 (  472)
  hydrogen bonds       : angle       3.47807 ( 1416)
  covalent geometry    : bond        0.00301 ( 8251)
  covalent geometry    : angle       0.45723 (11190)

*********************** 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: 21
    poor density    : 221
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8288 (ttmt) cc_final: 0.7959 (ttmt)
REVERT: A  108 ILE cc_start: 0.8442 (mm) cc_final: 0.8155 (mt)
REVERT: A  116 VAL cc_start: 0.8353 (p) cc_final: 0.8135 (p)
REVERT: A  124 GLU cc_start: 0.7554 (tp30) cc_final: 0.7072 (tm-30)
REVERT: A  125 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7135 (mm-30)
REVERT: A  155 ASP cc_start: 0.7555 (t70) cc_final: 0.7270 (t70)
REVERT: A  163 PHE cc_start: 0.8476 (t80) cc_final: 0.8230 (t80)
REVERT: A  209 ASP cc_start: 0.7552 (t0) cc_final: 0.7100 (t0)
REVERT: A  233 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7164 (tt0)
REVERT: A  287 VAL cc_start: 0.8179 (m) cc_final: 0.7906 (t)
REVERT: A  322 SER cc_start: 0.8464 (t) cc_final: 0.7997 (p)
REVERT: A  398 ILE cc_start: 0.8429 (mm) cc_final: 0.8087 (mt)
REVERT: A  401 MET cc_start: 0.7847 (mmm) cc_final: 0.7494 (mmm)
REVERT: A  406 PHE cc_start: 0.8050 (m-80) cc_final: 0.7815 (m-80)
REVERT: A  502 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.7354 (t70)
REVERT: A  511 MET cc_start: 0.8640 (tmm) cc_final: 0.7932 (ttt)
REVERT: A  580 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7495 (mm-30)
REVERT: A  588 LYS cc_start: 0.8243 (ttpp) cc_final: 0.7991 (ttmt)
REVERT: A  616 GLU cc_start: 0.7469 (mt-10) cc_final: 0.7082 (mm-30)
REVERT: A  849 GLU cc_start: 0.7264 (tt0) cc_final: 0.7021 (tt0)
REVERT: A  853 ILE cc_start: 0.7989 (mm) cc_final: 0.7519 (tt)
REVERT: A  866 GLU cc_start: 0.7567 (tp30) cc_final: 0.7239 (tp30)
REVERT: A  872 GLU cc_start: 0.7556 (tp30) cc_final: 0.7287 (tp30)
REVERT: A  968 LYS cc_start: 0.8485 (mttt) cc_final: 0.8247 (mttt)
REVERT: A 1035 TYR cc_start: 0.8288 (m-80) cc_final: 0.8024 (m-80)
REVERT: A 1048 LEU cc_start: 0.8244 (mt) cc_final: 0.8001 (mt)
REVERT: A 1057 VAL cc_start: 0.8764 (t) cc_final: 0.8531 (m)
REVERT: A 1066 TYR cc_start: 0.8615 (OUTLIER) cc_final: 0.7722 (m-80)
REVERT: A 1098 ILE cc_start: 0.8855 (mm) cc_final: 0.8540 (mt)
REVERT: A 1122 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7836 (mm-30)
  outliers start: 21
  outliers final: 18
  residues processed: 230
  average time/residue: 0.2202
  time to fit residues: 67.2568
Evaluate side-chains
  239 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 219
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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  407 SER
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  638 LYS
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 48 optimal weight:    0.6980
   chunk 7 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 94 optimal weight:    0.9980
   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 = 0.3632 r_free = 0.3632 target = 0.132667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.110592 restraints weight = 11611.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.58
r_work: 0.3197 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8251  Z= 0.139
  Angle     :  0.472   9.397  11190  Z= 0.239
  Chirality :  0.039   0.136   1343
  Planarity :  0.004   0.069   1379
  Dihedral  :  3.514  14.341   1093
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  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:  2.39 (0.26), residues: 1012
  helix:  2.12 (0.19), residues: 712
  sheet:  1.37 (0.80), residues: 43
  loop :  0.15 (0.41), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 635 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.014   0.001   PHE A 999 
 TYR   0.010   0.001   TYR A 984 
 ARG   0.005   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04245 (  472)
  hydrogen bonds       : angle       3.49737 ( 1416)
  covalent geometry    : bond        0.00319 ( 8251)
  covalent geometry    : angle       0.47225 (11190)

********************** 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
  246 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 221
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A   96 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7957 (ttmt)
REVERT: A  108 ILE cc_start: 0.8438 (mm) cc_final: 0.8155 (mt)
REVERT: A  116 VAL cc_start: 0.8359 (p) cc_final: 0.8144 (p)
REVERT: A  124 GLU cc_start: 0.7558 (tp30) cc_final: 0.7079 (tm-30)
REVERT: A  125 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7136 (mm-30)
REVERT: A  155 ASP cc_start: 0.7573 (t70) cc_final: 0.7295 (t70)
REVERT: A  163 PHE cc_start: 0.8477 (t80) cc_final: 0.8240 (t80)
REVERT: A  200 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8216 (ttm)
REVERT: A  209 ASP cc_start: 0.7540 (t0) cc_final: 0.7100 (t0)
REVERT: A  233 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7166 (tt0)
REVERT: A  287 VAL cc_start: 0.8170 (m) cc_final: 0.7920 (t)
REVERT: A  322 SER cc_start: 0.8459 (t) cc_final: 0.7987 (p)
REVERT: A  337 GLU cc_start: 0.7628 (mp0) cc_final: 0.7407 (mp0)
REVERT: A  398 ILE cc_start: 0.8438 (mm) cc_final: 0.8094 (mt)
REVERT: A  401 MET cc_start: 0.7812 (mmm) cc_final: 0.7460 (mmm)
REVERT: A  406 PHE cc_start: 0.8076 (m-80) cc_final: 0.7836 (m-80)
REVERT: A  502 HIS cc_start: 0.7565 (OUTLIER) cc_final: 0.7334 (t70)
REVERT: A  511 MET cc_start: 0.8629 (tmm) cc_final: 0.8016 (ttt)
REVERT: A  580 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7499 (mm-30)
REVERT: A  588 LYS cc_start: 0.8238 (ttpp) cc_final: 0.7981 (ttmt)
REVERT: A  616 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7106 (mm-30)
REVERT: A  853 ILE cc_start: 0.8000 (mm) cc_final: 0.7548 (tt)
REVERT: A  866 GLU cc_start: 0.7568 (tp30) cc_final: 0.7239 (tp30)
REVERT: A  872 GLU cc_start: 0.7563 (tp30) cc_final: 0.7305 (tp30)
REVERT: A  880 LYS cc_start: 0.8511 (tttt) cc_final: 0.8288 (tptp)
REVERT: A  968 LYS cc_start: 0.8481 (mttt) cc_final: 0.8251 (mttt)
REVERT: A 1035 TYR cc_start: 0.8269 (m-80) cc_final: 0.7989 (m-80)
REVERT: A 1048 LEU cc_start: 0.8242 (mt) cc_final: 0.8006 (mt)
REVERT: A 1057 VAL cc_start: 0.8737 (t) cc_final: 0.8496 (m)
REVERT: A 1066 TYR cc_start: 0.8609 (OUTLIER) cc_final: 0.7759 (m-80)
REVERT: A 1073 MET cc_start: 0.8134 (mmm) cc_final: 0.7579 (mmm)
REVERT: A 1106 GLN cc_start: 0.7880 (tm-30) cc_final: 0.7574 (tm-30)
REVERT: A 1107 MET cc_start: 0.6889 (ptt) cc_final: 0.6570 (ptp)
  outliers start: 25
  outliers final: 18
  residues processed: 231
  average time/residue: 0.2163
  time to fit residues: 66.1634
Evaluate side-chains
  239 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 218
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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  200 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  407 SER
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  502 HIS
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  627 LEU
Chi-restraints excluded: chain A residue  638 LYS
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue 1041 VAL
Chi-restraints excluded: chain A residue 1063 VAL
Chi-restraints excluded: chain A residue 1066 TYR
Chi-restraints excluded: chain A residue 1077 ILE
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:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 37 optimal weight:    0.5980
   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 886 GLN
A 955 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.132897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.110994 restraints weight = 11648.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3298 rms_B_bonded: 1.58
r_work: 0.3193 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8251  Z= 0.141
  Angle     :  0.479   9.412  11190  Z= 0.242
  Chirality :  0.039   0.143   1343
  Planarity :  0.004   0.068   1379
  Dihedral  :  3.527  14.942   1093
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 17.86 %
    Favored  : 79.64 %
  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:  2.32 (0.26), residues: 1012
  helix:  2.06 (0.19), residues: 713
  sheet:  1.55 (0.83), residues: 42
  loop :  0.14 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 419 
 HIS   0.004   0.001   HIS A1120 
 PHE   0.012   0.001   PHE A 766 
 TYR   0.012   0.001   TYR A 984 
 ARG   0.006   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04280 (  472)
  hydrogen bonds       : angle       3.51085 ( 1416)
  covalent geometry    : bond        0.00325 ( 8251)
  covalent geometry    : angle       0.47915 (11190)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4543.92 seconds
wall clock time: 79 minutes 5.16 seconds (4745.16 seconds total)